default search action
Google
Google Scholar
Semantic Scholar
Internet Archive Scholar
CiteSeerX
ORCIDBibTeX records: Zhiyong Lu
@article{DBLP:journals/corr/abs-2601-11560,
author = {Zifeng Wang and
Zheng Chen and
Ziwei Yang and
Xuan Wang and
Qiao Jin and
Yifan Peng and
Zhiyong Lu and
Jimeng Sun},
title = {DeepEvidence: Empowering Biomedical Discovery with Deep Knowledge
Graph Research},
journal = {CoRR},
volume = {abs/2601.11560},
year = {2026},
url = {https://doi.org/10.48550/arXiv.2601.11560},
doi = {10.48550/ARXIV.2601.11560},
eprinttype = {arXiv},
eprint = {2601.11560},
timestamp = {Tue, 17 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2601-11560.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LaiWTLL25,
author = {Po{-}Ting Lai and
Chih{-}Hsuan Wei and
Shubo Tian and
Robert Leaman and
Zhiyong Lu},
title = {Enhancing biomedical relation extraction with directionality},
journal = {Bioinform.},
volume = {41},
number = {Supplement{\_}1},
pages = {i68--i76},
year = {2025},
url = {https://doi.org/10.1093/bioinformatics/btaf226},
doi = {10.1093/BIOINFORMATICS/BTAF226},
timestamp = {Sun, 01 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LaiWTLL25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/ZhuHMMJCWCSL25,
author = {Qingqing Zhu and
Benjamin Hou and
Tejas Sudharshan Mathai and
Pritam Mukherjee and
Qiao Jin and
Xiuying Chen and
Zhizheng Wang and
Ruida Cheng and
Ronald M. Summers and
Zhiyong Lu},
title = {How well do multimodal LLMs interpret {CT} scans? An auto-evaluation
framework for analyses},
journal = {J. Biomed. Informatics},
volume = {168},
pages = {104864},
year = {2025},
url = {https://doi.org/10.1016/j.jbi.2025.104864},
doi = {10.1016/J.JBI.2025.104864},
timestamp = {Sat, 09 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbi/ZhuHMMJCWCSL25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mia/LinHWZWBCDDDGGHKMLPSSUV25,
author = {Mingquan Lin and
Gregory Holste and
Song Wang and
Yiliang Zhou and
Yishu Wei and
Imon Banerjee and
Pengyi Chen and
Tianjie Dai and
Yuexi Du and
Nicha C. Dvornek and
Yuyan Ge and
Zuwei Guo and
Shouhei Hanaoka and
Dongkyun Kim and
Pablo Messina and
Yang Lu and
Denis Parra and
Donghyun Son and
{\'{A}}lvaro Soto and
Aisha Urooj and
Ren{\'{e}} Vidal and
Yosuke Yamagishi and
Pingkun Yan and
Zefan Yang and
Ruichi Zhang and
Yang Zhou and
Leo Anthony Celi and
Ronald M. Summers and
Zhiyong Lu and
Hao Chen and
Adam E. Flanders and
George Shih and
Zhangyang Wang and
Yifan Peng},
title = {{CXR-LT} 2024: {A} {MICCAI} challenge on long-tailed, multi-label,
and zero-shot disease classification from chest X-ray},
journal = {Medical Image Anal.},
volume = {106},
pages = {103739},
year = {2025},
url = {https://doi.org/10.1016/j.media.2025.103739},
doi = {10.1016/J.MEDIA.2025.103739},
timestamp = {Wed, 25 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/mia/LinHWZWBCDDDGGHKMLPSSUV25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/npjdm/BhasuranJXYHCSHLH25,
author = {Balu Bhasuran and
Qiao Jin and
Yuzhang Xie and
Carl Yang and
Karim Hanna and
Jennifer Costa and
Cindy Shavor and
Wenshan Han and
Zhiyong Lu and
Zhe He},
title = {Preliminary analysis of the impact of lab results on large language
model generated differential diagnoses},
journal = {npj Digit. Medicine},
volume = {8},
number = {1},
year = {2025},
url = {https://doi.org/10.1038/s41746-025-01556-8},
doi = {10.1038/S41746-025-01556-8},
timestamp = {Sun, 07 Dec 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/npjdm/BhasuranJXYHCSHLH25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/npjdm/WangCDJLS25,
author = {Zifeng Wang and
Lang Cao and
Benjamin P. Danek and
Qiao Jin and
Zhiyong Lu and
Jimeng Sun},
title = {Accelerating clinical evidence synthesis with large language models},
journal = {npj Digit. Medicine},
volume = {8},
number = {1},
year = {2025},
url = {https://doi.org/10.1038/s41746-025-01840-7},
doi = {10.1038/S41746-025-01840-7},
timestamp = {Sun, 21 Sep 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/npjdm/WangCDJLS25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/npjdm/ZhangXJCFLRXLWP25,
author = {Gongbo Zhang and
Zihan Xu and
Qiao Jin and
Fangyi Chen and
Yilu Fang and
Yi Liu and
Justin F. Rousseau and
Ziyang Xu and
Zhiyong Lu and
Chunhua Weng and
Yifan Peng},
title = {Leveraging long context in retrieval augmented language models for
medical question answering},
journal = {npj Digit. Medicine},
volume = {8},
number = {1},
year = {2025},
url = {https://doi.org/10.1038/s41746-025-01651-w},
doi = {10.1038/S41746-025-01651-W},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/npjdm/ZhangXJCFLRXLWP25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tois/WangCZGGLGZ25,
author = {Tairan Wang and
Xiuying Chen and
Qingqing Zhu and
Taicheng Guo and
Shen Gao and
Zhiyong Lu and
Xin Gao and
Xiangliang Zhang},
title = {New Paradigm for Evaluating Scholar Summaries: {A} Facet-aware Metric
and a Meta-evaluation Benchmark},
journal = {{ACM} Trans. Inf. Syst.},
volume = {43},
number = {4},
pages = {100:1--100:25},
year = {2025},
url = {https://doi.org/10.1145/3733597},
doi = {10.1145/3733597},
timestamp = {Thu, 11 Sep 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tois/WangCZGGLGZ25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/acl/WangT0XHZLZ25,
author = {Xiao Wang and
Mengjue Tan and
Qiao Jin and
Guangzhi Xiong and
Yu Hu and
Aidong Zhang and
Zhiyong Lu and
Minjia Zhang},
editor = {Wanxiang Che and
Joyce Nabende and
Ekaterina Shutova and
Mohammad Taher Pilehvar},
title = {MedCite: Can Language Models Generate Verifiable Text for Medicine?},
booktitle = {Findings of the Association for Computational Linguistics, {ACL} 2025,
Vienna, Austria, July 27 - August 1, 2025},
series = {Findings of {ACL}},
volume = {{ACL} 2025},
pages = {18891--18913},
publisher = {Association for Computational Linguistics},
year = {2025},
url = {https://aclanthology.org/2025.findings-acl.967/},
timestamp = {Mon, 02 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/acl/WangT0XHZLZ25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hci/YeL25,
author = {Junnan Ye and
Zhiyong Lu},
editor = {Constantine Stephanidis and
Margherita Antona and
Stavroula Ntoa and
Gavriel Salvendy},
title = {Research on the Design of Community Two-Wheeled Electric Vehicle Parking
Facilities Based on Kano-QFD and {FBS-TRIZ} Models},
booktitle = {{HCI} International 2025 Posters - 27th International Conference on
Human-Computer Interaction, {HCII} 2025, Gothenburg, Sweden, June
22-27, 2025, Proceedings, Part {IV}},
series = {Communications in Computer and Information Science},
volume = {2525},
pages = {436--448},
publisher = {Springer},
year = {2025},
url = {https://doi.org/10.1007/978-3-031-94159-7\_46},
doi = {10.1007/978-3-031-94159-7\_46},
timestamp = {Sat, 19 Jul 2025 22:41:09 +0200},
biburl = {https://dblp.org/rec/conf/hci/YeL25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/mlmi-ws/WuLCCLPD25,
author = {Puzhen Wu and
Mingquan Lin and
Qingyu Chen and
Emily Y. Chew and
Zhiyong Lu and
Yifan Peng and
Hexin Dong},
editor = {Zhiming Cui and
Islem Rekik and
Heung{-}IL Suk and
Xi Ouyang and
Kaicong Sun and
Sheng Wang},
title = {AMD-Mamba: {A} Phenotype-Aware Multi-modal Framework for Robust {AMD}
Prognosis},
booktitle = {Machine Learning in Medical Imaging - 16th International Workshop,
{MLMI} 2025, Held in Conjunction with {MICCAI} 2025, Daejeon, South
Korea, September 23, 2025, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {16241},
pages = {150--160},
publisher = {Springer},
year = {2025},
url = {https://doi.org/10.1007/978-3-032-09513-8\_15},
doi = {10.1007/978-3-032-09513-8\_15},
timestamp = {Sat, 31 Jan 2026 13:02:32 +0100},
biburl = {https://dblp.org/rec/conf/mlmi-ws/WuLCCLPD25.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2501-14066,
author = {Benjamin Hou and
Tejas Sudharshan Mathai and
Pritam Mukherjee and
Xinya Wang and
Ronald M. Summers and
Zhiyong Lu},
title = {Efficient 2D {CT} Foundation Model for Contrast Phase Classification},
journal = {CoRR},
volume = {abs/2501.14066},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2501.14066},
doi = {10.48550/ARXIV.2501.14066},
eprinttype = {arXiv},
eprint = {2501.14066},
timestamp = {Fri, 28 Feb 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2501-14066.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2501-14079,
author = {Po{-}Ting Lai and
Chih{-}Hsuan Wei and
Shubo Tian and
Robert Leaman and
Zhiyong Lu},
title = {Enhancing Biomedical Relation Extraction with Directionality},
journal = {CoRR},
volume = {abs/2501.14079},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2501.14079},
doi = {10.48550/ARXIV.2501.14079},
eprinttype = {arXiv},
eprint = {2501.14079},
timestamp = {Wed, 26 Feb 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2501-14079.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2501-16255,
author = {Zifeng Wang and
Lang Cao and
Qiao Jin and
Joey Chan and
Nicholas Wan and
Behdad Afzali and
Hyunjin Cho and
Changin Choi and
Mehdi Emamverdi and
Manjot K. Gill and
Sun{-}Hyung Kim and
Yijia Li and
Yi Liu and
Hanley Ong and
Justin F. Rousseau and
Irfan Sheikh and
Jenny J. Wei and
Ziyang Xu and
Christopher M. Zallek and
Kyungsang Kim and
Yifan Peng and
Zhiyong Lu and
Jimeng Sun},
title = {A foundation model for human-AI collaboration in medical literature
mining},
journal = {CoRR},
volume = {abs/2501.16255},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2501.16255},
doi = {10.48550/ARXIV.2501.16255},
eprinttype = {arXiv},
eprint = {2501.16255},
timestamp = {Sat, 15 Nov 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2501-16255.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2502-13957,
author = {Guangzhi Xiong and
Qiao Jin and
Xiao Wang and
Yin Fang and
Haolin Liu and
Yifan Yang and
Fangyuan Chen and
Zhixing Song and
Dengyu Wang and
Minjia Zhang and
Zhiyong Lu and
Aidong Zhang},
title = {RAG-Gym: Optimizing Reasoning and Search Agents with Process Supervision},
journal = {CoRR},
volume = {abs/2502.13957},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2502.13957},
doi = {10.48550/ARXIV.2502.13957},
eprinttype = {arXiv},
eprint = {2502.13957},
timestamp = {Tue, 17 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2502-13957.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2504-05196,
author = {Tejas Sudharshan Mathai and
Sungwon Lee and
Thomas C. Shen and
Zhiyong Lu and
Ronald M. Summers},
title = {Universal Lymph Node Detection in Multiparametric {MRI} with Selective
Augmentation},
journal = {CoRR},
volume = {abs/2504.05196},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2504.05196},
doi = {10.48550/ARXIV.2504.05196},
eprinttype = {arXiv},
eprint = {2504.05196},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2504-05196.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2504-20059,
author = {Joey Chan and
Qiao Jin and
Nicholas Wan and
Charalampos S. Floudas and
Elisabetta Xue and
Zhiyong Lu},
title = {Recommending Clinical Trials for Online Patient Cases using Artificial
Intelligence},
journal = {CoRR},
volume = {abs/2504.20059},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2504.20059},
doi = {10.48550/ARXIV.2504.20059},
eprinttype = {arXiv},
eprint = {2504.20059},
timestamp = {Sun, 25 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2504-20059.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2505-07671,
author = {Xianrui Zhong and
Bowen Jin and
Siru Ouyang and
Yanzhen Shen and
Qiao Jin and
Yin Fang and
Zhiyong Lu and
Jiawei Han},
title = {Benchmarking Retrieval-Augmented Generation for Chemistry},
journal = {CoRR},
volume = {abs/2505.07671},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2505.07671},
doi = {10.48550/ARXIV.2505.07671},
eprinttype = {arXiv},
eprint = {2505.07671},
timestamp = {Sun, 07 Dec 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2505-07671.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2505-16097,
author = {Zifeng Wang and
Qiao Jin and
Jiacheng Lin and
Junyi Gao and
Jathurshan Pradeepkumar and
Pengcheng Jiang and
Benjamin P. Danek and
Zhiyong Lu and
Jimeng Sun},
title = {TrialPanorama: Database and Benchmark for Systematic Review and Design
of Clinical Trials},
journal = {CoRR},
volume = {abs/2505.16097},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2505.16097},
doi = {10.48550/ARXIV.2505.16097},
eprinttype = {arXiv},
eprint = {2505.16097},
timestamp = {Wed, 25 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2505-16097.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2506-02911,
author = {Yin Fang and
Qiao Jin and
Guangzhi Xiong and
Bowen Jin and
Xianrui Zhong and
Siru Ouyang and
Aidong Zhang and
Jiawei Han and
Zhiyong Lu},
title = {Cell-o1: Training LLMs to Solve Single-Cell Reasoning Puzzles with
Reinforcement Learning},
journal = {CoRR},
volume = {abs/2506.02911},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2506.02911},
doi = {10.48550/ARXIV.2506.02911},
eprinttype = {arXiv},
eprint = {2506.02911},
timestamp = {Mon, 02 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2506-02911.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2506-04303,
author = {Zhizheng Wang and
Chi{-}Ping Day and
Chih{-}Hsuan Wei and
Qiao Jin and
Robert Leaman and
Yifan Yang and
Shubo Tian and
Aodong Qiu and
Yin Fang and
Qingqing Zhu and
Xinghua Lu and
Zhiyong Lu},
title = {Knowledge-guided Contextual Gene Set Analysis Using Large Language
Models},
journal = {CoRR},
volume = {abs/2506.04303},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2506.04303},
doi = {10.48550/ARXIV.2506.04303},
eprinttype = {arXiv},
eprint = {2506.04303},
timestamp = {Mon, 21 Jul 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2506-04303.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2506-06605,
author = {Xiao Wang and
Mengjue Tan and
Qiao Jin and
Guangzhi Xiong and
Yu Hu and
Aidong Zhang and
Zhiyong Lu and
Minjia Zhang},
title = {MedCite: Can Language Models Generate Verifiable Text for Medicine?},
journal = {CoRR},
volume = {abs/2506.06605},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2506.06605},
doi = {10.48550/ARXIV.2506.06605},
eprinttype = {arXiv},
eprint = {2506.06605},
timestamp = {Mon, 02 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2506-06605.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2506-07984,
author = {Mingquan Lin and
Gregory Holste and
Song Wang and
Yiliang Zhou and
Yishu Wei and
Imon Banerjee and
Pengyi Chen and
Tianjie Dai and
Yuexi Du and
Nicha C. Dvornek and
Yuyan Ge and
Zuowei Guo and
Shouhei Hanaoka and
Dongkyun Kim and
Pablo Messina and
Yang Lu and
Denis Parra and
Donghyun Son and
{\'{A}}lvaro Soto and
Aisha Urooj and
Ren{\'{e}} Vidal and
Yosuke Yamagishi and
Zefan Yang and
Ruichi Zhang and
Yang Zhou and
Leo Anthony Celi and
Ronald M. Summers and
Zhiyong Lu and
Hao Chen and
Adam E. Flanders and
George Shih and
Zhangyang Wang and
Yifan Peng},
title = {{CXR-LT} 2024: {A} {MICCAI} challenge on long-tailed, multi-label,
and zero-shot disease classification from chest X-ray},
journal = {CoRR},
volume = {abs/2506.07984},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2506.07984},
doi = {10.48550/ARXIV.2506.07984},
eprinttype = {arXiv},
eprint = {2506.07984},
timestamp = {Mon, 15 Sep 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2506-07984.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2508-06453,
author = {Ruida Cheng and
Tejas Sudharshan Mathai and
Pritam Mukherjee and
Benjamin Hou and
Qingqing Zhu and
Zhiyong Lu and
Matthew J. McAuliffe and
Ronald M. Summers},
title = {Text Embedded Swin-UMamba for DeepLesion Segmentation},
journal = {CoRR},
volume = {abs/2508.06453},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2508.06453},
doi = {10.48550/ARXIV.2508.06453},
eprinttype = {arXiv},
eprint = {2508.06453},
timestamp = {Sat, 13 Sep 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2508-06453.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2509-08604,
author = {Anran Li and
Lingfei Qian and
Mengmeng Du and
Yu Yin and
Yan Hu and
Zihao Sun and
Yihang Fu and
Erica Stutz and
Xuguang Ai and
Qianqian Xie and
Rui Zhu and
Jimin Huang and
Yifan Yang and
Siru Liu and
Yih{-}Chung Tham and
Lucila Ohno{-}Machado and
Hyunghoon Cho and
Zhiyong Lu and
Hua Xu and
Qingyu Chen},
title = {Memorization in Large Language Models in Medicine: Prevalence, Characteristics,
and Implications},
journal = {CoRR},
volume = {abs/2509.08604},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2509.08604},
doi = {10.48550/ARXIV.2509.08604},
eprinttype = {arXiv},
eprint = {2509.08604},
timestamp = {Mon, 13 Oct 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2509-08604.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2509-10575,
author = {Zhizheng Wang and
Yifan Yang and
Qiao Jin and
Zhiyong Lu},
title = {Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set
Analysis},
journal = {CoRR},
volume = {abs/2509.10575},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2509.10575},
doi = {10.48550/ARXIV.2509.10575},
eprinttype = {arXiv},
eprint = {2509.10575},
timestamp = {Sun, 26 Oct 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2509-10575.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2509-25620,
author = {Zhenyue Qin and
Yang Liu and
Yu Yin and
Jinyu Ding and
Haoran Zhang and
Anran Li and
Dylan Campbell and
Xuansheng Wu and
Ke Zou and
Tiarnan D. L. Keenan and
Emily Y. Chew and
Zhiyong Lu and
Yih{-}Chung Tham and
Ninghao Liu and
Xiuzhen Zhang and
Qingyu Chen},
title = {{LMOD+:} {A} Comprehensive Multimodal Dataset and Benchmark for Developing
and Evaluating Multimodal Large Language Models in Ophthalmology},
journal = {CoRR},
volume = {abs/2509.25620},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2509.25620},
doi = {10.48550/ARXIV.2509.25620},
eprinttype = {arXiv},
eprint = {2509.25620},
timestamp = {Mon, 23 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2509-25620.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2510-09897,
author = {Wonbin Kweon and
Runchu Tian and
SeongKu Kang and
Pengcheng Jiang and
Zhiyong Lu and
Jiawei Han and
Hwanjo Yu},
title = {PairSem: LLM-Guided Pairwise Semantic Matching for Scientific Document
Retrieval},
journal = {CoRR},
volume = {abs/2510.09897},
year = {2025},
url = {https://doi.org/10.48550/arXiv.2510.09897},
doi = {10.48550/ARXIV.2510.09897},
eprinttype = {arXiv},
eprint = {2510.09897},
timestamp = {Tue, 11 Nov 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2510-09897.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TianJYLZCYCKCIKGL24,
author = {Shubo Tian and
Qiao Jin and
Lana Yeganova and
Po{-}Ting Lai and
Qingqing Zhu and
Xiuying Chen and
Yifan Yang and
Qingyu Chen and
Won Kim and
Donald C. Comeau and
Rezarta Islamaj and
Aadit Kapoor and
Xin Gao and
Zhiyong Lu},
title = {Opportunities and challenges for ChatGPT and large language models
in biomedicine and health},
journal = {Briefings Bioinform.},
volume = {25},
number = {1},
year = {2024},
url = {https://doi.org/10.1093/bib/bbad493},
doi = {10.1093/BIB/BBAD493},
timestamp = {Tue, 16 Dec 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/TianJYLZCYCKCIKGL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/TianJL24,
author = {Shubo Tian and
Qiao Jin and
Zhiyong Lu},
title = {Response to Letter to Editor 'Timely need for navigating the potential
and downsides of LLMs in healthcare and biomedicine'},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae211},
doi = {10.1093/BIB/BBAE211},
timestamp = {Tue, 16 Dec 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/TianJL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/IslamajLWLAJCSPCLPMTSHV24,
author = {Rezarta Islamaj and
Po{-}Ting Lai and
Chih{-}Hsuan Wei and
Ling Luo and
Tiago Melo Almeida and
Richard A. A. Jonker and
Sofia I R. Concei{\c{c}}{\~{a}}o and
Diana F. Sousa and
Cong{-}Phuoc Phan and
Jung{-}Hsien Chiang and
Jiru Li and
Dinghao Pan and
Wilailack Meesawad and
Richard Tzong{-}Han Tsai and
M. Janina Sarol and
Gibong Hong and
Airat Valiev and
Elena Tutubalina and
Shao{-}Man Lee and
Yi{-}Yu Hsu and
Mingjie Li and
Karin Verspoor and
Zhiyong Lu},
title = {The overview of the BioRED (Biomedical Relation Extraction Dataset)
track at BioCreative {VIII}},
journal = {Database J. Biol. Databases Curation},
volume = {2024},
year = {2024},
url = {https://doi.org/10.1093/database/baae069},
doi = {10.1093/DATABASE/BAAE069},
timestamp = {Wed, 25 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/IslamajLWLAJCSPCLPMTSHV24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/IslamajWLLCKMRSTWL24,
author = {Rezarta Islamaj and
Chih{-}Hsuan Wei and
Po{-}Ting Lai and
Ling Luo and
Cathleen Coss and
Preeti Gokal Kochar and
Nicholas Miliaras and
Oleg Rodionov and
Keiko Sekiya and
Dorothy Trinh and
Deborah Whitman and
Zhiyong Lu},
title = {The biomedical relationship corpus of the BioRED track at the BioCreative
{VIII} challenge and workshop},
journal = {Database J. Biol. Databases Curation},
volume = {2024},
year = {2024},
url = {https://doi.org/10.1093/database/baae071},
doi = {10.1093/DATABASE/BAAE071},
timestamp = {Mon, 03 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/IslamajWLLCKMRSTWL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JinYCL24,
author = {Qiao Jin and
Yifan Yang and
Qingyu Chen and
Zhiyong Lu},
title = {GeneGPT: augmenting large language models with domain tools for improved
access to biomedical information},
journal = {Bioinform.},
volume = {40},
number = {2},
year = {2024},
url = {https://doi.org/10.1093/bioinformatics/btae075},
doi = {10.1093/BIOINFORMATICS/BTAE075},
timestamp = {Tue, 28 Oct 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JinYCL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KelothHXP0ZSRW024,
author = {Vipina Kuttichi Keloth and
Yan Hu and
Qianqian Xie and
Xueqing Peng and
Yan Wang and
Andrew Zheng and
Melih Selek and
Kalpana Raja and
Chih{-}Hsuan Wei and
Qiao Jin and
Zhiyong Lu and
Qingyu Chen and
Hua Xu},
title = {Advancing entity recognition in biomedicine via instruction tuning
of large language models},
journal = {Bioinform.},
volume = {40},
number = {4},
year = {2024},
url = {https://doi.org/10.1093/bioinformatics/btae163},
doi = {10.1093/BIOINFORMATICS/BTAE163},
timestamp = {Sun, 01 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KelothHXP0ZSRW024.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Tian0CWL24,
author = {Shubo Tian and
Qingyu Chen and
Donald C. Comeau and
W. John Wilbur and
Zhiyong Lu},
title = {PubMed Computed Authors in 2024: an open resource of disambiguated
author names in biomedical literature},
journal = {Bioinform.},
volume = {40},
number = {11},
year = {2024},
url = {https://doi.org/10.1093/bioinformatics/btae672},
doi = {10.1093/BIOINFORMATICS/BTAE672},
timestamp = {Wed, 25 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Tian0CWL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cars/MathaiLSELS24,
author = {Tejas Sudharshan Mathai and
Sungwon Lee and
Thomas C. Shen and
Daniel C. Elton and
Zhiyong Lu and
Ronald M. Summers},
title = {Universal detection and segmentation of lymph nodes in multi-parametric
{MRI}},
journal = {Int. J. Comput. Assist. Radiol. Surg.},
volume = {19},
number = {1},
pages = {163--170},
year = {2024},
url = {https://doi.org/10.1007/s11548-023-02954-7},
doi = {10.1007/S11548-023-02954-7},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cars/MathaiLSELS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cmig/MathaiSELLS24,
author = {Tejas Sudharshan Mathai and
Thomas C. Shen and
Daniel C. Elton and
Sungwon Lee and
Zhiyong Lu and
Ronald M. Summers},
title = {Detection of abdominopelvic lymph nodes in multi-parametric {MRI}},
journal = {Comput. Medical Imaging Graph.},
volume = {114},
pages = {102363},
year = {2024},
url = {https://doi.org/10.1016/j.compmedimag.2024.102363},
doi = {10.1016/J.COMPMEDIMAG.2024.102363},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cmig/MathaiSELLS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jamia/LuPCGWT24,
author = {Zhiyong Lu and
Yifan Peng and
Trevor Cohen and
Marzyeh Ghassemi and
Chunhua Weng and
Shubo Tian},
title = {Large language models in biomedicine and health: current research
landscape and future directions},
journal = {J. Am. Medical Informatics Assoc.},
volume = {31},
number = {9},
pages = {1801--1811},
year = {2024},
url = {https://doi.org/10.1093/jamia/ocae202},
doi = {10.1093/JAMIA/OCAE202},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jamia/LuPCGWT24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jamia/HuCDPKZZLJLRX24,
author = {Yan Hu and
Qingyu Chen and
Jingcheng Du and
Xueqing Peng and
Vipina Kuttichi Keloth and
Xu Zuo and
Yujia Zhou and
Zehan Li and
Xiaoqian Jiang and
Zhiyong Lu and
Kirk Roberts and
Hua Xu},
title = {Improving large language models for clinical named entity recognition
via prompt engineering},
journal = {J. Am. Medical Informatics Assoc.},
volume = {31},
number = {9},
pages = {1812--1820},
year = {2024},
url = {https://doi.org/10.1093/jamia/ocad259},
doi = {10.1093/JAMIA/OCAD259},
timestamp = {Sun, 01 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jamia/HuCDPKZZLJLRX24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/ZhangJMCWCYWMPWLWP24,
author = {Gongbo Zhang and
Qiao Jin and
Denis Jered McInerney and
Yong Chen and
Fei Wang and
Curtis L. Cole and
Qian Yang and
Yanshan Wang and
Bradley A. Malin and
Mor Peleg and
Byron C. Wallace and
Zhiyong Lu and
Chunhua Weng and
Yifan Peng},
title = {Leveraging generative {AI} for clinical evidence synthesis needs to
ensure trustworthiness},
journal = {J. Biomed. Informatics},
volume = {153},
pages = {104640},
year = {2024},
url = {https://doi.org/10.1016/j.jbi.2024.104640},
doi = {10.1016/J.JBI.2024.104640},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbi/ZhangJMCWCYWMPWLWP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/YangLZPHL24,
author = {Yifan Yang and
Mingquan Lin and
Han Zhao and
Yifan Peng and
Furong Huang and
Zhiyong Lu},
title = {A survey of recent methods for addressing {AI} fairness and bias in
biomedicine},
journal = {J. Biomed. Informatics},
volume = {154},
pages = {104646},
year = {2024},
url = {https://doi.org/10.1016/j.jbi.2024.104646},
doi = {10.1016/J.JBI.2024.104646},
timestamp = {Sun, 06 Jul 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbi/YangLZPHL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/YinKXWKLXFC24,
author = {Yu Yin and
Hyunjae Kim and
Xiao Xiao and
Chih{-}Hsuan Wei and
Jaewoo Kang and
Zhiyong Lu and
Hua Xu and
Meng Fang and
Qingyu Chen},
title = {Augmenting biomedical named entity recognition with general-domain
resources},
journal = {J. Biomed. Informatics},
volume = {159},
pages = {104731},
year = {2024},
url = {https://doi.org/10.1016/j.jbi.2024.104731},
doi = {10.1016/J.JBI.2024.104731},
timestamp = {Mon, 09 Dec 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/YinKXWKLXFC24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mia/HolsteZWJLZYKMTJPRHVYKSKCLSSWP24,
author = {Gregory Holste and
Yiliang Zhou and
Song Wang and
Ajay Jaiswal and
Mingquan Lin and
Sherry Zhuge and
Yuzhe Yang and
Dongkyun Kim and
Trong{-}Hieu Nguyen Mau and
Minh{-}Triet Tran and
Jaehyup Jeong and
Wongi Park and
Jongbin Ryu and
Feng Hong and
Arsh Verma and
Yosuke Yamagishi and
Changhyun Kim and
Hyeryeong Seo and
Myungjoo Kang and
Leo Anthony Celi and
Zhiyong Lu and
Ronald M. Summers and
George Shih and
Zhangyang Wang and
Yifan Peng},
title = {Towards long-tailed, multi-label disease classification from chest
X-ray: Overview of the {CXR-LT} challenge},
journal = {Medical Image Anal.},
volume = {97},
pages = {103224},
year = {2024},
url = {https://doi.org/10.1016/j.media.2024.103224},
doi = {10.1016/J.MEDIA.2024.103224},
timestamp = {Mon, 18 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mia/HolsteZWJLZYKMTJPRHVYKSKCLSSWP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/npjdm/HolsteLZWLYTKCLWP24,
author = {Gregory Holste and
Mingquan Lin and
Ruiwen Zhou and
Fei Wang and
Lei Liu and
Qi Yan and
Sarah Van Tassel and
Kyle Kovacs and
Emily Y. Chew and
Zhiyong Lu and
Zhangyang Wang and
Yifan Peng},
title = {Harnessing the power of longitudinal medical imaging for eye disease
prognosis using Transformer-based sequence modeling},
journal = {npj Digit. Medicine},
volume = {7},
number = {1},
year = {2024},
url = {https://doi.org/10.1038/s41746-024-01207-4},
doi = {10.1038/S41746-024-01207-4},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/npjdm/HolsteLZWLYTKCLWP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/npjdm/HolsteLZWLYTKCLWP24a,
author = {Gregory Holste and
Mingquan Lin and
Ruiwen Zhou and
Fei Wang and
Lei Liu and
Qi Yan and
Sarah Van Tassel and
Kyle Kovacs and
Emily Y. Chew and
Zhiyong Lu and
Zhangyang Wang and
Yifan Peng},
title = {Author Correction: Harnessing the power of longitudinal medical imaging
for eye disease prognosis using Transformer-based sequence modeling},
journal = {npj Digit. Medicine},
volume = {7},
number = {1},
year = {2024},
url = {https://doi.org/10.1038/s41746-024-01243-0},
doi = {10.1038/S41746-024-01243-0},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/npjdm/HolsteLZWLYTKCLWP24a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/npjdm/JinCZXCCSRNLBALCBCPL24,
author = {Qiao Jin and
Fangyuan Chen and
Yiliang Zhou and
Ziyang Xu and
Justin M. Cheung and
Robert Chen and
Ronald M. Summers and
Justin F. Rousseau and
Peiyun Ni and
Marc J. Landsman and
Sally L. Baxter and
Subhi J. Al'Aref and
Yijia Li and
Alexander Chen and
Josef A. Brejt and
Michael F. Chiang and
Yifan Peng and
Zhiyong Lu},
title = {Hidden flaws behind expert-level accuracy of multimodal {GPT-4} vision
in medicine},
journal = {npj Digit. Medicine},
volume = {7},
number = {1},
year = {2024},
url = {https://doi.org/10.1038/s41746-024-01185-7},
doi = {10.1038/S41746-024-01185-7},
timestamp = {Tue, 17 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/npjdm/JinCZXCCSRNLBALCBCPL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/npjdm/ZhangJZWILPNSSCLWP24,
author = {Gongbo Zhang and
Qiao Jin and
Yiliang Zhou and
Song Wang and
Betina Idnay and
Yiming Luo and
Elizabeth Park and
Jordan G. Nestor and
Matthew E. Spotnitz and
Ali Soroush and
Thomas Campion and
Zhiyong Lu and
Chunhua Weng and
Yifan Peng},
title = {Closing the gap between open source and commercial large language
models for medical evidence summarization},
journal = {npj Digit. Medicine},
volume = {7},
number = {1},
year = {2024},
url = {https://doi.org/10.1038/s41746-024-01239-w},
doi = {10.1038/S41746-024-01239-W},
timestamp = {Mon, 18 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/npjdm/ZhangJZWILPNSSCLWP24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/acl/Xiong0LZ24,
author = {Guangzhi Xiong and
Qiao Jin and
Zhiyong Lu and
Aidong Zhang},
editor = {Lun{-}Wei Ku and
Andre Martins and
Vivek Srikumar},
title = {Benchmarking Retrieval-Augmented Generation for Medicine},
booktitle = {Findings of the Association for Computational Linguistics, {ACL} 2024,
Bangkok, Thailand and virtual meeting, August 11-16, 2024},
series = {Findings of {ACL}},
volume = {{ACL} 2024},
pages = {6233--6251},
publisher = {Association for Computational Linguistics},
year = {2024},
url = {https://doi.org/10.18653/v1/2024.findings-acl.372},
doi = {10.18653/V1/2024.FINDINGS-ACL.372},
timestamp = {Mon, 02 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/acl/Xiong0LZ24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icct/ZhangLL24,
author = {Hongmei Zhang and
Zhiyong Lu and
Kejia Liu},
title = {A Text-to-Speech Synthesis Method Based on Speaker Transfer},
booktitle = {24th {IEEE} International Conference on Communication Technology,
{ICCT} 2024, Chengdu, China, October 18-20, 2024},
pages = {1822--1826},
publisher = {{IEEE}},
year = {2024},
url = {https://doi.org/10.1109/ICCT62411.2024.10946354},
doi = {10.1109/ICCT62411.2024.10946354},
timestamp = {Wed, 18 Jun 2025 09:10:47 +0200},
biburl = {https://dblp.org/rec/conf/icct/ZhangLL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ichi/ZhuC0HMM0SL24,
author = {Qingqing Zhu and
Xiuying Chen and
Qiao Jin and
Benjamin Hou and
Tejas Sudharshan Mathai and
Pritam Mukherjee and
Xin Gao and
Ronald M. Summers and
Zhiyong Lu},
title = {Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation
for AI-generated Radiology Reports},
booktitle = {12th {IEEE} International Conference on Healthcare Informatics, {ICHI}
2024, Orlando, FL, USA, June 3-6, 2024},
pages = {402--411},
publisher = {{IEEE}},
year = {2024},
url = {https://doi.org/10.1109/ICHI61247.2024.00058},
doi = {10.1109/ICHI61247.2024.00058},
timestamp = {Mon, 03 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ichi/ZhuC0HMM0SL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nips/Khandekar0XDAAS24,
author = {Nikhil Khandekar and
Qiao Jin and
Guangzhi Xiong and
Soren Dunn and
Serina S. Applebaum and
Zain Anwar and
Maame Sarfo{-}Gyamfi and
Conrad W. Safranek and
Abid A Anwar and
Andrew Zhang and
Aidan Gilson and
Maxwell B. Singer and
Amisha D. Dave and
Andrew Taylor and
Aidong Zhang and
Qingyu Chen and
Zhiyong Lu},
editor = {Amir Globersons and
Lester Mackey and
Danielle Belgrave and
Angela Fan and
Ulrich Paquet and
Jakub M. Tomczak and
Cheng Zhang},
title = {MedCalc-Bench: Evaluating Large Language Models for Medical Calculations},
booktitle = {Advances in Neural Information Processing Systems 38: Annual Conference
on Neural Information Processing Systems 2024, NeurIPS 2024, Vancouver,
BC, Canada, December 10 - 15, 2024},
year = {2024},
url = {http://papers.nips.cc/paper\_files/paper/2024/hash/99e81750f3fdfcaf9613db2dbf4bd623-Abstract-Datasets\_and\_Benchmarks\_Track.html},
timestamp = {Mon, 02 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/nips/Khandekar0XDAAS24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@misc{DBLP:data/11/LaiCAABCFMPPPRRSWLLLB24,
author = {Po{-}Ting Lai and
Elisabeth Coudert and
Lucila Aimo and
Kristian B. Axelsen and
Lionel Breuza and
Edouard De Castro and
Marc Feuermann and
Anne Morgat and
Lucille Pourcel and
Ivo Pedruzzi and
Sylvain Poux and
Nicole Redaschi and
Catherine Rivoire and
Anastasia Sveshnikova and
Chih{-}Hsuan Wei and
Robert Leaman and
Ling Luo and
Zhiyong Lu and
Alan J. Bridge},
title = {EnzChemRED, a rich enzyme chemistry relation extraction dataset (Version
1)},
publisher = {Zenodo},
year = {2024},
month = apr,
howpublished = {\url{https://doi.org/10.5281/zenodo.11067998}},
note = {Accessed on YYYY-MM-DD.},
url = {https://doi.org/10.5281/zenodo.11067998},
doi = {10.5281/ZENODO.11067998},
timestamp = {Mon, 23 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/data/11/LaiCAABCFMPPPRRSWLLLB24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@misc{DBLP:data/11/WeiALLTLJWCL24,
author = {Chih{-}Hsuan Wei and
Alexis Allot and
Po{-}Ting Lai and
Robert Leaman and
Shubo Tian and
Ling Luo and
Qiao Jin and
Zhizheng Wang and
Qingyu Chen and
Zhiyong Lu},
title = {Archive of PubTator 3.0 source code and trained models (Version 1)},
publisher = {Zenodo},
year = {2024},
month = mar,
howpublished = {\url{https://doi.org/10.5281/zenodo.10839631}},
note = {Accessed on YYYY-MM-DD.},
url = {https://doi.org/10.5281/zenodo.10839631},
doi = {10.5281/ZENODO.10839631},
timestamp = {Wed, 11 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/data/11/WeiALLTLJWCL24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2401-08396,
author = {Qiao Jin and
Fangyuan Chen and
Yiliang Zhou and
Ziyang Xu and
Justin M. Cheung and
Robert Chen and
Ronald M. Summers and
Justin F. Rousseau and
Peiyun Ni and
Marc J. Landsman and
Sally L. Baxter and
Subhi J. Al'Aref and
Yijia Li and
Michael F. Chiang and
Yifan Peng and
Zhiyong Lu},
title = {Hidden Flaws Behind Expert-Level Accuracy of {GPT-4} Vision in Medicine},
journal = {CoRR},
volume = {abs/2401.08396},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2401.08396},
doi = {10.48550/ARXIV.2401.08396},
eprinttype = {arXiv},
eprint = {2401.08396},
timestamp = {Tue, 17 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2401-08396.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2401-11048,
author = {Chih{-}Hsuan Wei and
Alexis Allot and
Po{-}Ting Lai and
Robert Leaman and
Shubo Tian and
Ling Luo and
Qiao Jin and
Zhizheng Wang and
Qingyu Chen and
Zhiyong Lu},
title = {PubTator 3.0: an AI-powered Literature Resource for Unlocking Biomedical
Knowledge},
journal = {CoRR},
volume = {abs/2401.11048},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2401.11048},
doi = {10.48550/ARXIV.2401.11048},
eprinttype = {arXiv},
eprint = {2401.11048},
timestamp = {Thu, 01 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2401-11048.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2401-13867,
author = {Yifan Yang and
Xiaoyu Liu and
Qiao Jin and
Furong Huang and
Zhiyong Lu},
title = {Unmasking and Quantifying Racial Bias of Large Language Models in
Medical Report Generation},
journal = {CoRR},
volume = {abs/2401.13867},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2401.13867},
doi = {10.48550/ARXIV.2401.13867},
eprinttype = {arXiv},
eprint = {2401.13867},
timestamp = {Wed, 16 Apr 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2401-13867.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2401-16578,
author = {Qingqing Zhu and
Xiuying Chen and
Qiao Jin and
Benjamin Hou and
Tejas Sudharshan Mathai and
Pritam Mukherjee and
Xin Gao and
Ronald M. Summers and
Zhiyong Lu},
title = {Leveraging Professional Radiologists' Expertise to Enhance LLMs' Evaluation
for Radiology Reports},
journal = {CoRR},
volume = {abs/2401.16578},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2401.16578},
doi = {10.48550/ARXIV.2401.16578},
eprinttype = {arXiv},
eprint = {2401.16578},
timestamp = {Tue, 06 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2401-16578.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2402-01693,
author = {Zhe He and
Balu Bhasuran and
Qiao Jin and
Shubo Tian and
Karim Hanna and
Cindy Shavor and
Lisbeth Y. Garcia Arguello and
Patrick Murray and
Zhiyong Lu},
title = {Quality of Answers of Generative Large Language Models vs Peer Patients
for Interpreting Lab Test Results for Lay Patients: Evaluation Study},
journal = {CoRR},
volume = {abs/2402.01693},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2402.01693},
doi = {10.48550/ARXIV.2402.01693},
eprinttype = {arXiv},
eprint = {2402.01693},
timestamp = {Fri, 09 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2402-01693.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2402-03484,
author = {Ashley Shin and
Qiao Jin and
James T. Anibal and
Zhiyong Lu},
title = {Harnessing PubMed User Query Logs for Post Hoc Explanations of Recommended
Similar Articles},
journal = {CoRR},
volume = {abs/2402.03484},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2402.03484},
doi = {10.48550/ARXIV.2402.03484},
eprinttype = {arXiv},
eprint = {2402.03484},
timestamp = {Tue, 26 Nov 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2402-03484.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2402-04247,
author = {Xiangru Tang and
Qiao Jin and
Kunlun Zhu and
Tongxin Yuan and
Yichi Zhang and
Wangchunshu Zhou and
Meng Qu and
Yilun Zhao and
Jian Tang and
Zhuosheng Zhang and
Arman Cohan and
Zhiyong Lu and
Mark Gerstein},
title = {Prioritizing Safeguarding Over Autonomy: Risks of {LLM} Agents for
Science},
journal = {CoRR},
volume = {abs/2402.04247},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2402.04247},
doi = {10.48550/ARXIV.2402.04247},
eprinttype = {arXiv},
eprint = {2402.04247},
timestamp = {Sun, 15 Mar 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2402-04247.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2402-08250,
author = {Yifan Yang and
Mingquan Lin and
Han Zhao and
Yifan Peng and
Furong Huang and
Zhiyong Lu},
title = {A survey of recent methods for addressing {AI} fairness and bias in
biomedicine},
journal = {CoRR},
volume = {abs/2402.08250},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2402.08250},
doi = {10.48550/ARXIV.2402.08250},
eprinttype = {arXiv},
eprint = {2402.08250},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2402-08250.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2402-13178,
author = {Guangzhi Xiong and
Qiao Jin and
Zhiyong Lu and
Aidong Zhang},
title = {Benchmarking Retrieval-Augmented Generation for Medicine},
journal = {CoRR},
volume = {abs/2402.13178},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2402.13178},
doi = {10.48550/ARXIV.2402.13178},
eprinttype = {arXiv},
eprint = {2402.13178},
timestamp = {Mon, 02 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2402-13178.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2402-13225,
author = {Qiao Jin and
Zhizheng Wang and
Yifan Yang and
Qingqing Zhu and
Donald Wright and
Thomas Huang and
W. John Wilbur and
Zhe He and
Andrew Taylor and
Qingyu Chen and
Zhiyong Lu},
title = {AgentMD: Empowering Language Agents for Risk Prediction with Large-Scale
Clinical Tool Learning},
journal = {CoRR},
volume = {abs/2402.13225},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2402.13225},
doi = {10.48550/ARXIV.2402.13225},
eprinttype = {arXiv},
eprint = {2402.13225},
timestamp = {Thu, 01 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2402-13225.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2402-14359,
author = {Xiuying Chen and
Tairan Wang and
Qingqing Zhu and
Taicheng Guo and
Shen Gao and
Zhiyong Lu and
Xin Gao and
Xiangliang Zhang},
title = {Rethinking Scientific Summarization Evaluation: Grounding Explainable
Metrics on Facet-aware Benchmark},
journal = {CoRR},
volume = {abs/2402.14359},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2402.14359},
doi = {10.48550/ARXIV.2402.14359},
eprinttype = {arXiv},
eprint = {2402.14359},
timestamp = {Mon, 03 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2402-14359.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2403-05680,
author = {Qingqing Zhu and
Benjamin Hou and
Tejas Sudharshan Mathai and
Pritam Mukherjee and
Qiao Jin and
Xiuying Chen and
Zhizheng Wang and
Ruida Cheng and
Ronald M. Summers and
Zhiyong Lu},
title = {Decomposing Vision-based {LLM} Predictions for Auto-Evaluation with
{GPT-4}},
journal = {CoRR},
volume = {abs/2403.05680},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2403.05680},
doi = {10.48550/ARXIV.2403.05680},
eprinttype = {arXiv},
eprint = {2403.05680},
timestamp = {Thu, 01 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2403-05680.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2404-14209,
author = {Po{-}Ting Lai and
Elisabeth Coudert and
Lucila Aimo and
Kristian B. Axelsen and
Lionel Breuza and
Edouard De Castro and
Marc Feuermann and
Anne Morgat and
Lucille Pourcel and
Ivo Pedruzzi and
Sylvain Poux and
Nicole Redaschi and
Catherine Rivoire and
Anastasia Sveshnikova and
Chih{-}Hsuan Wei and
Robert Leaman and
Ling Luo and
Zhiyong Lu and
Alan J. Bridge},
title = {EnzChemRED, a rich enzyme chemistry relation extraction dataset},
journal = {CoRR},
volume = {abs/2404.14209},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2404.14209},
doi = {10.48550/ARXIV.2404.14209},
eprinttype = {arXiv},
eprint = {2404.14209},
timestamp = {Sat, 25 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2404-14209.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2405-08780,
author = {Gregory Holste and
Mingquan Lin and
Ruiwen Zhou and
Fei Wang and
Lei Liu and
Qi Yan and
Sarah Van Tassel and
Kyle Kovacs and
Emily Y. Chew and
Zhiyong Lu and
Zhangyang Wang and
Yifan Peng},
title = {Harnessing the power of longitudinal medical imaging for eye disease
prognosis using Transformer-based sequence modeling},
journal = {CoRR},
volume = {abs/2405.08780},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2405.08780},
doi = {10.48550/ARXIV.2405.08780},
eprinttype = {arXiv},
eprint = {2405.08780},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2405-08780.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2405-16205,
author = {Zhizheng Wang and
Qiao Jin and
Chih{-}Hsuan Wei and
Shubo Tian and
Po{-}Ting Lai and
Qingqing Zhu and
Chi{-}Ping Day and
Christina Ross and
Zhiyong Lu},
title = {GeneAgent: Self-verification Language Agent for Gene Set Knowledge
Discovery using Domain Databases},
journal = {CoRR},
volume = {abs/2405.16205},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2405.16205},
doi = {10.48550/ARXIV.2405.16205},
eprinttype = {arXiv},
eprint = {2405.16205},
timestamp = {Thu, 01 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2405-16205.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2406-03688,
author = {Benjamin Hou and
Qingqing Zhu and
Tejas Sudharshan Mathai and
Qiao Jin and
Zhiyong Lu and
Ronald M. Summers},
title = {Shadow and Light: Digitally Reconstructed Radiographs for Disease
Classification},
journal = {CoRR},
volume = {abs/2406.03688},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2406.03688},
doi = {10.48550/ARXIV.2406.03688},
eprinttype = {arXiv},
eprint = {2406.03688},
timestamp = {Thu, 10 Jul 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2406-03688.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2406-10671,
author = {Yu Yin and
Hyunjae Kim and
Xiao Xiao and
Chih{-}Hsuan Wei and
Jaewoo Kang and
Zhiyong Lu and
Hua Xu and
Meng Fang and
Qingyu Chen},
title = {Augmenting Biomedical Named Entity Recognition with General-domain
Resources},
journal = {CoRR},
volume = {abs/2406.10671},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2406.10671},
doi = {10.48550/ARXIV.2406.10671},
eprinttype = {arXiv},
eprint = {2406.10671},
timestamp = {Thu, 18 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2406-10671.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2406-12036,
author = {Nikhil Khandekar and
Qiao Jin and
Guangzhi Xiong and
Soren Dunn and
Serina S. Applebaum and
Zain Anwar and
Maame Sarfo{-}Gyamfi and
Conrad W. Safranek and
Abid A Anwar and
Andrew Zhang and
Aidan Gilson and
Maxwell B. Singer and
Amisha D. Dave and
Andrew Taylor and
Aidong Zhang and
Qingyu Chen and
Zhiyong Lu},
title = {MedCalc-Bench: Evaluating Large Language Models for Medical Calculations},
journal = {CoRR},
volume = {abs/2406.12036},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2406.12036},
doi = {10.48550/ARXIV.2406.12036},
eprinttype = {arXiv},
eprint = {2406.12036},
timestamp = {Mon, 02 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2406-12036.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2406-12259,
author = {Yifan Yang and
Qiao Jin and
Furong Huang and
Zhiyong Lu},
title = {Adversarial Attacks on Large Language Models in Medicine},
journal = {CoRR},
volume = {abs/2406.12259},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2406.12259},
doi = {10.48550/ARXIV.2406.12259},
eprinttype = {arXiv},
eprint = {2406.12259},
timestamp = {Wed, 16 Apr 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2406-12259.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2406-17755,
author = {Zifeng Wang and
Lang Cao and
Benjamin P. Danek and
Yichi Zhang and
Qiao Jin and
Zhiyong Lu and
Jimeng Sun},
title = {Accelerating Clinical Evidence Synthesis with Large Language Models},
journal = {CoRR},
volume = {abs/2406.17755},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2406.17755},
doi = {10.48550/ARXIV.2406.17755},
eprinttype = {arXiv},
eprint = {2406.17755},
timestamp = {Mon, 16 Mar 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2406-17755.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2408-00588,
author = {Gongbo Zhang and
Qiao Jin and
Yiliang Zhou and
Song Wang and
Betina Ross S. Idnay and
Yiming Luo and
Elizabeth Park and
Jordan G. Nestor and
Matthew E. Spotnitz and
Ali Soroush and
Thomas Campion and
Zhiyong Lu and
Chunhua Weng and
Yifan Peng},
title = {Closing the gap between open-source and commercial large language
models for medical evidence summarization},
journal = {CoRR},
volume = {abs/2408.00588},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2408.00588},
doi = {10.48550/ARXIV.2408.00588},
eprinttype = {arXiv},
eprint = {2408.00588},
timestamp = {Thu, 25 Dec 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2408-00588.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2408-00727,
author = {Guangzhi Xiong and
Qiao Jin and
Xiao Wang and
Minjia Zhang and
Zhiyong Lu and
Aidong Zhang},
title = {Improving Retrieval-Augmented Generation in Medicine with Iterative
Follow-up Questions},
journal = {CoRR},
volume = {abs/2408.00727},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2408.00727},
doi = {10.48550/ARXIV.2408.00727},
eprinttype = {arXiv},
eprint = {2408.00727},
timestamp = {Mon, 02 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2408-00727.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2409-13902,
author = {Aidan Gilson and
Xuguang Ai and
Thilaka Arunachalam and
Ziyou Chen and
Ki Xiong Cheong and
Amisha D. Dave and
Cameron Duic and
Mercy Kibe and
Annette Kaminaka and
Minali Prasad and
Fares Siddig and
Maxwell B. Singer and
Wendy Wong and
Qiao Jin and
Tiarnan D. L. Keenan and
Xia Hu and
Emily Y. Chew and
Zhiyong Lu and
Hua Xu and
Ron A. Adelman and
Yih{-}Chung Tham and
Qingyu Chen},
title = {Enhancing Large Language Models with Domain-specific Retrieval Augment
Generation: {A} Case Study on Long-form Consumer Health Question Answering
in Ophthalmology},
journal = {CoRR},
volume = {abs/2409.13902},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2409.13902},
doi = {10.48550/ARXIV.2409.13902},
eprinttype = {arXiv},
eprint = {2409.13902},
timestamp = {Wed, 14 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2409-13902.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2409-15087,
author = {Qingyu Chen and
Tiarnan D. L. Keenan and
Elvira Agr{\'{o}}n and
Alexis Allot and
Emily Guan and
Bryant Duong and
Amr S. Elsawy and
Benjamin Hou and
Cancan Xue and
Sanjeeb Bhandari and
Geoff Broadhead and
Chantal Cousineau{-}Krieger and
Ellen Davis and
William G. Gensheimer and
David Grasic and
Seema Gupta and
Luis Haddock and
Eleni Konstantinou and
Tania Lamba and
Michele Maiberger and
Dimosthenis Mantopoulos and
Mitul C. Mehta and
Ayman G. Nahri and
Mutaz AL{-}Nawaflh and
Arnold Oshinsky and
Brittany E. Powell and
Boonkit Purt and
Soo Shin and
Hillary Stiefel and
Alisa T. Thavikulwat and
Keith Wroblewski and
Tham Yih Chung and
Chui Ming Gemmy Cheung and
Ching{-}Yu Cheng and
Emily Y. Chew and
Michelle R. Hribar and
Michael F. Chiang and
Zhiyong Lu},
title = {Towards Accountable AI-Assisted Eye Disease Diagnosis: Workflow Design,
External Validation, and Continual Learning},
journal = {CoRR},
volume = {abs/2409.15087},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2409.15087},
doi = {10.48550/ARXIV.2409.15087},
eprinttype = {arXiv},
eprint = {2409.15087},
timestamp = {Mon, 21 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2409-15087.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2410-12793,
author = {Betina Idnay and
Zihan Xu and
William G. Adams and
Mohammad Adibuzzaman and
Nicholas R. Anderson and
Neil Bahroos and
Douglas S. Bell and
Cody Bumgardner and
Thomas R. Campion Jr. and
Victor M. Castro and
James J. Cimino and
I. Glenn Cohen and
David A. Dorr and
Peter L. Elkin and
Jungwei W. Fan and
Todd Ferris and
David J. Foran and
David A. Hanauer and
Mike Hogarth and
Kun Huang and
Jayashree Kalpathy{-}Cramer and
Manoj Kandpal and
Niranjan S. Karnik and
Avnish Katoch and
Albert M. Lai and
Christophe G. Lambert and
Lang Li and
Christopher J. Lindsell and
Jinze Liu and
Zhiyong Lu and
Yuan Luo and
Peter McGarvey and
Eneida A. Mendon{\c{c}}a and
Parsa Mirhaji and
Shawn N. Murphy and
John D. Osborne and
Ioannis Ch. Paschalidis and
Paul A. Harris and
Fred W. Prior and
Nicholas J. Shaheen and
Nawar Shara and
Ida Sim and
Umberto Tachinardi and
Lemuel R. Waitman and
Rosalind J. Wright and
Adrian H. Zai and
Kai Zheng and
Sandra Soo{-}Jin Lee and
Bradley A. Malin and
Karthik Natarajan and
W. Nicholson Price and
Rui Zhang and
Yiye Zhang and
Hua Xu and
Jiang Bian and
Chunhua Weng and
Yifan Peng},
title = {Environment Scan of Generative {AI} Infrastructure for Clinical and
Translational Science},
journal = {CoRR},
volume = {abs/2410.12793},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2410.12793},
doi = {10.48550/ARXIV.2410.12793},
eprinttype = {arXiv},
eprint = {2410.12793},
timestamp = {Wed, 25 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2410-12793.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2410-18460,
author = {Yifan Yang and
Qiao Jin and
Qingqing Zhu and
Zhizheng Wang and
Francisco Erramuspe {\'{A}}lvarez and
Nicholas Wan and
Benjamin Hou and
Zhiyong Lu},
title = {Beyond Multiple-Choice Accuracy: Real-World Challenges of Implementing
Large Language Models in Healthcare},
journal = {CoRR},
volume = {abs/2410.18460},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2410.18460},
doi = {10.48550/ARXIV.2410.18460},
eprinttype = {arXiv},
eprint = {2410.18460},
timestamp = {Thu, 01 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2410-18460.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2410-18856,
author = {Qiao Jin and
Nicholas Wan and
Robert Leaman and
Shubo Tian and
Zhizheng Wang and
Yifan Yang and
Zifeng Wang and
Guangzhi Xiong and
Po{-}Ting Lai and
Qingqing Zhu and
Benjamin Hou and
Maame Sarfo{-}Gyamfi and
Gongbo Zhang and
Aidan Gilson and
Balu Bhasuran and
Zhe He and
Aidong Zhang and
Jimeng Sun and
Chunhua Weng and
Ronald M. Summers and
Qingyu Chen and
Yifan Peng and
Zhiyong Lu},
title = {Demystifying Large Language Models for Medicine: {A} Primer},
journal = {CoRR},
volume = {abs/2410.18856},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2410.18856},
doi = {10.48550/ARXIV.2410.18856},
eprinttype = {arXiv},
eprint = {2410.18856},
timestamp = {Mon, 02 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2410-18856.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2411-02523,
author = {Balu Bhasuran and
Qiao Jin and
Yuzhang Xie and
Carl Yang and
Karim Hanna and
Jennifer Costa and
Cindy Shavor and
Zhiyong Lu and
Zhe He},
title = {Evaluating the Impact of Lab Test Results on Large Language Models
Generated Differential Diagnoses from Clinical Case Vignettes},
journal = {CoRR},
volume = {abs/2411.02523},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2411.02523},
doi = {10.48550/ARXIV.2411.02523},
eprinttype = {arXiv},
eprint = {2411.02523},
timestamp = {Mon, 03 Feb 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2411-02523.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2411-05897,
author = {Nicholas Wan and
Qiao Jin and
Joey Chan and
Guangzhi Xiong and
Serina S. Applebaum and
Aidan Gilson and
Reid McMurry and
R. Andrew Taylor and
Aidong Zhang and
Qingyu Chen and
Zhiyong Lu},
title = {Humans Continue to Outperform Large Language Models in Complex Clinical
Decision-Making: {A} Study with Medical Calculators},
journal = {CoRR},
volume = {abs/2411.05897},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2411.05897},
doi = {10.48550/ARXIV.2411.05897},
eprinttype = {arXiv},
eprint = {2411.05897},
timestamp = {Mon, 02 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2411-05897.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2411-14487,
author = {Yifan Yang and
Qiao Jin and
Robert Leaman and
Xiaoyu Liu and
Guangzhi Xiong and
Maame Sarfo{-}Gyamfi and
Changlin Gong and
Santiago Ferri{\`{e}}re{-}Steinert and
W. John Wilbur and
Xiaojun Li and
Jiaxin Yuan and
Bang An and
Kelvin S. Castro and
Francisco Erramuspe {\'{A}}lvarez and
Mat{\'{\i}}as Stockle and
Aidong Zhang and
Furong Huang and
Zhiyong Lu},
title = {Ensuring Safety and Trust: Analyzing the Risks of Large Language Models
in Medicine},
journal = {CoRR},
volume = {abs/2411.14487},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2411.14487},
doi = {10.48550/ARXIV.2411.14487},
eprinttype = {arXiv},
eprint = {2411.14487},
timestamp = {Mon, 02 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2411-14487.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2412-15271,
author = {Gongbo Zhang and
Zihan Xu and
Qiao Jin and
Fangyi Chen and
Yilu Fang and
Yi Liu and
Justin F. Rousseau and
Ziyang Xu and
Zhiyong Lu and
Chunhua Weng and
Yifan Peng},
title = {A MapReduce Approach to Effectively Utilize Long Context Information
in Retrieval Augmented Language Models},
journal = {CoRR},
volume = {abs/2412.15271},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2412.15271},
doi = {10.48550/ARXIV.2412.15271},
eprinttype = {arXiv},
eprint = {2412.15271},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2412-15271.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/LeamanIAAA0BCEH23,
author = {Robert Leaman and
Rezarta Islamaj and
Virginia Adams and
Mohammed Alliheedi and
Jo{\~{a}}o Rafael Almeida and
Rui Antunes and
Robert Bevan and
Yung{-}Chun Chang and
Arslan Erdengasileng and
Matthew Hodgskiss and
Ryuki Ida and
Hyunjae Kim and
Keqiao Li and
Robert E. Mercer and
Lukr{\'{e}}cia Mertov{\'{a}} and
Ghadeer Mobasher and
Hoo{-}Chang Shin and
Mujeen Sung and
Tomoki Tsujimura and
Wen{-}Chao Yeh and
Zhiyong Lu},
title = {Chemical identification and indexing in full-text articles: an overview
of the NLM-Chem track at BioCreative {VII}},
journal = {Database J. Biol. Databases Curation},
volume = {2023},
year = {2023},
url = {https://doi.org/10.1093/database/baad005},
doi = {10.1093/DATABASE/BAAD005},
timestamp = {Thu, 25 Dec 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/LeamanIAAA0BCEH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuoWLLCL23,
author = {Ling Luo and
Chih{-}Hsuan Wei and
Po{-}Ting Lai and
Robert Leaman and
Qingyu Chen and
Zhiyong Lu},
title = {{AIONER:} all-in-one scheme-based biomedical named entity recognition
using deep learning},
journal = {Bioinform.},
volume = {39},
number = {5},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad310},
doi = {10.1093/BIOINFORMATICS/BTAD310},
timestamp = {Tue, 28 Oct 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuoWLLCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JinKCCYWL23,
author = {Qiao Jin and
Won Kim and
Qingyu Chen and
Donald C. Comeau and
Lana Yeganova and
W. John Wilbur and
Zhiyong Lu},
title = {MedCPT: Contrastive Pre-trained Transformers with large-scale PubMed
search logs for zero-shot biomedical information retrieval},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad651},
doi = {10.1093/BIOINFORMATICS/BTAD651},
timestamp = {Tue, 28 Oct 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JinKCCYWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeiLILL23,
author = {Chih{-}Hsuan Wei and
Ling Luo and
Rezarta Islamaj and
Po{-}Ting Lai and
Zhiyong Lu},
title = {GNorm2: an improved gene name recognition and normalization system},
journal = {Bioinform.},
volume = {39},
number = {10},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad599},
doi = {10.1093/BIOINFORMATICS/BTAD599},
timestamp = {Tue, 28 Oct 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeiLILL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrozaWDDHBDLLR23,
author = {Tudor Groza and
Honghan Wu and
Marcel E. Dinger and
Daniel Danis and
Coleman Hilton and
Anita Bagley and
Jon R. Davids and
Ling Luo and
Zhiyong Lu and
Peter N. Robinson},
title = {Term-BLAST-like alignment tool for concept recognition in noisy clinical
texts},
journal = {Bioinform.},
volume = {39},
number = {12},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad716},
doi = {10.1093/BIOINFORMATICS/BTAD716},
timestamp = {Mon, 03 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/GrozaWDDHBDLLR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/cars/MathaiLSLS23,
author = {Tejas Sudharshan Mathai and
Sungwon Lee and
Thomas C. Shen and
Zhiyong Lu and
Ronald M. Summers},
title = {Universal lymph node detection in {T2} {MRI} using neural networks},
journal = {Int. J. Comput. Assist. Radiol. Surg.},
volume = {18},
number = {2},
pages = {313--318},
year = {2023},
url = {https://doi.org/10.1007/s11548-022-02782-1},
doi = {10.1007/S11548-022-02782-1},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/cars/MathaiLSLS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/SunLZXWLP23,
author = {Zhaoyi Sun and
Mingquan Lin and
Qingqing Zhu and
Qianqian Xie and
Fei Wang and
Zhiyong Lu and
Yifan Peng},
title = {A scoping review on multimodal deep learning in biomedical images
and texts},
journal = {J. Biomed. Informatics},
volume = {146},
pages = {104482},
year = {2023},
url = {https://doi.org/10.1016/j.jbi.2023.104482},
doi = {10.1016/J.JBI.2023.104482},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbi/SunLZXWLP23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/LaiWLCL23,
author = {Po{-}Ting Lai and
Chih{-}Hsuan Wei and
Ling Luo and
Qingyu Chen and
Zhiyong Lu},
title = {BioREx: Improving biomedical relation extraction by leveraging heterogeneous
datasets},
journal = {J. Biomed. Informatics},
volume = {146},
pages = {104487},
year = {2023},
url = {https://doi.org/10.1016/j.jbi.2023.104487},
doi = {10.1016/J.JBI.2023.104487},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbi/LaiWLCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SayersBBCCCFFFFHKKKKLLLMMMMPPRSTWYT23,
author = {Eric W. Sayers and
Evan E. Bolton and
J. Rodney Brister and
Kathi Canese and
Jessica Chan and
Donald C. Comeau and
Catherine M. Farrell and
Michael Feldgarden and
Anna M. Fine and
Kathryn Funk and
Eneida Hatcher and
Sivakumar Kannan and
Christopher Kelly and
Sunghwan Kim and
William Klimke and
Melissa J. Landrum and
Stacy Lathrop and
Zhiyong Lu and
Thomas L. Madden and
Adriana J. Malheiro and
Aron Marchler{-}Bauer and
Terence D. Murphy and
Lon Phan and
Shashikant Pujar and
Sanjida H. Rangwala and
Valerie A. Schneider and
Tony Tse and
Jiyao Wang and
Jian Ye and
Barton W. Trawick and
Kim D. Pruitt and
Stephen T. Sherry},
title = {Database resources of the National Center for Biotechnology Information
in 2023},
journal = {Nucleic Acids Res.},
volume = {51},
number = {{D1}},
pages = {29--38},
year = {2023},
url = {https://doi.org/10.1093/nar/gkac1032},
doi = {10.1093/NAR/GKAC1032},
timestamp = {Tue, 14 Oct 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SayersBBCCCFFFFHKKKKLLLMMMMPPRSTWYT23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ChenALWAGXL23,
author = {Qingyu Chen and
Alexis Allot and
Robert Leaman and
Chih{-}Hsuan Wei and
Elaheh Aghaarabi and
John J. Guerrerio and
Lilly Xu and
Zhiyong Lu},
title = {LitCovid in 2022: an information resource for the {COVID-19} literature},
journal = {Nucleic Acids Res.},
volume = {51},
number = {{D1}},
pages = {1512--1518},
year = {2023},
url = {https://doi.org/10.1093/nar/gkac1005},
doi = {10.1093/NAR/GKAC1005},
timestamp = {Fri, 18 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ChenALWAGXL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/patterns/LeamanIACWL23,
author = {Robert Leaman and
Rezarta Islamaj and
Alexis Allot and
Qingyu Chen and
W. John Wilbur and
Zhiyong Lu},
title = {Comprehensively identifying Long Covid articles with human-in-the-loop
machine learning},
journal = {Patterns},
volume = {4},
number = {1},
pages = {100659},
year = {2023},
url = {https://doi.org/10.1016/j.patter.2022.100659},
doi = {10.1016/J.PATTER.2022.100659},
timestamp = {Tue, 28 Mar 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/patterns/LeamanIACWL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pr/LiuLSL23,
author = {Xingsheng Liu and
Anhu Li and
Jianfeng Sun and
Zhiyong Lu},
title = {Trigonometric projection statistics histograms for 3D local feature
representation and shape description},
journal = {Pattern Recognit.},
volume = {143},
pages = {109727},
year = {2023},
url = {https://doi.org/10.1016/j.patcog.2023.109727},
doi = {10.1016/J.PATCOG.2023.109727},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/pr/LiuLSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/clef/Shin0L23,
author = {Ashley Shin and
Qiao Jin and
Zhiyong Lu},
editor = {Mohammad Aliannejadi and
Guglielmo Faggioli and
Nicola Ferro and
Michalis Vlachos},
title = {Multi-stage Literature Retrieval System Trained by PubMed Search Logs
for Biomedical Question Answering},
booktitle = {Working Notes of the Conference and Labs of the Evaluation Forum {(CLEF}
2023), Thessaloniki, Greece, September 18th to 21st, 2023},
series = {{CEUR} Workshop Proceedings},
volume = {3497},
pages = {178--189},
publisher = {CEUR-WS.org},
year = {2023},
url = {https://ceur-ws.org/Vol-3497/paper-016.pdf},
timestamp = {Wed, 25 Oct 2023 17:24:28 +0200},
biburl = {https://dblp.org/rec/conf/clef/Shin0L23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/micad/MathaiLSLS23,
author = {Tejas Sudharshan Mathai and
Sungwon Lee and
Thomas C. Shen and
Zhiyong Lu and
Ronald M. Summers},
editor = {Khan M. Iftekharuddin and
Weijie Chen},
title = {Universal lymph node detection in multiparametric {MRI} with selective
augmentation},
booktitle = {Medical Imaging 2023: Computer-Aided Diagnosis, San Diego, CA, USA,
February 19-23, 2023},
series = {{SPIE} Proceedings},
volume = {12465},
publisher = {{SPIE}},
year = {2023},
url = {https://doi.org/10.1117/12.2655270},
doi = {10.1117/12.2655270},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/micad/MathaiLSLS23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/miccai/ZhuMMPSL23,
author = {Qingqing Zhu and
Tejas Sudharshan Mathai and
Pritam Mukherjee and
Yifan Peng and
Ronald M. Summers and
Zhiyong Lu},
editor = {Hayit Greenspan and
Anant Madabhushi and
Parvin Mousavi and
Septimiu E. Salcudean and
James Duncan and
Tanveer F. Syeda{-}Mahmood and
Russell H. Taylor},
title = {Utilizing Longitudinal Chest X-Rays and Reports to Pre-fill Radiology
Reports},
booktitle = {Medical Image Computing and Computer Assisted Intervention - {MICCAI}
2023 - 26th International Conference, Vancouver, BC, Canada, October
8-12, 2023, Proceedings, Part {V}},
series = {Lecture Notes in Computer Science},
volume = {14224},
pages = {189--198},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-3-031-43904-9\_19},
doi = {10.1007/978-3-031-43904-9\_19},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/miccai/ZhuMMPSL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/miip/ElsawyK0SCL23,
author = {Amr S. Elsawy and
Tiarnan D. Kenan and
Qingyu Chen and
Xiaoshuang Shi and
Emily Y. Chew and
Zhiyong Lu},
editor = {Olivier Colliot and
Ivana Isgum},
title = {Attention-based 3D convolutional networks for detection of geographic
atrophy from optical coherence tomography scans},
booktitle = {Medical Imaging 2023: Image Processing, San Diego, CA, USA, February
19-23, 2023},
series = {{SPIE} Proceedings},
volume = {12464},
publisher = {{SPIE}},
year = {2023},
url = {https://doi.org/10.1117/12.2654487},
doi = {10.1117/12.2654487},
timestamp = {Wed, 27 Nov 2024 12:15:53 +0100},
biburl = {https://dblp.org/rec/conf/miip/ElsawyK0SCL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sigir/0001SL23,
author = {Qiao Jin and
Andrew Shin and
Zhiyong Lu},
editor = {Hsin{-}Hsi Chen and
Wei{-}Jou (Edward) Duh and
Hen{-}Hsen Huang and
Makoto P. Kato and
Josiane Mothe and
Barbara Poblete},
title = {{LADER:} Log-Augmented DEnse Retrieval for Biomedical Literature Search},
booktitle = {Proceedings of the 46th International {ACM} {SIGIR} Conference on
Research and Development in Information Retrieval, {SIGIR} 2023, Taipei,
Taiwan, July 23-27, 2023},
pages = {2092--2097},
publisher = {{ACM}},
year = {2023},
url = {https://doi.org/10.1145/3539618.3592005},
doi = {10.1145/3539618.3592005},
timestamp = {Wed, 25 Feb 2026 08:28:08 +0100},
biburl = {https://dblp.org/rec/conf/sigir/0001SL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2302-01588,
author = {Li Fang and
Qingyu Chen and
Chih{-}Hsuan Wei and
Zhiyong Lu and
Kai Wang},
title = {Bioformer: an efficient transformer language model for biomedical
text mining},
journal = {CoRR},
volume = {abs/2302.01588},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2302.01588},
doi = {10.48550/ARXIV.2302.01588},
eprinttype = {arXiv},
eprint = {2302.01588},
timestamp = {Fri, 10 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2302-01588.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2302-09636,
author = {Xinyue Hu and
Lin Gu and
Kazuma Kobayashi and
Qiyuan An and
Qingyu Chen and
Zhiyong Lu and
Chang Su and
Tatsuya Harada and
Yingying Zhu},
title = {Interpretable Medical Image Visual Question Answering via Multi-Modal
Relationship Graph Learning},
journal = {CoRR},
volume = {abs/2302.09636},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2302.09636},
doi = {10.48550/ARXIV.2302.09636},
eprinttype = {arXiv},
eprint = {2302.09636},
timestamp = {Tue, 14 Oct 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2302-09636.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2304-04590,
author = {Qiao Jin and
Andrew Shin and
Zhiyong Lu},
title = {{LADER:} Log-Augmented DEnse Retrieval for Biomedical Literature Search},
journal = {CoRR},
volume = {abs/2304.04590},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2304.04590},
doi = {10.48550/ARXIV.2304.04590},
eprinttype = {arXiv},
eprint = {2304.04590},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2304-04590.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2304-09667,
author = {Qiao Jin and
Yifan Yang and
Qingyu Chen and
Zhiyong Lu},
title = {GeneGPT: Augmenting Large Language Models with Domain Tools for Improved
Access to Biomedical Information},
journal = {CoRR},
volume = {abs/2304.09667},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2304.09667},
doi = {10.48550/ARXIV.2304.09667},
eprinttype = {arXiv},
eprint = {2304.09667},
timestamp = {Wed, 16 Apr 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2304-09667.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2305-16326,
author = {Qingyu Chen and
Jingcheng Du and
Yan Hu and
Vipina Kuttichi Keloth and
Xueqing Peng and
Kalpana Raja and
Rui Zhang and
Zhiyong Lu and
Hua Xu},
title = {Large language models in biomedical natural language processing: benchmarks,
baselines, and recommendations},
journal = {CoRR},
volume = {abs/2305.16326},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2305.16326},
doi = {10.48550/ARXIV.2305.16326},
eprinttype = {arXiv},
eprint = {2305.16326},
timestamp = {Wed, 17 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2305-16326.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2306-08749,
author = {Qingqing Zhu and
Tejas Sudharshan Mathai and
Pritam Mukherjee and
Yifan Peng and
Ronald M. Summers and
Zhiyong Lu},
title = {Utilizing Longitudinal Chest X-Rays and Reports to Pre-Fill Radiology
Reports},
journal = {CoRR},
volume = {abs/2306.08749},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2306.08749},
doi = {10.48550/ARXIV.2306.08749},
eprinttype = {arXiv},
eprint = {2306.08749},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2306-08749.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2306-10070,
author = {Shubo Tian and
Qiao Jin and
Lana Yeganova and
Po{-}Ting Lai and
Qingqing Zhu and
Xiuying Chen and
Yifan Yang and
Qingyu Chen and
Won Kim and
Donald C. Comeau and
Rezarta Islamaj and
Aadit Kapoor and
Xin Gao and
Zhiyong Lu},
title = {Opportunities and Challenges for ChatGPT and Large Language Models
in Biomedicine and Health},
journal = {CoRR},
volume = {abs/2306.10070},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2306.10070},
doi = {10.48550/ARXIV.2306.10070},
eprinttype = {arXiv},
eprint = {2306.10070},
timestamp = {Wed, 16 Apr 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2306-10070.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2306-11189,
author = {Po{-}Ting Lai and
Chih{-}Hsuan Wei and
Ling Luo and
Qingyu Chen and
Zhiyong Lu},
title = {BioREx: Improving Biomedical Relation Extraction by Leveraging Heterogeneous
Datasets},
journal = {CoRR},
volume = {abs/2306.11189},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2306.11189},
doi = {10.48550/ARXIV.2306.11189},
eprinttype = {arXiv},
eprint = {2306.11189},
timestamp = {Fri, 23 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2306-11189.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2307-00589,
author = {Qiao Jin and
Won Kim and
Qingyu Chen and
Donald C. Comeau and
Lana Yeganova and
W. John Wilbur and
Zhiyong Lu},
title = {BioCPT: Contrastive Pre-trained Transformers with Large-scale PubMed
Search Logs for Zero-shot Biomedical Information Retrieval},
journal = {CoRR},
volume = {abs/2307.00589},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2307.00589},
doi = {10.48550/ARXIV.2307.00589},
eprinttype = {arXiv},
eprint = {2307.00589},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2307-00589.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2307-07362,
author = {Zhaoyi Sun and
Mingquan Lin and
Qingqing Zhu and
Qianqian Xie and
Fei Wang and
Zhiyong Lu and
Yifan Peng},
title = {A scoping review on multimodal deep learning in biomedical images
and texts},
journal = {CoRR},
volume = {abs/2307.07362},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2307.07362},
doi = {10.48550/ARXIV.2307.07362},
eprinttype = {arXiv},
eprint = {2307.07362},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2307-07362.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2307-09683,
author = {Qiao Jin and
Robert Leaman and
Zhiyong Lu},
title = {PubMed and Beyond: Recent Advances and Best Practices in Biomedical
Literature Search},
journal = {CoRR},
volume = {abs/2307.09683},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2307.09683},
doi = {10.48550/ARXIV.2307.09683},
eprinttype = {arXiv},
eprint = {2307.09683},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2307-09683.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2307-15051,
author = {Qiao Jin and
Zifeng Wang and
Charalampos S. Floudas and
Jimeng Sun and
Zhiyong Lu},
title = {Matching Patients to Clinical Trials with Large Language Models},
journal = {CoRR},
volume = {abs/2307.15051},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2307.15051},
doi = {10.48550/ARXIV.2307.15051},
eprinttype = {arXiv},
eprint = {2307.15051},
timestamp = {Fri, 06 Dec 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2307-15051.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2310-16112,
author = {Gregory Holste and
Yiliang Zhou and
Song Wang and
Ajay Jaiswal and
Mingquan Lin and
Sherry Zhuge and
Yuzhe Yang and
Dongkyun Kim and
Trong{-}Hieu Nguyen Mau and
Minh{-}Triet Tran and
Jaehyup Jeong and
Wongi Park and
Jongbin Ryu and
Feng Hong and
Arsh Verma and
Yosuke Yamagishi and
Changhyun Kim and
Hyeryeong Seo and
Myungjoo Kang and
Leo Anthony Celi and
Zhiyong Lu and
Ronald M. Summers and
George Shih and
Zhangyang Wang and
Yifan Peng},
title = {Towards long-tailed, multi-label disease classification from chest
X-ray: Overview of the {CXR-LT} challenge},
journal = {CoRR},
volume = {abs/2310.16112},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2310.16112},
doi = {10.48550/ARXIV.2310.16112},
eprinttype = {arXiv},
eprint = {2310.16112},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2310-16112.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2311-11211,
author = {Gongbo Zhang and
Qiao Jin and
Denis Jered McInerney and
Yong Chen and
Fei Wang and
Curtis L. Cole and
Qian Yang and
Yanshan Wang and
Bradley A. Malin and
Mor Peleg and
Byron C. Wallace and
Zhiyong Lu and
Chunhua Weng and
Yifan Peng},
title = {Leveraging Generative {AI} for Clinical Evidence Summarization Needs
to Achieve Trustworthiness},
journal = {CoRR},
volume = {abs/2311.11211},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2311.11211},
doi = {10.48550/ARXIV.2311.11211},
eprinttype = {arXiv},
eprint = {2311.11211},
timestamp = {Sun, 07 Dec 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2311-11211.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2311-16588,
author = {Rui Yang and
Qingcheng Zeng and
Keen You and
Yujie Qiao and
Lucas Huang and
Chiachun Hsieh and
Benjamin Rosand and
Jeremy Goldwasser and
Amisha D. Dave and
Tiarnan D. L. Keenan and
Emily Y. Chew and
Dragomir Radev and
Zhiyong Lu and
Hua Xu and
Qingyu Chen and
Irene Li},
title = {MedGen: {A} Python Natural Language Processing Toolkit for Medical
Text Processing},
journal = {CoRR},
volume = {abs/2311.16588},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2311.16588},
doi = {10.48550/ARXIV.2311.16588},
eprinttype = {arXiv},
eprint = {2311.16588},
timestamp = {Sat, 13 Sep 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2311-16588.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LuoLWAL22,
author = {Ling Luo and
Po{-}Ting Lai and
Chih{-}Hsuan Wei and
Cecilia N. Arighi and
Zhiyong Lu},
title = {BioRED: a rich biomedical relation extraction dataset},
journal = {Briefings Bioinform.},
volume = {23},
number = {5},
year = {2022},
url = {https://doi.org/10.1093/bib/bbac282},
doi = {10.1093/BIB/BBAC282},
timestamp = {Sun, 02 Nov 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LuoLWAL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/0001WL0IL22,
author = {Ling Luo and
Chih{-}Hsuan Wei and
Po{-}Ting Lai and
Qingyu Chen and
Rezarta Islamaj and
Zhiyong Lu},
title = {Assigning species information to corresponding genes by a sequence
labeling framework},
journal = {Database J. Biol. Databases Curation},
volume = {2022},
number = {2022},
year = {2022},
url = {https://doi.org/10.1093/database/baac090},
doi = {10.1093/DATABASE/BAAC090},
timestamp = {Mon, 05 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/0001WL0IL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/ChenALIDFKXZBBB22,
author = {Qingyu Chen and
Alexis Allot and
Robert Leaman and
Rezarta Islamaj and
Jingcheng Du and
Li Fang and
Wang Kai and
Shuo Xu and
Yuefu Zhang and
Parsa Bagherzadeh and
Sabine Bergler and
Aakash Bhatnagar and
Nidhir Bhavsar and
Yung{-}Chun Chang and
Sheng{-}Jie Lin and
Wentai Tang and
Hongtong Zhang and
Ilija Tavchioski and
Senja Pollak and
Shubo Tian and
Jinfeng Zhang and
Yulia Otmakhova and
Antonio Jimeno{-}Yepes and
Hang Dong and
Honghan Wu and
Richard Dufour and
Yanis Labrak and
Niladri Chatterjee and
Kushagri Tandon and
Fr{\'{e}}jus A. A. Laleye and
Lo{\"{\i}}c Rakotoson and
Emmanuele Chersoni and
Jinghang Gu and
Annemarie Friedrich and
Subhash Chandra Pujari and
Mariia Chizhikova and
Naveen Sivadasan and
Saipradeep Vg and
Zhiyong Lu},
title = {Multi-label classification for biomedical literature: an overview
of the BioCreative {VII} LitCovid Track for {COVID-19} literature
topic annotations},
journal = {Database J. Biol. Databases Curation},
volume = {2022},
number = {2022},
year = {2022},
url = {https://doi.org/10.1093/database/baac069},
doi = {10.1093/DATABASE/BAAC069},
timestamp = {Wed, 12 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/ChenALIDFKXZBBB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/Crecy-LagardHAB22,
author = {Val{\'{e}}rie de Cr{\'{e}}cy{-}Lagard and
Rocio Amorin de Hegedus and
Cecilia N. Arighi and
Jill Babor and
Alex Bateman and
Ian Blaby and
Crysten Blaby{-}Haas and
Alan J. Bridge and
Stephen K. Burley and
Stacey Cleveland and
Lucy J. Colwell and
Ana Conesa and
Christian Dallago and
Antoine Danchin and
Anita de Waard and
Adam Deutschbauer and
Raquel Dias and
Yousong Ding and
Gang Fang and
Iddo Friedberg and
John Gerlt and
Joshua Goldford and
Mark Gorelik and
Benjamin M. Gyori and
Christopher S. Henry and
Geoffrey Hutinet and
Marshall Jaroch and
Peter D. Karp and
Liudmyla Kondratova and
Zhiyong Lu and
Aron Marchler{-}Bauer and
Maria Jesus Martin and
Claire D. McWhite and
Gaurav D. Moghe and
Paul Monaghan and
Anne Morgat and
Christopher J. Mungall and
Darren A. Natale and
William C. Nelson and
Se{\'{a}}n I. O'Donoghue and
Christine A. Orengo and
Katherine H. O'Toole and
Predrag Radivojac and
Colbie Reed and
Richard J. Roberts and
Dmitri Rodionov and
Irina A. Rodionova and
Jeffrey DePons and
Lana Saleh and
Gloria M. Sheynkman and
Fran{\c{c}}oise Thibaud{-}Nissen and
Paul D. Thomas and
Peter Uetz and
David Vallenet and
Erica Watson Carter and
Peter Weigele and
Valerie Wood and
Elisha M. Wood{-}Charlson and
Jin Xu},
title = {A roadmap for the functional annotation of protein families: a community
perspective},
journal = {Database J. Biol. Databases Curation},
volume = {2022},
number = {2022},
year = {2022},
url = {https://doi.org/10.1093/database/baac062},
doi = {10.1093/DATABASE/BAAC062},
timestamp = {Sun, 07 Dec 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/Crecy-LagardHAB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/IslamajLCCDFGKM22,
author = {Rezarta Islamaj and
Robert Leaman and
David Cissel and
Cathleen Coss and
Joseph Denicola and
Carol Fisher and
Rob Guzman and
Preeti Gokal Kochar and
Nicholas Miliaras and
Zoe Punske and
Keiko Sekiya and
Dorothy Trinh and
Deborah Whitman and
Susan Schmidt and
Zhiyong Lu},
title = {NLM-Chem-BC7: manually annotated full-text resources for chemical
entity annotation and indexing in biomedical articles},
journal = {Database J. Biol. Databases Curation},
volume = {2022},
number = {2022},
year = {2022},
url = {https://doi.org/10.1093/database/baac102},
doi = {10.1093/DATABASE/BAAC102},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/IslamajLCCDFGKM22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/LuoLWL22,
author = {Ling Luo and
Po{-}Ting Lai and
Chih{-}Hsuan Wei and
Zhiyong Lu},
title = {A sequence labeling framework for extracting drug-protein relations
from biomedical literature},
journal = {Database J. Biol. Databases Curation},
volume = {2022},
number = {2022},
year = {2022},
url = {https://doi.org/10.1093/database/baac058},
doi = {10.1093/DATABASE/BAAC058},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/LuoLWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeiARML22,
author = {Chih{-}Hsuan Wei and
Alexis Allot and
Kevin Riehle and
Aleksandar Milosavljevic and
Zhiyong Lu},
title = {tmVar 3.0: an improved variant concept recognition and normalization
tool},
journal = {Bioinform.},
volume = {38},
number = {18},
pages = {4449--4451},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac537},
doi = {10.1093/BIOINFORMATICS/BTAC537},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeiARML22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/YanLLVOXGSRL22,
author = {Shankai Yan and
Ling Luo and
Po{-}Ting Lai and
Daniel Veltri and
Andrew J. Oler and
Sandhya Xirasagar and
Rajarshi Ghosh and
Morgan Similuk and
Peter N. Robinson and
Zhiyong Lu},
title = {PhenoRerank: {A} re-ranking model for phenotypic concept recognition
pre-trained on human phenotype ontology},
journal = {J. Biomed. Informatics},
volume = {129},
pages = {104059},
year = {2022},
url = {https://doi.org/10.1016/j.jbi.2022.104059},
doi = {10.1016/J.JBI.2022.104059},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbi/YanLLVOXGSRL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/KimYCWL22,
author = {Won Kim and
Lana Yeganova and
Donald C. Comeau and
W. John Wilbur and
Zhiyong Lu},
title = {Towards a unified search: Improving PubMed retrieval with full text},
journal = {J. Biomed. Informatics},
volume = {134},
pages = {104211},
year = {2022},
url = {https://doi.org/10.1016/j.jbi.2022.104211},
doi = {10.1016/J.JBI.2022.104211},
timestamp = {Sun, 22 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbi/KimYCWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/mia/WangZLESTPLS22,
author = {Shuai Wang and
Yingying Zhu and
Sungwon Lee and
Daniel C. Elton and
Thomas C. Shen and
Youbao Tang and
Yifan Peng and
Zhiyong Lu and
Ronald M. Summers},
title = {Global-Local attention network with multi-task uncertainty loss for
abnormal lymph node detection in {MR} images},
journal = {Medical Image Anal.},
volume = {77},
pages = {102345},
year = {2022},
url = {https://doi.org/10.1016/j.media.2021.102345},
doi = {10.1016/J.MEDIA.2021.102345},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/mia/WangZLESTPLS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SayersBBCCCCFKK22,
author = {Eric W. Sayers and
Evan E. Bolton and
J. Rodney Brister and
Kathi Canese and
Jessica Chan and
Donald C. Comeau and
Ryan Connor and
Kathryn Funk and
Chris Kelly and
Sunghwan Kim and
Tom Madej and
Aron Marchler{-}Bauer and
Christopher J. Lanczycki and
Stacy Lathrop and
Zhiyong Lu and
Fran{\c{c}}oise Thibaud{-}Nissen and
Terence D. Murphy and
Lon Phan and
Yuri Skripchenko and
Tony Tse and
Jiyao Wang and
Rebecca Williams and
Barton W. Trawick and
Kim D. Pruitt and
Stephen T. Sherry},
title = {Database resources of the national center for biotechnology information},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{D1}},
pages = {20--26},
year = {2022},
url = {https://doi.org/10.1093/nar/gkab1112},
doi = {10.1093/NAR/GKAB1112},
timestamp = {Tue, 14 Oct 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SayersBBCCCCFKK22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/natmi/Diaz-PintoRASZL22,
author = {Andres Diaz{-}Pinto and
Nishant Ravikumar and
Rahman Attar and
Avan Suinesiaputra and
Yitian Zhao and
Eylem Levelt and
Erica Dall' Armellina and
Marco Lorenzi and
Qingyu Chen and
Tiarnan D. L. Keenan and
Elvira Agr{\'{o}}n and
Emily Y. Chew and
Zhiyong Lu and
Chris P. Gale and
Richard P. Gale and
Sven Plein and
Alejandro F. Frangi},
title = {Predicting myocardial infarction through retinal scans and minimal
personal information},
journal = {Nat. Mach. Intell.},
volume = {4},
number = {1},
pages = {55--61},
year = {2022},
url = {https://doi.org/10.1038/s42256-021-00427-7},
doi = {10.1038/S42256-021-00427-7},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/natmi/Diaz-PintoRASZL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/pr/ShiPCKTLTCSL22,
author = {Xiaoshuang Shi and
Yifan Peng and
Qingyu Chen and
Tiarnan D. Keenan and
Alisa T. Thavikulwat and
Sungwon Lee and
Yuxing Tang and
Emily Y. Chew and
Ronald M. Summers and
Zhiyong Lu},
title = {Robust convolutional neural networks against adversarial attacks on
medical images},
journal = {Pattern Recognit.},
volume = {132},
pages = {108923},
year = {2022},
url = {https://doi.org/10.1016/j.patcog.2022.108923},
doi = {10.1016/J.PATCOG.2022.108923},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/pr/ShiPCKTLTCSL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/ChenDAL22,
author = {Qingyu Chen and
Jingcheng Du and
Alexis Allot and
Zhiyong Lu},
title = {LitMC-BERT: Transformer-Based Multi-Label Classification of Biomedical
Literature With An Application on {COVID-19} Literature Curation},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {19},
number = {5},
pages = {2584--2595},
year = {2022},
url = {https://doi.org/10.1109/TCBB.2022.3173562},
doi = {10.1109/TCBB.2022.3173562},
timestamp = {Sun, 19 Jan 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcbb/ChenDAL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/0001KABBCDGGGKL22,
author = {Qingyu Chen and
Tiarnan D. Keenan and
Alexis Allot and
Sanjeeb Bhandari and
Geoff Broadhead and
Chantal Cousineau{-}Krieger and
Ellen Davis and
William G. Gensheimer and
David Grasic and
Seema Gupta and
Eleni Konstantinou and
Tania Lamba and
Michele Maiberger and
Arnold Oshinsky and
Brittany E. Powell and
Boonkit Purt and
Soo Shin and
Hillary Steifel and
Alisa T. Thavikulwat and
Keith Wroblewski and
Sirisha Koirala and
Tom Murickan and
Michael F. Chiang and
Michelle R. Hribar and
Emily Y. Chew and
Zhiyong Lu},
title = {Automated and Accessible Diagnosis of Age-related Macular Degeneration:
a Comparative Analysis of the impact of machine learning models in
clinical diagnostic Workflows},
booktitle = {{AMIA} 2022, American Medical Informatics Association Annual Symposium,
Washington, DC, USA, November 5-9, 2022},
publisher = {{AMIA}},
year = {2022},
url = {https://knowledge.amia.org/76677-amia-1.4637602/f002-1.4642717/f002-1.4642718/7006-1.4642734/7003-1.4642731},
timestamp = {Tue, 22 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/0001KABBCDGGGKL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/0001KAECL22,
author = {Qingyu Chen and
Tiarnan D. Keenan and
Elvira Agr{\'{o}}n and
Amr S. Elsawy and
Emily Y. Chew and
Zhiyong Lu},
title = {Deep learning automated diagnosis and quantitative classification
of cataract type and severity: quantifying the effectiveness and usability
of deep learning-assisted disease diagnosis models with 14 ophthalmologists
and multi-center validations},
booktitle = {{AMIA} 2022, American Medical Informatics Association Annual Symposium,
Washington, DC, USA, November 5-9, 2022},
publisher = {{AMIA}},
year = {2022},
url = {https://knowledge.amia.org/76677-amia-1.4637602/f007-1.4641746/f007-1.4641747/340-1.4642099/502-1.4642096},
timestamp = {Wed, 17 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/0001KAECL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/0001LWAL22,
author = {Ling Luo and
Po{-}Ting Lai and
Chih{-}Hsuan Wei and
Cecilia N. Arighi and
Zhiyong Lu},
title = {BioRED: {A} Comprehensive Biomedical Relation Extraction Dataset},
booktitle = {{AMIA} 2022, American Medical Informatics Association Annual Symposium,
Washington, DC, USA, November 5-9, 2022},
publisher = {{AMIA}},
year = {2022},
url = {https://knowledge.amia.org/76677-amia-1.4637602/f007-1.4641746/f007-1.4641747/37-1.4641961/222-1.4641958},
timestamp = {Wed, 17 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/0001LWAL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/YanLFVOGWSWL22,
author = {Shankai Yan and
Ling Luo and
Li Fang and
Daniel Veltri and
Andrew J. Oler and
Rajarshi Ghosh and
Chih{-}Hsuan Wei and
Morgan Similuk and
Kai Wang and
Zhiyong Lu},
title = {PhenoGene: Disease-gene prioritization using graph embedding on patient
phenotypic profiles},
booktitle = {{AMIA} 2022, American Medical Informatics Association Annual Symposium,
Washington, DC, USA, November 5-9, 2022},
publisher = {{AMIA}},
year = {2022},
url = {https://knowledge.amia.org/76677-amia-1.4637602/f007-1.4641746/f007-1.4641747/358-1.4641772/347-1.4641769},
timestamp = {Wed, 17 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/YanLFVOGWSWL22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ichi/WangLDSLP22,
author = {Song Wang and
Mingquan Lin and
Ying Ding and
George Shih and
Zhiyong Lu and
Yifan Peng},
title = {Radiology Text Analysis System (RadText): Architecture and Evaluation},
booktitle = {10th {IEEE} International Conference on Healthcare Informatics, {ICHI}
2022, Rochester, MN, USA, June 11-14, 2022},
pages = {288--296},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/ICHI54592.2022.00050},
doi = {10.1109/ICHI54592.2022.00050},
timestamp = {Mon, 18 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ichi/WangLDSLP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/micad/MathaiLESPLS22,
author = {Tejas Sudharshan Mathai and
Sungwon Lee and
Daniel C. Elton and
Thomas C. Shen and
Yifan Peng and
Zhiyong Lu and
Ronald M. Summers},
editor = {Karen Drukker and
Khan M. Iftekharuddin},
title = {Lymph node detection in {T2} {MRI} with transformers},
booktitle = {Medical Imaging 2022: Computer-Aided Diagnosis, San Diego, CA, USA,
February 20-24, 2022 / online, March 21-27, 2022},
series = {{SPIE} Proceedings},
volume = {12033},
publisher = {{SPIE}},
year = {2022},
url = {https://doi.org/10.1117/12.2613273},
doi = {10.1117/12.2613273},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/micad/MathaiLESPLS22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/miccai/LeeWCKGCLWP22,
author = {Junghwan Lee and
Tingyi Wanyan and
Qingyu Chen and
Tiarnan D. L. Keenan and
Benjamin S. Glicksberg and
Emily Y. Chew and
Zhiyong Lu and
Fei Wang and
Yifan Peng},
editor = {Chunfeng Lian and
Xiaohuan Cao and
Islem Rekik and
Xuanang Xu and
Zhiming Cui},
title = {Predicting Age-related Macular Degeneration Progression with Longitudinal
Fundus Images Using Deep Learning},
booktitle = {Machine Learning in Medical Imaging - 13th International Workshop,
{MLMI} 2022, Held in Conjunction with {MICCAI} 2022, Singapore, September
18, 2022, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13583},
pages = {11--20},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-21014-3\_2},
doi = {10.1007/978-3-031-21014-3\_2},
timestamp = {Fri, 16 Jan 2026 08:42:12 +0100},
biburl = {https://dblp.org/rec/conf/miccai/LeeWCKGCLWP22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2201-07317,
author = {Qiyuan An and
Ruijiang Li and
Lin Gu and
Hao Zhang and
Qingyu Chen and
Zhiyong Lu and
Fei Wang and
Yingying Zhu},
title = {A Privacy-Preserving Unsupervised Domain Adaptation Framework for
Clinical Text Analysis},
journal = {CoRR},
volume = {abs/2201.07317},
year = {2022},
url = {https://arxiv.org/abs/2201.07317},
eprinttype = {arXiv},
eprint = {2201.07317},
timestamp = {Wed, 14 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2201-07317.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2204-00622,
author = {Tejas Sudharshan Mathai and
Sungwon Lee and
Thomas C. Shen and
Zhiyong Lu and
Ronald M. Summers},
title = {Universal Lymph Node Detection in {T2} {MRI} using Neural Networks},
journal = {CoRR},
volume = {abs/2204.00622},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2204.00622},
doi = {10.48550/ARXIV.2204.00622},
eprinttype = {arXiv},
eprint = {2204.00622},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2204-00622.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2204-03637,
author = {Chih{-}Hsuan Wei and
Alexis Allot and
Kevin Riehle and
Aleksandar Milosavljevic and
Zhiyong Lu},
title = {tmVar 3.0: an improved variant concept recognition and normalization
tool},
journal = {CoRR},
volume = {abs/2204.03637},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2204.03637},
doi = {10.48550/ARXIV.2204.03637},
eprinttype = {arXiv},
eprint = {2204.03637},
timestamp = {Wed, 13 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2204-03637.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2204-04263,
author = {Ling Luo and
Po{-}Ting Lai and
Chih{-}Hsuan Wei and
Cecilia N. Arighi and
Zhiyong Lu},
title = {BioRED: {A} Comprehensive Biomedical Relation Extraction Dataset},
journal = {CoRR},
volume = {abs/2204.04263},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2204.04263},
doi = {10.48550/ARXIV.2204.04263},
eprinttype = {arXiv},
eprint = {2204.04263},
timestamp = {Wed, 11 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2204-04263.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2204-08649,
author = {Qingyu Chen and
Jingcheng Du and
Alexis Allot and
Zhiyong Lu},
title = {LitMC-BERT: transformer-based multi-label classification of biomedical
literature with an application on {COVID-19} literature curation},
journal = {CoRR},
volume = {abs/2204.08649},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2204.08649},
doi = {10.48550/ARXIV.2204.08649},
eprinttype = {arXiv},
eprint = {2204.08649},
timestamp = {Mon, 25 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2204-08649.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2204-09599,
author = {Song Wang and
Mingquan Lin and
Ying Ding and
George Shih and
Zhiyong Lu and
Yifan Peng},
title = {Radiology Text Analysis System (RadText): Architecture and Evaluation},
journal = {CoRR},
volume = {abs/2204.09599},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2204.09599},
doi = {10.48550/ARXIV.2204.09599},
eprinttype = {arXiv},
eprint = {2204.09599},
timestamp = {Mon, 18 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2204-09599.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2204-09781,
author = {Qingyu Chen and
Alexis Allot and
Robert Leaman and
Rezarta Islamaj Dogan and
Jingcheng Du and
Li Fang and
Wang Kai and
Shuo Xu and
Yuefu Zhang and
Parsa Bagherzadeh and
Sabine Bergler and
Aakash Bhatnagar and
Nidhir Bhavsar and
Yung{-}Chun Chang and
Sheng{-}Jie Lin and
Wentai Tang and
Hongtong Zhang and
Ilija Tavchioski and
Shubo Tian and
Jinfeng Zhang and
Yulia Otmakhova and
Antonio Jimeno{-}Yepes and
Hang Dong and
Honghan Wu and
Richard Dufour and
Yanis Labrak and
Niladri Chatterjee and
Kushagri Tandon and
Fr{\'{e}}jus A. A. Laleye and
Lo{\"{\i}}c Rakotoson and
Emmanuele Chersoni and
Jinghang Gu and
Annemarie Friedrich and
Subhash Chandra Pujari and
Mariia Chizhikova and
Naveen Sivadasan and
Zhiyong Lu},
title = {Multi-label classification for biomedical literature: an overview
of the BioCreative {VII} LitCovid Track for {COVID-19} literature
topic annotations},
journal = {CoRR},
volume = {abs/2204.09781},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2204.09781},
doi = {10.48550/ARXIV.2204.09781},
eprinttype = {arXiv},
eprint = {2204.09781},
timestamp = {Fri, 14 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2204-09781.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2205-03853,
author = {Ling Luo and
Chih{-}Hsuan Wei and
Po{-}Ting Lai and
Qingyu Chen and
Rezarta Islamaj Dogan and
Zhiyong Lu},
title = {Assigning Species Information to Corresponding Genes by a Sequence
Labeling Framework},
journal = {CoRR},
volume = {abs/2205.03853},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2205.03853},
doi = {10.48550/ARXIV.2205.03853},
eprinttype = {arXiv},
eprint = {2205.03853},
timestamp = {Wed, 11 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2205-03853.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2209-08124,
author = {Robert Leaman and
Rezarta Islamaj Dogan and
Alexis Allot and
Qingyu Chen and
W. John Wilbur and
Zhiyong Lu},
title = {Comprehensive identification of Long Covid articles with human-in-the-loop
machine learning},
journal = {CoRR},
volume = {abs/2209.08124},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2209.08124},
doi = {10.48550/ARXIV.2209.08124},
eprinttype = {arXiv},
eprint = {2209.08124},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2209-08124.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2209-13428,
author = {Qingyu Chen and
Alexis Allot and
Robert Leaman and
Chih{-}Hsuan Wei and
Elaheh Aghaarabi and
John J. Guerrerio and
Lilly Xu and
Zhiyong Lu},
title = {LitCovid in 2022: an information resource for the {COVID-19} literature},
journal = {CoRR},
volume = {abs/2209.13428},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2209.13428},
doi = {10.48550/ARXIV.2209.13428},
eprinttype = {arXiv},
eprint = {2209.13428},
timestamp = {Thu, 06 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2209-13428.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2211-16944,
author = {Ling Luo and
Chih{-}Hsuan Wei and
Po{-}Ting Lai and
Robert Leaman and
Qingyu Chen and
Zhiyong Lu},
title = {{AIONER:} All-in-one scheme-based biomedical named entity recognition
using deep learning},
journal = {CoRR},
volume = {abs/2211.16944},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2211.16944},
doi = {10.48550/ARXIV.2211.16944},
eprinttype = {arXiv},
eprint = {2211.16944},
timestamp = {Fri, 02 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2211-16944.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LeeWL21,
author = {Kyubum Lee and
Chih{-}Hsuan Wei and
Zhiyong Lu},
title = {Recent advances of automated methods for searching and extracting
genomic variant information from biomedical literature},
journal = {Briefings Bioinform.},
volume = {22},
number = {3},
year = {2021},
url = {https://doi.org/10.1093/bib/bbaa142},
doi = {10.1093/BIB/BBAA142},
timestamp = {Tue, 16 Dec 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LeeWL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/ZhaoSLW21,
author = {Sendong Zhao and
Chang Su and
Zhiyong Lu and
Fei Wang},
title = {Recent advances in biomedical literature mining},
journal = {Briefings Bioinform.},
volume = {22},
number = {3},
year = {2021},
url = {https://doi.org/10.1093/bib/bbaa057},
doi = {10.1093/BIB/BBAA057},
timestamp = {Tue, 16 Dec 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/ZhaoSLW21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LaiL21,
author = {Po{-}Ting Lai and
Zhiyong Lu},
title = {{BERT-GT:} cross-sentence n-ary relation extraction with {BERT} and
Graph Transformer},
journal = {Bioinform.},
volume = {36},
number = {24},
pages = {5678--5685},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btaa1087},
doi = {10.1093/BIOINFORMATICS/BTAA1087},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LaiL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuoYLVOXGSRL21,
author = {Ling Luo and
Shankai Yan and
Po{-}Ting Lai and
Daniel Veltri and
Andrew J. Oler and
Sandhya Xirasagar and
Rajarshi Ghosh and
Morgan Similuk and
Peter N. Robinson and
Zhiyong Lu},
title = {PhenoTagger: a hybrid method for phenotype concept recognition using
human phenotype ontology},
journal = {Bioinform.},
volume = {37},
number = {13},
pages = {1884--1890},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab019},
doi = {10.1093/BIOINFORMATICS/BTAB019},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuoYLVOXGSRL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jamia/0001KAPADKLCCWM21,
author = {Qingyu Chen and
Tiarnan D. L. Keenan and
Alexis Allot and
Yifan Peng and
Elvira Agr{\'{o}}n and
Amitha Domalpally and
Caroline C. W. Klaver and
Daniel T. Luttikhuizen and
Marcus H. Colyer and
Catherine A. Cukras and
Henry E. Wiley and
M. Teresa Magone and
Chantal Cousineau{-}Krieger and
Wai T. Wong and
Yingying Zhu and
Emily Y. Chew and
Zhiyong Lu},
title = {Multimodal, multitask, multiattention {(M3)} deep learning detection
of reticular pseudodrusen: Toward automated and accessible classification
of age-related macular degeneration},
journal = {J. Am. Medical Informatics Assoc.},
volume = {28},
number = {6},
pages = {1135--1148},
year = {2021},
url = {https://doi.org/10.1093/jamia/ocaa302},
doi = {10.1093/JAMIA/OCAA302},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jamia/0001KAPADKLCCWM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/DoganWCMPRSWL21,
author = {Rezarta Islamaj Dogan and
Chih{-}Hsuan Wei and
David Cissel and
Nicholas Miliaras and
Olga Printseva and
Oleg Rodionov and
Keiko Sekiya and
Janice Ward and
Zhiyong Lu},
title = {NLM-Gene, a richly annotated gold standard dataset for gene entities
that addresses ambiguity and multi-species gene recognition},
journal = {J. Biomed. Informatics},
volume = {118},
pages = {103779},
year = {2021},
url = {https://doi.org/10.1016/j.jbi.2021.103779},
doi = {10.1016/J.JBI.2021.103779},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/DoganWCMPRSWL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SayersBBBBCCF0K21,
author = {Eric W. Sayers and
Jeffrey Beck and
Evan Bolton and
Devon Bourexis and
James R. Brister and
Kathi Canese and
Donald C. Comeau and
Kathryn Funk and
Sunghwan Kim and
William Klimke and
Aron Marchler{-}Bauer and
Melissa J. Landrum and
Stacy Lathrop and
Zhiyong Lu and
Thomas L. Madden and
Nuala A. O'Leary and
Lon Phan and
Sanjida H. Rangwala and
Valerie A. Schneider and
Yuri Skripchenko and
Jiyao Wang and
Jian Ye and
Barton W. Trawick and
Kim D. Pruitt and
Stephen T. Sherry},
title = {Database resources of the National Center for Biotechnology Information},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D10--D17},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa892},
doi = {10.1093/NAR/GKAA892},
timestamp = {Tue, 14 Oct 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SayersBBBBCCF0K21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/0001AL21,
author = {Qingyu Chen and
Alexis Allot and
Zhiyong Lu},
title = {LitCovid: an open database of {COVID-19} literature},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D1534--D1540},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa952},
doi = {10.1093/NAR/GKAA952},
timestamp = {Tue, 01 Jun 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/0001AL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AllotLCLL21,
author = {Alexis Allot and
Kyubum Lee and
Qingyu Chen and
Ling Luo and
Zhiyong Lu},
title = {LitSuggest: a web-based system for literature recommendation and curation
using machine learning},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Webserver-Issue},
pages = {352--358},
year = {2021},
url = {https://doi.org/10.1093/nar/gkab326},
doi = {10.1093/NAR/GKAB326},
timestamp = {Tue, 06 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/AllotLCLL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tbd/PengTLZSL21,
author = {Yifan Peng and
Yuxing Tang and
Sungwon Lee and
Yingying Zhu and
Ronald M. Summers and
Zhiyong Lu},
title = {{COVID-19-CT-CXR:} {A} Freely Accessible and Weakly Labeled Chest
X-Ray and {CT} Image Collection on {COVID-19} From Biomedical Literature},
journal = {{IEEE} Trans. Big Data},
volume = {7},
number = {1},
pages = {3--12},
year = {2021},
url = {https://doi.org/10.1109/TBDATA.2020.3035935},
doi = {10.1109/TBDATA.2020.3035935},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tbd/PengTLZSL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tip/ShiXXCLLG21,
author = {Xiaoshuang Shi and
Fuyong Xing and
Kaidi Xu and
Pingjun Chen and
Yun Liang and
Zhiyong Lu and
Zhenhua Guo},
title = {Loss-Based Attention for Interpreting Image-Level Prediction of Convolutional
Neural Networks},
journal = {{IEEE} Trans. Image Process.},
volume = {30},
pages = {1662--1675},
year = {2021},
url = {https://doi.org/10.1109/TIP.2020.3046875},
doi = {10.1109/TIP.2020.3046875},
timestamp = {Thu, 27 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tip/ShiXXCLLG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tmi/PaulSLBPLS21,
author = {Angshuman Paul and
Thomas C. Shen and
Sungwon Lee and
Niranjan Balachandar and
Yifan Peng and
Zhiyong Lu and
Ronald M. Summers},
title = {Generalized Zero-Shot Chest X-Ray Diagnosis Through Trait-Guided Multi-View
Semantic Embedding With Self-Training},
journal = {{IEEE} Trans. Medical Imaging},
volume = {40},
number = {10},
pages = {2642--2655},
year = {2021},
url = {https://doi.org/10.1109/TMI.2021.3054817},
doi = {10.1109/TMI.2021.3054817},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tmi/PaulSLBPLS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/0001DAL21,
author = {Qingyu Chen and
Jingcheng Du and
Alexis Allot and
Zhiyong Lu},
title = {{AM2BERT:} attention guided and regularized transformer-based multi-label
classification model for {COVID-19} literature curation},
booktitle = {{AMIA} 2021, American Medical Informatics Association Annual Symposium,
San Diego, CA, USA, October 30, 2021 - November 3, 2021},
publisher = {{AMIA}},
year = {2021},
url = {https://knowledge.amia.org/74229-amia-1.4622266/t005-1.4625076/t005-1.4625077/3576396-1.4625861/3577513-1.4625858},
timestamp = {Wed, 17 Apr 2024 11:46:53 +0200},
biburl = {https://dblp.org/rec/conf/amia/0001DAL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/0001KCL21,
author = {Qingyu Chen and
Tiarnan D. Keenan and
Emily Y. Chew and
Zhiyong Lu},
title = {Deep learning detection of reticular pseudodrusen using multi-modal,
multi-task, and multi-attention mechanisms: towards automated and
accessible classification of age-related macular degeneration},
booktitle = {{AMIA} 2021, American Medical Informatics Association Annual Symposium,
San Diego, CA, USA, October 30, 2021 - November 3, 2021},
publisher = {{AMIA}},
year = {2021},
url = {https://knowledge.amia.org/74229-amia-1.4622266/t004-1.4626008/t004-1.4626009/3577601-1.4626388/3577532-1.4626385},
timestamp = {Wed, 17 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/0001KCL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/GhahramaniBLCKC21,
author = {Gregory C. Ghahramani and
Matthew Brendel and
Mingquan Lin and
Qingyu Chen and
Tiarnan D. Keenan and
Kun Chen and
Emily Y. Chew and
Zhiyong Lu and
Yifan Peng and
Fei Wang},
title = {Multi-task deep learning-based survival analysis on the prognosis
of late {AMD} using the longitudinal data in {AREDS}},
booktitle = {{AMIA} 2021, American Medical Informatics Association Annual Symposium,
San Diego, CA, USA, October 30, 2021 - November 3, 2021},
publisher = {{AMIA}},
year = {2021},
url = {https://knowledge.amia.org/74229-amia-1.4622266/t003-1.4626466/t003-1.4626467/3577667-1.4626711/3577402-1.4626708},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/GhahramaniBLCKC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/IslamajKKL21,
author = {Rezarta Islamaj and
Dongseop Kwon and
Sun Kim and
Zhiyong Lu},
title = {TeamTat: {A} Collaborative Text Annotation Tool for Creating Gold-Standard
Corpora},
booktitle = {{AMIA} 2021, American Medical Informatics Association Annual Symposium,
San Diego, CA, USA, October 30, 2021 - November 3, 2021},
publisher = {{AMIA}},
year = {2021},
url = {https://knowledge.amia.org/74229-amia-1.4622266/t004-1.4626008/t004-1.4626009/3577378-1.4626283/3577172-1.4626280},
timestamp = {Wed, 17 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/IslamajKKL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/IslamajLCCFGKTW21,
author = {Rezarta Islamaj and
Robert Leaman and
David Cissel and
Cathleen Coss and
Carol Fisher and
Rob Guzman and
Preeti Gokal Kochar and
Dorothy Trinh and
Deborah Whitman and
Keiko Sekiya and
Zhiyong Lu},
title = {NLM-Chem, a Gold-Standard Corpus for Chemical Entity Recognition in
PubMed Full Text Literature},
booktitle = {{AMIA} 2021, American Medical Informatics Association Annual Symposium,
San Diego, CA, USA, October 30, 2021 - November 3, 2021},
publisher = {{AMIA}},
year = {2021},
url = {https://knowledge.amia.org/74229-amia-1.4622266/t004-1.4626008/t004-1.4626009/3577172-1.4626280/3577205-1.4626277},
timestamp = {Wed, 17 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/IslamajLCCFGKTW21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/Leaman0AL21,
author = {Robert Leaman and
Qingyu Chen and
Alexis Allot and
Zhiyong Lu},
title = {Long Covid: {A} Comprehensive Collection of Articles Regarding Long-Haul
Symptoms in {COVID-19} Survivors},
booktitle = {{AMIA} 2021, American Medical Informatics Association Annual Symposium,
San Diego, CA, USA, October 30, 2021 - November 3, 2021},
publisher = {{AMIA}},
year = {2021},
url = {https://knowledge.amia.org/74229-amia-1.4622266/t004-1.4626008/t004-1.4626009/3577551-1.4626235/3632350-1.4626232},
timestamp = {Wed, 17 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/Leaman0AL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/McDonaldBCDL21,
author = {Clement J. McDonald and
Patricia Flatley Brennan and
Michael F. Chiang and
Joshua C. Denny and
Zhiyong Lu},
title = {Informatics-izing the National Institutes of Health},
booktitle = {{AMIA} 2021, American Medical Informatics Association Annual Symposium,
San Diego, CA, USA, October 30, 2021 - November 3, 2021},
publisher = {{AMIA}},
year = {2021},
url = {https://knowledge.amia.org/74229-amia-1.4622266/t002-1.4626813/t002-1.4626814/3577541-1.4626908/3577403-1.4626905},
timestamp = {Wed, 21 Jan 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/amia/McDonaldBCDL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/Yeganova0CWL21,
author = {Lana Yeganova and
Won Kim and
Donald C. Comeau and
W. John Wilbur and
Zhiyong Lu},
title = {Improving PubMed Retrieval by Integrating Abstract and Full Text Search},
booktitle = {{AMIA} 2021, American Medical Informatics Association Annual Symposium,
San Diego, CA, USA, October 30, 2021 - November 3, 2021},
publisher = {{AMIA}},
year = {2021},
url = {https://knowledge.amia.org/74229-amia-1.4622266/t004-1.4626008/t004-1.4626009/3577495-1.4626034/3577262-1.4626031},
timestamp = {Wed, 17 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/Yeganova0CWL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/YeganovaKCWL21,
author = {Lana Yeganova and
Won Kim and
Donald C. Comeau and
W. John Wilbur and
Zhiyong Lu},
editor = {Dina Demner{-}Fushman and
Kevin Bretonnel Cohen and
Sophia Ananiadou and
Junichi Tsujii},
title = {Measuring the relative importance of full text sections for information
retrieval from scientific literature},
booktitle = {Proceedings of the 20th Workshop on Biomedical Language Processing,
BioNLP@NAACL-HLT 2021, Online, June 11, 2021},
pages = {247--256},
publisher = {Association for Computational Linguistics},
year = {2021},
url = {https://doi.org/10.18653/v1/2021.bionlp-1.27},
doi = {10.18653/V1/2021.BIONLP-1.27},
timestamp = {Fri, 06 Aug 2021 00:41:22 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/YeganovaKCWL21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccvw/ZouJZCLW21,
author = {Wenbin Zou and
Mingchao Jiang and
Yunchen Zhang and
Liang Chen and
Zhiyong Lu and
Yi Wu},
title = {SDWNet: {A} Straight Dilated Network with Wavelet Transformation for
image Deblurring},
booktitle = {{IEEE/CVF} International Conference on Computer Vision Workshops,
{ICCVW} 2021, Montreal, QC, Canada, October 11-17, 2021},
pages = {1895--1904},
publisher = {{IEEE}},
year = {2021},
url = {https://doi.org/10.1109/ICCVW54120.2021.00216},
doi = {10.1109/ICCVW54120.2021.00216},
timestamp = {Wed, 16 Oct 2024 17:46:29 +0200},
biburl = {https://dblp.org/rec/conf/iccvw/ZouJZCLW21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icic/WeiLLZ21,
author = {Cong Wei and
Zhiyong Lu and
Zhiyong Lin and
Chong Zhong},
editor = {De{-}Shuang Huang and
Kang{-}Hyun Jo and
Jianqiang Li and
Valeriya V. Gribova and
Abir Hussain},
title = {Research on Deep Neural Network Model Compression Based on Quantification
Pruning and Huffmann Encoding},
booktitle = {Intelligent Computing Theories and Application - 17th International
Conference, {ICIC} 2021, Shenzhen, China, August 12-15, 2021, Proceedings,
Part {II}},
series = {Lecture Notes in Computer Science},
volume = {12837},
pages = {522--531},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-84529-2\_44},
doi = {10.1007/978-3-030-84529-2\_44},
timestamp = {Tue, 20 Aug 2024 07:54:43 +0200},
biburl = {https://dblp.org/rec/conf/icic/WeiLLZ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbi/PaulSPLS21,
author = {Angshuman Paul and
Thomas C. Shen and
Yifan Peng and
Zhiyong Lu and
Ronald M. Summers},
title = {Learning Few-Shot Chest X-Ray Diagnosis Using Images From The Published
Scientific Literature},
booktitle = {18th {IEEE} International Symposium on Biomedical Imaging, {ISBI}
2021, Nice, France, April 13-16, 2021},
pages = {344--348},
publisher = {{IEEE}},
year = {2021},
url = {https://doi.org/10.1109/ISBI48211.2021.9434059},
doi = {10.1109/ISBI48211.2021.9434059},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbi/PaulSPLS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/miccai/ZhuWCLSELS21,
author = {Yingying Zhu and
Shuai Wang and
Qingyu Chen and
Sungwon Lee and
Thomas C. Shen and
Daniel C. Elton and
Zhiyong Lu and
Ronald M. Summers},
editor = {Chunfeng Lian and
Xiaohuan Cao and
Islem Rekik and
Xuanang Xu and
Pingkun Yan},
title = {Learning Structure from Visual Semantic Features and Radiology Ontology
for Lymph Node Classification on {MRI}},
booktitle = {Machine Learning in Medical Imaging - 12th International Workshop,
{MLMI} 2021, Held in Conjunction with {MICCAI} 2021, Strasbourg, France,
September 27, 2021, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12966},
pages = {101--109},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-87589-3\_11},
doi = {10.1007/978-3-030-87589-3\_11},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/miccai/ZhuWCLSELS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/miccai/MathaiLESPLS21,
author = {Tejas Sudharshan Mathai and
Sungwon Lee and
Daniel C. Elton and
Thomas C. Shen and
Yifan Peng and
Zhiyong Lu and
Ronald M. Summers},
editor = {Chunfeng Lian and
Xiaohuan Cao and
Islem Rekik and
Xuanang Xu and
Pingkun Yan},
title = {Detection of Lymph Nodes in {T2} {MRI} Using Neural Network Ensembles},
booktitle = {Machine Learning in Medical Imaging - 12th International Workshop,
{MLMI} 2021, Held in Conjunction with {MICCAI} 2021, Strasbourg, France,
September 27, 2021, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12966},
pages = {682--691},
publisher = {Springer},
year = {2021},
url = {https://doi.org/10.1007/978-3-030-87589-3\_70},
doi = {10.1007/978-3-030-87589-3\_70},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/miccai/MathaiLESPLS21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2101-04158,
author = {Po{-}Ting Lai and
Zhiyong Lu},
title = {{BERT-GT:} Cross-sentence n-ary relation extraction with {BERT} and
Graph Transformer},
journal = {CoRR},
volume = {abs/2101.04158},
year = {2021},
url = {https://arxiv.org/abs/2101.04158},
eprinttype = {arXiv},
eprint = {2101.04158},
timestamp = {Thu, 21 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2101-04158.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2110-05803,
author = {Wenbin Zou and
Mingchao Jiang and
Yunchen Zhang and
Liang Chen and
Zhiyong Lu and
Yi Wu},
title = {SDWNet: {A} Straight Dilated Network with Wavelet Transformation for
Image Deblurring},
journal = {CoRR},
volume = {abs/2110.05803},
year = {2021},
url = {https://arxiv.org/abs/2110.05803},
eprinttype = {arXiv},
eprint = {2110.05803},
timestamp = {Tue, 19 Dec 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2110-05803.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2111-04885,
author = {Tejas Sudharshan Mathai and
Sungwon Lee and
Daniel C. Elton and
Thomas C. Shen and
Yifan Peng and
Zhiyong Lu and
Ronald M. Summers},
title = {Lymph Node Detection in {T2} {MRI} with Transformers},
journal = {CoRR},
volume = {abs/2111.04885},
year = {2021},
url = {https://arxiv.org/abs/2111.04885},
eprinttype = {arXiv},
eprint = {2111.04885},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2111-04885.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2111-09733,
author = {Tian Ye and
Mingchao Jiang and
Yunchen Zhang and
Liang Chen and
ErKang Chen and
Pen Chen and
Zhiyong Lu},
title = {Perceiving and Modeling Density is All You Need for Image Dehazing},
journal = {CoRR},
volume = {abs/2111.09733},
year = {2021},
url = {https://arxiv.org/abs/2111.09733},
eprinttype = {arXiv},
eprint = {2111.09733},
timestamp = {Thu, 25 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2111-09733.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DaiYLHMZ20,
author = {Suyang Dai and
Ronghui You and
Zhiyong Lu and
Xiaodi Huang and
Hiroshi Mamitsuka and
Shanfeng Zhu},
title = {FullMeSH: improving large-scale MeSH indexing with full text},
journal = {Bioinform.},
volume = {36},
number = {5},
pages = {1533--1541},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btz756},
doi = {10.1093/BIOINFORMATICS/BTZ756},
timestamp = {Sun, 28 Sep 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/DaiYLHMZ20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeiZFZL20,
author = {Xiaoqiong Wei and
Chengxin Zhang and
P. L. Freddolino and
Yang Zhang and
Zhiyong Lu},
title = {Detecting Gene Ontology misannotations using taxon-specific rate ratio
comparisons},
journal = {Bioinform.},
volume = {36},
number = {16},
pages = {4383--4388},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa548},
doi = {10.1093/BIOINFORMATICS/BTAA548},
timestamp = {Tue, 10 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeiZFZL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SunHJHL20,
author = {Zexuan Sun and
Shujun Huang and
Peiran Jiang and
Pingzhao Hu and
Zhiyong Lu},
title = {{DTF:} Deep Tensor Factorization for predicting anticancer drug synergy},
journal = {Bioinform.},
volume = {36},
number = {16},
pages = {4483--4489},
year = {2020},
url = {https://doi.org/10.1093/bioinformatics/btaa287},
doi = {10.1093/BIOINFORMATICS/BTAA287},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SunHJHL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jamia/YeganovaKCBWL20,
author = {Lana Yeganova and
Sun Kim and
Qingyu Chen and
Grigory Balasanov and
W. John Wilbur and
Zhiyong Lu},
title = {Better synonyms for enriching biomedical search},
journal = {J. Am. Medical Informatics Assoc.},
volume = {27},
number = {12},
pages = {1894--1902},
year = {2020},
url = {https://doi.org/10.1093/jamia/ocaa151},
doi = {10.1093/JAMIA/OCAA151},
timestamp = {Thu, 16 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jamia/YeganovaKCBWL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/midm/ChenDKWL20,
author = {Qingyu Chen and
Jingcheng Du and
Sun Kim and
W. John Wilbur and
Zhiyong Lu},
title = {Deep learning with sentence embeddings pre-trained on biomedical corpora
improves the performance of finding similar sentences in electronic
medical records},
journal = {{BMC} Medical Informatics Decis. Mak.},
volume = {20-S},
number = {1},
pages = {73},
year = {2020},
url = {https://doi.org/10.1186/s12911-020-1044-0},
doi = {10.1186/S12911-020-1044-0},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/midm/ChenDKWL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SayersBBBCCFK0K20,
author = {Eric W. Sayers and
Jeffrey Beck and
J. Rodney Brister and
Evan Bolton and
Kathi Canese and
Donald C. Comeau and
Kathryn Funk and
Anne Ketter and
Sunghwan Kim and
Avi Kimchi and
Paul A. Kitts and
Anatoliy Kuznetsov and
Stacy Lathrop and
Zhiyong Lu and
Kelly M. McGarvey and
Thomas L. Madden and
Terence D. Murphy and
Nuala A. O'Leary and
Lon Phan and
Valerie A. Schneider and
Fran{\c{c}}oise Thibaud{-}Nissen and
Barton W. Trawick and
Kim D. Pruitt and
James Ostell},
title = {Database resources of the National Center for Biotechnology Information},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D9--D16},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz899},
doi = {10.1093/NAR/GKZ899},
timestamp = {Tue, 01 Apr 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SayersBBBCCFK0K20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/DoganKKL20,
author = {Rezarta Islamaj Dogan and
Dongseop Kwon and
Sun Kim and
Zhiyong Lu},
title = {TeamTat: a collaborative text annotation tool},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Webserver-Issue},
pages = {W5--W11},
year = {2020},
url = {https://doi.org/10.1093/nar/gkaa333},
doi = {10.1093/NAR/GKAA333},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/DoganKKL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/npjdm/PengK0AAWCL20,
author = {Yifan Peng and
Tiarnan D. Keenan and
Qingyu Chen and
Elvira Agr{\'{o}}n and
Alexis Allot and
Wai T. Wong and
Emily Y. Chew and
Zhiyong Lu},
title = {Predicting risk of late age-related macular degeneration using deep
learning},
journal = {npj Digit. Medicine},
volume = {3},
year = {2020},
url = {https://doi.org/10.1038/s41746-020-00317-z},
doi = {10.1038/S41746-020-00317-Z},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/npjdm/PengK0AAWCL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/npjdm/TangTP0BRBLH0S20,
author = {Yuxing Tang and
Youbao Tang and
Yifan Peng and
Ke Yan and
Mohammadhadi Bagheri and
Bernadette A. Redd and
Catherine J. Brandon and
Zhiyong Lu and
Mei Han and
Jing Xiao and
Ronald M. Summers},
title = {Automated abnormality classification of chest radiographs using deep
convolutional neural networks},
journal = {npj Digit. Medicine},
volume = {3},
year = {2020},
url = {https://doi.org/10.1038/s41746-020-0273-z},
doi = {10.1038/S41746-020-0273-Z},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/npjdm/TangTP0BRBLH0S20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ChenLYKWL20,
author = {Qingyu Chen and
Kyubum Lee and
Shankai Yan and
Sun Kim and
Chih{-}Hsuan Wei and
Zhiyong Lu},
title = {BioConceptVec: Creating and evaluating literature-based biomedical
concept embeddings on a large scale},
journal = {PLoS Comput. Biol.},
volume = {16},
number = {4},
year = {2020},
url = {https://doi.org/10.1371/journal.pcbi.1007617},
doi = {10.1371/JOURNAL.PCBI.1007617},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/ChenLYKWL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/acl-clinicalnlp/PengLESTCWZSL20,
author = {Yifan Peng and
Sungwon Lee and
Daniel C. Elton and
Thomas C. Shen and
Yuxing Tang and
Qingyu Chen and
Shuai Wang and
Yingying Zhu and
Ronald M. Summers and
Zhiyong Lu},
editor = {Anna Rumshisky and
Kirk Roberts and
Steven Bethard and
Tristan Naumann},
title = {Automatic recognition of abdominal lymph nodes from clinical text},
booktitle = {Proceedings of the 3rd Clinical Natural Language Processing Workshop,
ClinicalNLP@EMNLP 2020, Online, November 19, 2020},
pages = {101--110},
publisher = {Association for Computational Linguistics},
year = {2020},
url = {https://doi.org/10.18653/v1/2020.clinicalnlp-1.12},
doi = {10.18653/V1/2020.CLINICALNLP-1.12},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/acl-clinicalnlp/PengLESTCWZSL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/0001KPAHTLWCL20,
author = {Qingyu Chen and
Tiarnan D. Keenan and
Yifan Peng and
Elvira Agr{\'{o}}n and
Christopher Hwang and
Alisa T. Thavikulwat and
Debora Lee and
Wai T. Wong and
Emily Y. Chew and
Zhiyong Lu},
title = {Detection of reticular pseudodrusen using deep learning},
booktitle = {{AMIA} 2020, American Medical Informatics Association Annual Symposium,
Virtual Event, USA, November 14-18, 2020},
publisher = {{AMIA}},
year = {2020},
url = {https://knowledge.amia.org/72332-amia-1.4602255/t004-1.4605866/t004-1.4605867/3414198-1.4606168/3416568-1.4606165},
timestamp = {Mon, 30 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/0001KPAHTLWCL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/PengCL20,
author = {Yifan Peng and
Qingyu Chen and
Zhiyong Lu},
editor = {Dina Demner{-}Fushman and
Kevin Bretonnel Cohen and
Sophia Ananiadou and
Junichi Tsujii},
title = {An Empirical Study of Multi-Task Learning on {BERT} for Biomedical
Text Mining},
booktitle = {Proceedings of the 19th SIGBioMed Workshop on Biomedical Language
Processing, BioNLP 2020, Online, July 9, 2020},
pages = {205--214},
publisher = {Association for Computational Linguistics},
year = {2020},
url = {https://doi.org/10.18653/v1/2020.bionlp-1.22},
doi = {10.18653/V1/2020.BIONLP-1.22},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/PengCL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/emnlp/LeamanL20,
author = {Robert Leaman and
Zhiyong Lu},
editor = {Karin Verspoor and
Kevin Bretonnel Cohen and
Michael Conway and
Berry de Bruijn and
Mark Dredze and
Rada Mihalcea and
Byron C. Wallace},
title = {A Comprehensive Dictionary and Term Variation Analysis for {COVID-19}
and SARS-CoV-2},
booktitle = {Proceedings of the 1st Workshop on {NLP} for COVID-19@ {EMNLP} 2020,
Online, December 2020},
publisher = {Association for Computational Linguistics},
year = {2020},
url = {https://doi.org/10.18653/v1/2020.nlpcovid19-2.32},
doi = {10.18653/V1/2020.NLPCOVID19-2.32},
timestamp = {Thu, 17 Feb 2022 16:43:16 +0100},
biburl = {https://dblp.org/rec/conf/emnlp/LeamanL20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/miccai/PaulSBTPLS20a,
author = {Angshuman Paul and
Thomas C. Shen and
Niranjan Balachandar and
Yuxing Tang and
Yifan Peng and
Zhiyong Lu and
Ronald M. Summers},
editor = {Jaime S. Cardoso and
Hien Van Nguyen and
Nicholas Heller and
Pedro Henriques Abreu and
Ivana Isgum and
Wilson Silva and
Ricardo P. M. Cruz and
Jos{\'{e}} Pereira Amorim and
Vishal Patel and
Badri Roysam and
S. Kevin Zhou and
Steve B. Jiang and
Ngan Le and
Khoa Luu and
Raphael Sznitman and
Veronika Cheplygina and
Diana Mateus and
Emanuele Trucco and
Samaneh Abbasi{-}Sureshjani},
title = {COMe-SEE: Cross-modality Semantic Embedding Ensemble for Generalized
Zero-Shot Diagnosis of Chest Radiographs},
booktitle = {Interpretable and Annotation-Efficient Learning for Medical Image
Computing - Third International Workshop, iMIMIC 2020, Second International
Workshop, {MIL3ID} 2020, and 5th International Workshop, {LABELS}
2020, Held in Conjunction with {MICCAI} 2020, Lima, Peru, October
4-8, 2020, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {12446},
pages = {103--111},
publisher = {Springer},
year = {2020},
url = {https://doi.org/10.1007/978-3-030-61166-8\_11},
doi = {10.1007/978-3-030-61166-8\_11},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/miccai/PaulSBTPLS20a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2004-11894,
author = {Rezarta Islamaj Dogan and
Dongseop Kwon and
Sun Kim and
Zhiyong Lu},
title = {TeamTat: a collaborative text annotation tool},
journal = {CoRR},
volume = {abs/2004.11894},
year = {2020},
url = {https://arxiv.org/abs/2004.11894},
eprinttype = {arXiv},
eprint = {2004.11894},
timestamp = {Tue, 28 Apr 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2004-11894.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2005-02799,
author = {Yifan Peng and
Qingyu Chen and
Zhiyong Lu},
title = {An Empirical Study of Multi-Task Learning on {BERT} for Biomedical
Text Mining},
journal = {CoRR},
volume = {abs/2005.02799},
year = {2020},
url = {https://arxiv.org/abs/2005.02799},
eprinttype = {arXiv},
eprint = {2005.02799},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2005-02799.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2006-06177,
author = {Yifan Peng and
Yuxing Tang and
Sungwon Lee and
Yingying Zhu and
Ronald M. Summers and
Zhiyong Lu},
title = {{COVID-19-CT-CXR:} a freely accessible and weakly labeled chest X-ray
and {CT} image collection on {COVID-19} from biomedical literature},
journal = {CoRR},
volume = {abs/2006.06177},
year = {2020},
url = {https://arxiv.org/abs/2006.06177},
eprinttype = {arXiv},
eprint = {2006.06177},
timestamp = {Sun, 17 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2006-06177.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2007-09550,
author = {Yifan Peng and
Tiarnan D. Keenan and
Qingyu Chen and
Elvira Agr{\'{o}}n and
Alexis Allot and
Wai T. Wong and
Emily Y. Chew and
Zhiyong Lu},
title = {Predicting risk of late age-related macular degeneration using deep
learning},
journal = {CoRR},
volume = {abs/2007.09550},
year = {2020},
url = {https://arxiv.org/abs/2007.09550},
eprinttype = {arXiv},
eprint = {2007.09550},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2007-09550.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2008-03397,
author = {Lana Yeganova and
Rezarta Islamaj Dogan and
Qingyu Chen and
Robert Leaman and
Alexis Allot and
Chih{-}Hsuan Wei and
Donald C. Comeau and
Won Kim and
Yifan Peng and
W. John Wilbur and
Zhiyong Lu},
title = {Navigating the landscape of {COVID-19} research through literature
analysis: {A} bird's eye view},
journal = {CoRR},
volume = {abs/2008.03397},
year = {2020},
url = {https://arxiv.org/abs/2008.03397},
eprinttype = {arXiv},
eprint = {2008.03397},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2008-03397.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2009-08478,
author = {Ling Luo and
Shankai Yan and
Po{-}Ting Lai and
Daniel Veltri and
Andrew J. Oler and
Sandhya Xirasagar and
Rajarshi Ghosh and
Morgan Similuk and
Peter N. Robinson and
Zhiyong Lu},
title = {PhenoTagger: {A} Hybrid Method for Phenotype Concept Recognition using
Human Phenotype Ontology},
journal = {CoRR},
volume = {abs/2009.08478},
year = {2020},
url = {https://arxiv.org/abs/2009.08478},
eprinttype = {arXiv},
eprint = {2009.08478},
timestamp = {Wed, 01 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2009-08478.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2010-14588,
author = {Robert Leaman and
Zhiyong Lu},
title = {A Comprehensive Dictionary and Term Variation Analysis for {COVID-19}
and SARS-CoV-2},
journal = {CoRR},
volume = {abs/2010.14588},
year = {2020},
url = {https://arxiv.org/abs/2010.14588},
eprinttype = {arXiv},
eprint = {2010.14588},
timestamp = {Mon, 02 Nov 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2010-14588.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2010-16413,
author = {Qingyu Chen and
Robert Leaman and
Alexis Allot and
Ling Luo and
Chih{-}Hsuan Wei and
Shankai Yan and
Zhiyong Lu},
title = {Artificial Intelligence {(AI)} in Action: Addressing the {COVID-19}
Pandemic with Natural Language Processing {(NLP)}},
journal = {CoRR},
volume = {abs/2010.16413},
year = {2020},
url = {https://arxiv.org/abs/2010.16413},
eprinttype = {arXiv},
eprint = {2010.16413},
timestamp = {Wed, 11 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2010-16413.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2011-05142,
author = {Qingyu Chen and
Tiarnan D. L. Keenan and
Alexis Allot and
Yifan Peng and
Elvira Agr{\'{o}}n and
Amitha Domalpally and
Caroline C. W. Klaver and
Daniel T. Luttikhuizen and
Marcus H. Colyer and
Catherine A. Cukras and
Henry E. Wiley and
M. Teresa Magone and
Chantal Cousineau{-}Krieger and
Wai T. Wong and
Yingying Zhu and
Emily Y. Chew and
Zhiyong Lu},
title = {Multi-modal, multi-task, multi-attention {(M3)} deep learning detection
of reticular pseudodrusen: towards automated and accessible classification
of age-related macular degeneration},
journal = {CoRR},
volume = {abs/2011.05142},
year = {2020},
url = {https://arxiv.org/abs/2011.05142},
eprinttype = {arXiv},
eprint = {2011.05142},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2011-05142.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/DoganKCWCAMCEPV19,
author = {Rezarta Islamaj Dogan and
Sun Kim and
Andrew Chatr{-}aryamontri and
Chih{-}Hsuan Wei and
Donald C. Comeau and
Rui Antunes and
S{\'{e}}rgio Matos and
Qingyu Chen and
Aparna Elangovan and
Nagesh C. Panyam and
Karin Verspoor and
Hongfang Liu and
Yanshan Wang and
Zhuang Liu and
Berna Altinel and
Zehra Melce H{\"{u}}s{\"{u}}nbeyi and
Arzucan {\"{O}}zg{\"{u}}r and
Aris Fergadis and
Chen{-}Kai Wang and
Hong{-}Jie Dai and
Tung Tran and
Ramakanth Kavuluru and
Ling Luo and
Albert Steppi and
Jinfeng Zhang and
Jinchan Qu and
Zhiyong Lu},
title = {Overview of the BioCreative {VI} Precision Medicine Track: mining
protein interactions and mutations for precision medicine},
journal = {Database J. Biol. Databases Curation},
volume = {2019},
pages = {bay147},
year = {2019},
url = {https://doi.org/10.1093/database/bay147},
doi = {10.1093/DATABASE/BAY147},
timestamp = {Tue, 14 Oct 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/DoganKCWCAMCEPV19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/HsuCWKL19,
author = {Yi{-}Yu Hsu and
Mindy Clyne and
Chih{-}Hsuan Wei and
Muin J. Khoury and
Zhiyong Lu},
title = {Using deep learning to identify translational research in genomic
medicine beyond bench to bedside},
journal = {Database J. Biol. Databases Curation},
volume = {2019},
pages = {baz010},
year = {2019},
url = {https://doi.org/10.1093/database/baz010},
doi = {10.1093/DATABASE/BAZ010},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/HsuCWKL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/DoganWXGTYZML19,
author = {Rezarta Islamaj Dogan and
W. John Wilbur and
Natalie Xie and
Noreen R. Gonzales and
Narmada Thanki and
Roxanne A. Yamashita and
Chanjuan Zheng and
Aron Marchler{-}Bauer and
Zhiyong Lu},
title = {PubMed Text Similarity Model and its application to curation efforts
in the Conserved Domain Database},
journal = {Database J. Biol. Databases Curation},
volume = {2019},
pages = {baz064},
year = {2019},
url = {https://doi.org/10.1093/database/baz064},
doi = {10.1093/DATABASE/BAZ064},
timestamp = {Thu, 01 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/DoganWXGTYZML19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ComeauWDL19,
author = {Donald C. Comeau and
Chih{-}Hsuan Wei and
Rezarta Islamaj Dogan and
Zhiyong Lu},
title = {{PMC} text mining subset in BioC: about three million full-text articles
and growing},
journal = {Bioinform.},
volume = {35},
number = {18},
pages = {3533--3535},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/btz070},
doi = {10.1093/BIOINFORMATICS/BTZ070},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ComeauWDL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jamia/DuCPXTL19,
author = {Jingcheng Du and
Qingyu Chen and
Yifan Peng and
Yang Xiang and
Cui Tao and
Zhiyong Lu},
title = {ML-Net: multi-label classification of biomedical texts with deep neural
networks},
journal = {J. Am. Medical Informatics Assoc.},
volume = {26},
number = {11},
pages = {1279--1285},
year = {2019},
url = {https://doi.org/10.1093/jamia/ocz085},
doi = {10.1093/JAMIA/OCZ085},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jamia/DuCPXTL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SayersABBCCCFFH19,
author = {Eric W. Sayers and
Richa Agarwala and
Evan Bolton and
J. Rodney Brister and
Kathi Canese and
Karen Clark and
Ryan Connor and
Nicolas Fiorini and
Kathryn Funk and
Timothy Hefferon and
J. Bradley Holmes and
Sunghwan Kim and
Avi Kimchi and
Paul A. Kitts and
Stacy Lathrop and
Zhiyong Lu and
Thomas L. Madden and
Aron Marchler{-}Bauer and
Lon Phan and
Valerie A. Schneider and
Conrad L. Schoch and
Kim D. Pruitt and
James Ostell},
title = {Database resources of the National Center for Biotechnology Information},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Database-Issue},
pages = {D23--D28},
year = {2019},
url = {https://doi.org/10.1093/nar/gky1069},
doi = {10.1093/NAR/GKY1069},
timestamp = {Thu, 01 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SayersABBCCCFFH19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/WeiALL19,
author = {Chih{-}Hsuan Wei and
Alexis Allot and
Robert Leaman and
Zhiyong Lu},
title = {PubTator central: automated concept annotation for biomedical full
text articles},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Webserver-Issue},
pages = {W587--W593},
year = {2019},
url = {https://doi.org/10.1093/nar/gkz389},
doi = {10.1093/NAR/GKZ389},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/WeiALL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/Allot0KACWL19,
author = {Alexis Allot and
Qingyu Chen and
Sun Kim and
Roberto Vera Alvarez and
Donald C. Comeau and
W. John Wilbur and
Zhiyong Lu},
title = {LitSense: making sense of biomedical literature at sentence level},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Webserver-Issue},
pages = {W594--W599},
year = {2019},
url = {https://doi.org/10.1093/nar/gkz289},
doi = {10.1093/NAR/GKZ289},
timestamp = {Sat, 25 Dec 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/Allot0KACWL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/PengK0AWCL19,
author = {Yifan Peng and
Tiarnan D. Keenan and
Qingyu Chen and
Elvira Agr{\'{o}}n and
Wai T. Wong and
Emily Y. Chew and
Zhiyong Lu},
title = {A deep learning-based survival model for prediction of progression
in late Age-related Macular Degeneration {(AMD)} from color fundus
photographs},
booktitle = {{AMIA} 2019, American Medical Informatics Association Annual Symposium,
Washington, DC, USA, November 16-20, 2019},
publisher = {{AMIA}},
year = {2019},
url = {https://knowledge.amia.org/69862-amia-1.4570936/t006-1.4574499/t006-1.4574500/3202289-1.4574612/3199497-1.4574609},
timestamp = {Mon, 30 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/PengK0AWCL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/WeiLLL19,
author = {Chih{-}Hsuan Wei and
Kyubum Lee and
Robert Leaman and
Zhiyong Lu},
editor = {Xinghua Mindy Shi and
Michael Buck and
Jian Ma and
Pierangelo Veltri},
title = {Biomedical Mention Disambiguation using a Deep Learning Approach},
booktitle = {Proceedings of the 10th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, {BCB} 2019, Niagara
Falls, NY, USA, September 7-10, 2019},
pages = {307--313},
publisher = {{ACM}},
year = {2019},
url = {https://doi.org/10.1145/3307339.3342162},
doi = {10.1145/3307339.3342162},
timestamp = {Sun, 25 Jul 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bcb/WeiLLL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/ChenDKWL19,
author = {Qingyu Chen and
Jingcheng Du and
Sun Kim and
W. John Wilbur and
Zhiyong Lu},
editor = {Xinghua Mindy Shi and
Michael Buck and
Jian Ma and
Pierangelo Veltri},
title = {Evaluation of Five Sentence Similarity Models on Electronic Medical
Records},
booktitle = {Proceedings of the 10th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, {BCB} 2019, Niagara
Falls, NY, USA, September 7-10, 2019},
pages = {533},
publisher = {{ACM}},
year = {2019},
url = {https://doi.org/10.1145/3307339.3343239},
doi = {10.1145/3307339.3343239},
timestamp = {Fri, 03 Jan 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/ChenDKWL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/WeiALL19,
author = {Chih{-}Hsuan Wei and
Alexis Allot and
Robert Leaman and
Zhiyong Lu},
editor = {Xinghua Mindy Shi and
Michael Buck and
Jian Ma and
Pierangelo Veltri},
title = {A Text-Mining System for Concept Annotation in Biomedical Full Text
Articles},
booktitle = {Proceedings of the 10th {ACM} International Conference on Bioinformatics,
Computational Biology and Health Informatics, {BCB} 2019, Niagara
Falls, NY, USA, September 7-10, 2019},
pages = {540},
publisher = {{ACM}},
year = {2019},
url = {https://doi.org/10.1145/3307339.3343246},
doi = {10.1145/3307339.3343246},
timestamp = {Sun, 19 Jan 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/WeiALL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/PengYL19,
author = {Yifan Peng and
Shankai Yan and
Zhiyong Lu},
editor = {Dina Demner{-}Fushman and
Kevin Bretonnel Cohen and
Sophia Ananiadou and
Junichi Tsujii},
title = {Transfer Learning in Biomedical Natural Language Processing: An Evaluation
of {BERT} and ELMo on Ten Benchmarking Datasets},
booktitle = {Proceedings of the 18th BioNLP Workshop and Shared Task, BioNLP@ACL
2019, Florence, Italy, August 1, 2019},
pages = {58--65},
publisher = {Association for Computational Linguistics},
year = {2019},
url = {https://doi.org/10.18653/v1/w19-5006},
doi = {10.18653/V1/W19-5006},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/PengYL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cvpr/YanPSBLS19,
author = {Ke Yan and
Yifan Peng and
Veit Sandfort and
Mohammadhadi Bagheri and
Zhiyong Lu and
Ronald M. Summers},
title = {Holistic and Comprehensive Annotation of Clinically Significant Findings
on Diverse {CT} Images: Learning From Radiology Reports and Label
Ontology},
booktitle = {{IEEE} Conference on Computer Vision and Pattern Recognition, {CVPR}
2019, Long Beach, CA, USA, June 16-20, 2019},
pages = {8523--8532},
publisher = {Computer Vision Foundation / {IEEE}},
year = {2019},
url = {http://openaccess.thecvf.com/content\_CVPR\_2019/html/Yan\_Holistic\_and\_Comprehensive\_Annotation\_of\_Clinically\_Significant\_Findings\_on\_Diverse\_CVPR\_2019\_paper.html},
doi = {10.1109/CVPR.2019.00872},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cvpr/YanPSBLS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ichi/ChenPL19,
author = {Qingyu Chen and
Yifan Peng and
Zhiyong Lu},
title = {BioSentVec: creating sentence embeddings for biomedical texts},
booktitle = {2019 {IEEE} International Conference on Healthcare Informatics, {ICHI}
2019, Xi'an, China, June 10-13, 2019},
pages = {1--5},
publisher = {{IEEE}},
year = {2019},
url = {https://doi.org/10.1109/ICHI.2019.8904728},
doi = {10.1109/ICHI.2019.8904728},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ichi/ChenPL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ichi/PengYSSL19,
author = {Yifan Peng and
Ke Yan and
Veit Sandfort and
Ronald M. Summers and
Zhiyong Lu},
title = {A self-attention based deep learning method for lesion attribute detection
from {CT} reports},
booktitle = {2019 {IEEE} International Conference on Healthcare Informatics, {ICHI}
2019, Xi'an, China, June 10-13, 2019},
pages = {1--5},
publisher = {{IEEE}},
year = {2019},
url = {https://doi.org/10.1109/ICHI.2019.8904668},
doi = {10.1109/ICHI.2019.8904668},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ichi/PengYSSL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbi/YanPLS19,
author = {Ke Yan and
Yifan Peng and
Zhiyong Lu and
Ronald M. Summers},
title = {Fine-Grained Lesion Annotation in {CT} Images With Knowledge Mined
From Radiology Reports},
booktitle = {16th {IEEE} International Symposium on Biomedical Imaging, {ISBI}
2019, Venice, Italy, April 8-11, 2019},
pages = {285--288},
publisher = {{IEEE}},
year = {2019},
url = {https://doi.org/10.1109/ISBI.2019.8759336},
doi = {10.1109/ISBI.2019.8759336},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbi/YanPLS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/miccai/YanTPSBLS19,
author = {Ke Yan and
Youbao Tang and
Yifan Peng and
Veit Sandfort and
Mohammadhadi Bagheri and
Zhiyong Lu and
Ronald M. Summers},
editor = {Dinggang Shen and
Tianming Liu and
Terry M. Peters and
Lawrence H. Staib and
Caroline Essert and
Sean Zhou and
Pew{-}Thian Yap and
Ali R. Khan},
title = {{MULAN:} Multitask Universal Lesion Analysis Network for Joint Lesion
Detection, Tagging, and Segmentation},
booktitle = {Medical Image Computing and Computer Assisted Intervention - {MICCAI}
2019 - 22nd International Conference, Shenzhen, China, October 13-17,
2019, Proceedings, Part {VI}},
series = {Lecture Notes in Computer Science},
volume = {11769},
pages = {194--202},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-030-32226-7\_22},
doi = {10.1007/978-3-030-32226-7\_22},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/miccai/YanTPSBLS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/GonzalezLLWBCDF19,
author = {Graciela Gonzalez and
Zhiyong Lu and
Robert Leaman and
Davy Weissenbacher and
Mary Regina Boland and
Yong Chen and
Jingcheng Du and
Juliane Fluck and
Casey S. Greene and
John H. Holmes and
Aditya Kashyap and
Rikke Linnemann Nielsen and
Zhengqing Ouyang and
Sebastian Schaaf and
Jaclyn N. Taroni and
Cui Tao and
Yuping Zhang and
Hongfang Liu},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Marylyn D. Ritchie and
Teri E. Klein},
title = {Text Mining and Machine Learning for Precision Medicine},
booktitle = {Biocomputing 2019: Proceedings of the Pacific Symposium, The Big Island
of Hawaii, Hawaii, USA, January 3-7, 2019},
pages = {449--454},
year = {2019},
url = {http://psb.stanford.edu/psb-online/proceedings/psb19/wkshop-text.pdf},
timestamp = {Wed, 09 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/psb/GonzalezLLWBCDF19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/sp/19/WangPLLBS19,
author = {Xiaosong Wang and
Yifan Peng and
Le Lu and
Zhiyong Lu and
Mohammadhadi Bagheri and
Ronald M. Summers},
editor = {Le Lu and
Xiaosong Wang and
Gustavo Carneiro and
Lin Yang},
title = {ChestX-ray: Hospital-Scale Chest X-ray Database and Benchmarks on
Weakly Supervised Classification and Localization of Common Thorax
Diseases},
booktitle = {Deep Learning and Convolutional Neural Networks for Medical Imaging
and Clinical Informatics},
series = {Advances in Computer Vision and Pattern Recognition},
pages = {369--392},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-030-13969-8\_18},
doi = {10.1007/978-3-030-13969-8\_18},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/books/sp/19/WangPLLBS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:books/sp/19/WangPLLS19,
author = {Xiaosong Wang and
Yifan Peng and
Le Lu and
Zhiyong Lu and
Ronald M. Summers},
editor = {Le Lu and
Xiaosong Wang and
Gustavo Carneiro and
Lin Yang},
title = {Automatic Classification and Reporting of Multiple Common Thorax Diseases
Using Chest Radiographs},
booktitle = {Deep Learning and Convolutional Neural Networks for Medical Imaging
and Clinical Informatics},
series = {Advances in Computer Vision and Pattern Recognition},
pages = {393--412},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-030-13969-8\_19},
doi = {10.1007/978-3-030-13969-8\_19},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/books/sp/19/WangPLLS19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1901-06103,
author = {Yijia Zhang and
Zhiyong Lu},
title = {Exploring Semi-supervised Variational Autoencoders for Biomedical
Relation Extraction},
journal = {CoRR},
volume = {abs/1901.06103},
year = {2019},
url = {http://arxiv.org/abs/1901.06103},
eprinttype = {arXiv},
eprint = {1901.06103},
timestamp = {Tue, 18 May 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1901-06103.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1903-01505,
author = {Ke Yan and
Yifan Peng and
Zhiyong Lu and
Ronald M. Summers},
title = {Fine-grained lesion annotation in {CT} images with knowledge mined
from radiology reports},
journal = {CoRR},
volume = {abs/1903.01505},
year = {2019},
url = {http://arxiv.org/abs/1903.01505},
eprinttype = {arXiv},
eprint = {1903.01505},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1903-01505.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1904-04661,
author = {Ke Yan and
Yifan Peng and
Veit Sandfort and
Mohammadhadi Bagheri and
Zhiyong Lu and
Ronald M. Summers},
title = {Holistic and Comprehensive Annotation of Clinically Significant Findings
on Diverse {CT} Images: Learning from Radiology Reports and Label
Ontology},
journal = {CoRR},
volume = {abs/1904.04661},
year = {2019},
url = {http://arxiv.org/abs/1904.04661},
eprinttype = {arXiv},
eprint = {1904.04661},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1904-04661.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1904-13018,
author = {Yifan Peng and
Ke Yan and
Veit Sandfort and
Ronald M. Summers and
Zhiyong Lu},
title = {A self-attention based deep learning method for lesion attribute detection
from {CT} reports},
journal = {CoRR},
volume = {abs/1904.13018},
year = {2019},
url = {http://arxiv.org/abs/1904.13018},
eprinttype = {arXiv},
eprint = {1904.13018},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1904-13018.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1906-03153,
author = {Tiarnan D. Keenan and
Shazia Dharssi and
Yifan Peng and
Qingyu Chen and
Elvira Agr{\'{o}}n and
Wai T. Wong and
Zhiyong Lu and
Emily Y. Chew},
title = {A deep learning approach for automated detection of geographic atrophy
from color fundus photographs},
journal = {CoRR},
volume = {abs/1906.03153},
year = {2019},
url = {http://arxiv.org/abs/1906.03153},
eprinttype = {arXiv},
eprint = {1906.03153},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1906-03153.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1906-05474,
author = {Yifan Peng and
Shankai Yan and
Zhiyong Lu},
title = {Transfer Learning in Biomedical Natural Language Processing: An Evaluation
of {BERT} and ELMo on Ten Benchmarking Datasets},
journal = {CoRR},
volume = {abs/1906.05474},
year = {2019},
url = {http://arxiv.org/abs/1906.05474},
eprinttype = {arXiv},
eprint = {1906.05474},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1906-05474.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1908-04373,
author = {Ke Yan and
Youbao Tang and
Yifan Peng and
Veit Sandfort and
Mohammadhadi Bagheri and
Zhiyong Lu and
Ronald M. Summers},
title = {{MULAN:} Multitask Universal Lesion Analysis Network for Joint Lesion
Detection, Tagging, and Segmentation},
journal = {CoRR},
volume = {abs/1908.04373},
year = {2019},
url = {http://arxiv.org/abs/1908.04373},
eprinttype = {arXiv},
eprint = {1908.04373},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1908-04373.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1909-03044,
author = {Qingyu Chen and
Jingcheng Du and
Sun Kim and
W. John Wilbur and
Zhiyong Lu},
title = {Deep learning with sentence embeddings pre-trained on biomedical corpora
improves the performance of finding similar sentences in electronic
medical records},
journal = {CoRR},
volume = {abs/1909.03044},
year = {2019},
url = {http://arxiv.org/abs/1909.03044},
eprinttype = {arXiv},
eprint = {1909.03044},
timestamp = {Fri, 03 Jan 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1909-03044.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1909-10416,
author = {Chih{-}Hsuan Wei and
Kyubum Lee and
Robert Leaman and
Zhiyong Lu},
title = {Biomedical Mention Disambiguation using a Deep Learning Approach},
journal = {CoRR},
volume = {abs/1909.10416},
year = {2019},
url = {http://arxiv.org/abs/1909.10416},
eprinttype = {arXiv},
eprint = {1909.10416},
timestamp = {Fri, 27 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1909-10416.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1912-10846,
author = {Qingyu Chen and
Kyubum Lee and
Shankai Yan and
Sun Kim and
Chih{-}Hsuan Wei and
Zhiyong Lu},
title = {BioConceptVec: creating and evaluating literature-based biomedical
concept embeddings on a large scale},
journal = {CoRR},
volume = {abs/1912.10846},
year = {2019},
url = {http://arxiv.org/abs/1912.10846},
eprinttype = {arXiv},
eprint = {1912.10846},
timestamp = {Fri, 03 Jan 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-1912-10846.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/YeganovaKCWL18,
author = {Lana Yeganova and
Won Kim and
Donald C. Comeau and
W. John Wilbur and
Zhiyong Lu},
title = {A Field Sensor: computing the composition and intent of PubMed queries},
journal = {Database J. Biol. Databases Curation},
volume = {2018},
pages = {bay052},
year = {2018},
url = {https://doi.org/10.1093/database/bay052},
doi = {10.1093/DATABASE/BAY052},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/YeganovaKCWL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/PengRKL18,
author = {Yifan Peng and
Anthony Rios and
Ramakanth Kavuluru and
Zhiyong Lu},
title = {Extracting chemical-protein relations with ensembles of {SVM} and
deep learning models},
journal = {Database J. Biol. Databases Curation},
volume = {2018},
pages = {bay073},
year = {2018},
url = {https://doi.org/10.1093/database/bay073},
doi = {10.1093/DATABASE/BAY073},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/PengRKL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/HsuWL18,
author = {Yi{-}Yu Hsu and
Chih{-}Hsuan Wei and
Zhiyong Lu},
title = {Assisting document triage for human kinome curation via machine learning},
journal = {Database J. Biol. Databases Curation},
volume = {2018},
pages = {bay091},
year = {2018},
url = {https://doi.org/10.1093/database/bay091},
doi = {10.1093/DATABASE/BAY091},
timestamp = {Thu, 01 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/HsuWL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/FioriniCBRGLMOK18,
author = {Nicolas Fiorini and
Kathi Canese and
Rostyslav Bryzgunov and
Ievgeniia Radetska and
Asta Gindulyte and
Martin Latterner and
Vadim Miller and
Maxim Osipov and
Michael Kholodov and
Grisha Starchenko and
Evgeny Kireev and
Zhiyong Lu},
title = {PubMed Labs: an experimental system for improving biomedical literature
search},
journal = {Database J. Biol. Databases Curation},
volume = {2018},
pages = {bay094},
year = {2018},
url = {https://doi.org/10.1093/database/bay094},
doi = {10.1093/DATABASE/BAY094},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/FioriniCBRGLMOK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/GobeillGDMKHWLR18,
author = {Julien Gobeill and
Pascale Gaudet and
Daniel Dopp and
Adam Morrone and
Indika Kahanda and
Yi{-}Yu Hsu and
Chih{-}Hsuan Wei and
Zhiyong Lu and
Patrick Ruch},
title = {Overview of the BioCreative {VI} text-mining services for Kinome Curation
Track},
journal = {Database J. Biol. Databases Curation},
volume = {2018},
pages = {bay104},
year = {2018},
url = {https://doi.org/10.1093/database/bay104},
doi = {10.1093/DATABASE/BAY104},
timestamp = {Thu, 01 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/GobeillGDMKHWLR18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeiPFMHL18,
author = {Chih{-}Hsuan Wei and
Lon Phan and
Juliana Feltz and
Rama Maiti and
Tim Hefferon and
Zhiyong Lu},
title = {tmVar 2.0: integrating genomic variant information from literature
with dbSNP and ClinVar for precision medicine},
journal = {Bioinform.},
volume = {34},
number = {1},
pages = {80--87},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/btx541},
doi = {10.1093/BIOINFORMATICS/BTX541},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeiPFMHL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RiosKL18,
author = {Anthony Rios and
Ramakanth Kavuluru and
Zhiyong Lu},
title = {Generalizing biomedical relation classification with neural adversarial
domain adaptation},
journal = {Bioinform.},
volume = {34},
number = {17},
pages = {2973--2981},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty190},
doi = {10.1093/BIOINFORMATICS/BTY190},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RiosKL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KwonKWLL18,
author = {Dongseop Kwon and
Sun Kim and
Chih{-}Hsuan Wei and
Robert Leaman and
Zhiyong Lu},
title = {ezTag: tagging biomedical concepts via interactive learning},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Webserver-Issue},
pages = {W523--W529},
year = {2018},
url = {https://doi.org/10.1093/nar/gky428},
doi = {10.1093/NAR/GKY428},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/KwonKWLL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AllotPWLPL18,
author = {Alexis Allot and
Yifan Peng and
Chih{-}Hsuan Wei and
Kyubum Lee and
Lon Phan and
Zhiyong Lu},
title = {LitVar: a semantic search engine for linking genomic variant data
in PubMed and {PMC}},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Webserver-Issue},
pages = {W530--W536},
year = {2018},
url = {https://doi.org/10.1093/nar/gky355},
doi = {10.1093/NAR/GKY355},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/AllotPWLPL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LeeFMWMPBBCXL18,
author = {Kyubum Lee and
Maria Livia Famiglietti and
Aoife McMahon and
Chih{-}Hsuan Wei and
Jacqueline A. L. MacArthur and
Sylvain Poux and
Lionel Breuza and
Alan J. Bridge and
Fiona Cunningham and
Ioannis Xenarios and
Zhiyong Lu},
title = {Scaling up data curation using deep learning: An application to literature
triage in genomic variation resources},
journal = {PLoS Comput. Biol.},
volume = {14},
number = {8},
year = {2018},
url = {https://doi.org/10.1371/journal.pcbi.1006390},
doi = {10.1371/JOURNAL.PCBI.1006390},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/LeeFMWMPBBCXL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/FioriniL18,
author = {Nicolas Fiorini and
Zhiyong Lu},
title = {Online evaluation of PubMed's new relevance search algorithm},
booktitle = {{AMIA} 2018, American Medical Informatics Association Annual Symposium,
San Francisco, CA, November 3-7, 2018},
publisher = {{AMIA}},
year = {2018},
url = {https://knowledge.amia.org/67852-amia-1.4259402/t006-1.4263223/t006-1.4263224/2975477-1.4263492/2976531-1.4263489},
timestamp = {Wed, 17 Apr 2024 11:47:15 +0200},
biburl = {https://dblp.org/rec/conf/amia/FioriniL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/LuF18,
author = {Zhiyong Lu and
Nicolas Fiorini},
title = {Experimenting new search and user interface in PubMed Labs},
booktitle = {{AMIA} 2018, American Medical Informatics Association Annual Symposium,
San Francisco, CA, November 3-7, 2018},
publisher = {{AMIA}},
year = {2018},
url = {https://knowledge.amia.org/67852-amia-1.4259402/t006-1.4263223/t006-1.4263224/2974973-1.4263399/2976996-1.4263396},
timestamp = {Wed, 17 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/LuF18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/ChenKWL18,
author = {Qingyu Chen and
Sun Kim and
W. John Wilbur and
Zhiyong Lu},
editor = {Amarda Shehu and
Cathy H. Wu and
Christina Boucher and
Jing Li and
Hongfang Liu and
Mihai Pop},
title = {Sentence Similarity Measures Revisited: Ranking Sentences in PubMed
Documents},
booktitle = {Proceedings of the 2018 {ACM} International Conference on Bioinformatics,
Computational Biology, and Health Informatics, {BCB} 2018, Washington,
DC, USA, August 29 - September 01, 2018},
pages = {531--532},
publisher = {{ACM}},
year = {2018},
url = {https://doi.org/10.1145/3233547.3233640},
doi = {10.1145/3233547.3233640},
timestamp = {Mon, 10 Jun 2024 20:41:10 +0200},
biburl = {https://dblp.org/rec/conf/bcb/ChenKWL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/YeganovaCKWL18,
author = {Lana Yeganova and
Donald C. Comeau and
Won Kim and
W. John Wilbur and
Zhiyong Lu},
editor = {Dina Demner{-}Fushman and
Kevin Bretonnel Cohen and
Sophia Ananiadou and
Junichi Tsujii},
title = {SingleCite: Towards an improved Single Citation Search in PubMed},
booktitle = {Proceedings of the BioNLP 2018 workshop, Melbourne, Australia, July
19, 2018},
pages = {151--155},
publisher = {Association for Computational Linguistics},
year = {2018},
url = {https://doi.org/10.18653/v1/w18-2318},
doi = {10.18653/V1/W18-2318},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/YeganovaCKWL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/KimYCWL18,
author = {Won Kim and
Lana Yeganova and
Donald C. Comeau and
W. John Wilbur and
Zhiyong Lu},
editor = {Dina Demner{-}Fushman and
Kevin Bretonnel Cohen and
Sophia Ananiadou and
Junichi Tsujii},
title = {MeSH-based dataset for measuring the relevance of text retrieval},
booktitle = {Proceedings of the BioNLP 2018 workshop, Melbourne, Australia, July
19, 2018},
pages = {161--165},
publisher = {Association for Computational Linguistics},
year = {2018},
url = {https://doi.org/10.18653/v1/w18-2320},
doi = {10.18653/V1/W18-2320},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/KimYCWL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cvpr/WangPLLS18,
author = {Xiaosong Wang and
Yifan Peng and
Le Lu and
Zhiyong Lu and
Ronald M. Summers},
title = {TieNet: Text-Image Embedding Network for Common Thorax Disease Classification
and Reporting in Chest X-Rays},
booktitle = {2018 {IEEE} Conference on Computer Vision and Pattern Recognition,
{CVPR} 2018, Salt Lake City, UT, USA, June 18-22, 2018},
pages = {9049--9058},
publisher = {Computer Vision Foundation / {IEEE} Computer Society},
year = {2018},
url = {http://openaccess.thecvf.com/content\_cvpr\_2018/html/Wang\_TieNet\_Text-Image\_Embedding\_CVPR\_2018\_paper.html},
doi = {10.1109/CVPR.2018.00943},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cvpr/WangPLLS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/naacl/FioriniL18,
author = {Nicolas Fiorini and
Zhiyong Lu},
editor = {Srinivas Bangalore and
Jennifer Chu{-}Carroll and
Yunyao Li},
title = {Personalized neural language models for real-world query auto completion},
booktitle = {Proceedings of the 2018 Conference of the North American Chapter of
the Association for Computational Linguistics: Human Language Technologies,
{NAACL-HLT} 2018, New Orleans, Louisiana, USA, June 1-6, 2018, Volume
3 (Industry Papers)},
pages = {208--215},
publisher = {Association for Computational Linguistics},
year = {2018},
url = {https://doi.org/10.18653/v1/n18-3026},
doi = {10.18653/V1/N18-3026},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/naacl/FioriniL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/www/MohanFKL18,
author = {Sunil Mohan and
Nicolas Fiorini and
Sun Kim and
Zhiyong Lu},
editor = {Pierre{-}Antoine Champin and
Fabien Gandon and
Mounia Lalmas and
Panagiotis G. Ipeirotis},
title = {A Fast Deep Learning Model for Textual Relevance in Biomedical Information
Retrieval},
booktitle = {Proceedings of the 2018 World Wide Web Conference on World Wide Web,
{WWW} 2018, Lyon, France, April 23-27, 2018},
pages = {77--86},
publisher = {{ACM}},
year = {2018},
url = {https://doi.org/10.1145/3178876.3186049},
doi = {10.1145/3178876.3186049},
timestamp = {Fri, 16 Apr 2021 10:04:12 +0200},
biburl = {https://dblp.org/rec/conf/www/MohanFKL18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1801-04334,
author = {Xiaosong Wang and
Yifan Peng and
Le Lu and
Zhiyong Lu and
Ronald M. Summers},
title = {TieNet: Text-Image Embedding Network for Common Thorax Disease Classification
and Reporting in Chest X-rays},
journal = {CoRR},
volume = {abs/1801.04334},
year = {2018},
url = {http://arxiv.org/abs/1801.04334},
eprinttype = {arXiv},
eprint = {1801.04334},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1801-04334.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1802-01255,
author = {Yifan Peng and
Anthony Rios and
Ramakanth Kavuluru and
Zhiyong Lu},
title = {Chemical-protein relation extraction with ensembles of SVM, CNN, and
{RNN} models},
journal = {CoRR},
volume = {abs/1802.01255},
year = {2018},
url = {http://arxiv.org/abs/1802.01255},
eprinttype = {arXiv},
eprint = {1802.01255},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1802-01255.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1802-10078,
author = {Sunil Mohan and
Nicolas Fiorini and
Sun Kim and
Zhiyong Lu},
title = {A Fast Deep Learning Model for Textual Relevance in Biomedical Information
Retrieval},
journal = {CoRR},
volume = {abs/1802.10078},
year = {2018},
url = {http://arxiv.org/abs/1802.10078},
eprinttype = {arXiv},
eprint = {1802.10078},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1802-10078.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1804-05957,
author = {Donald C. Comeau and
Chih{-}Hsuan Wei and
Rezarta Islamaj Dogan and
Zhiyong Lu},
title = {{PMC} text mining subset in BioC: 2.3 million full text articles and
growing},
journal = {CoRR},
volume = {abs/1804.05957},
year = {2018},
url = {http://arxiv.org/abs/1804.05957},
eprinttype = {arXiv},
eprint = {1804.05957},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1804-05957.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1804-06439,
author = {Nicolas Fiorini and
Zhiyong Lu},
title = {Personalized neural language models for real-world query auto completion},
journal = {CoRR},
volume = {abs/1804.06439},
year = {2018},
url = {http://arxiv.org/abs/1804.06439},
eprinttype = {arXiv},
eprint = {1804.06439},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1804-06439.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1806-04004,
author = {Nicolas Fiorini and
Kathi Canese and
Rostyslav Bryzgunov and
Ievgeniia Radetska and
Asta Gindulyte and
Martin Latterner and
Vadim Miller and
Maxim Osipov and
Michael Kholodov and
Grisha Starchenko and
Evgeny Kireev and
Zhiyong Lu},
title = {PubMed Labs: An experimental platform for improving biomedical literature
search},
journal = {CoRR},
volume = {abs/1806.04004},
year = {2018},
url = {http://arxiv.org/abs/1806.04004},
eprinttype = {arXiv},
eprint = {1806.04004},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1806-04004.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1810-09302,
author = {Qingyu Chen and
Yifan Peng and
Zhiyong Lu},
title = {BioSentVec: creating sentence embeddings for biomedical texts},
journal = {CoRR},
volume = {abs/1810.09302},
year = {2018},
url = {http://arxiv.org/abs/1810.09302},
eprinttype = {arXiv},
eprint = {1810.09302},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1810-09302.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1811-05475,
author = {Jingcheng Du and
Qingyu Chen and
Yifan Peng and
Yang Xiang and
Cui Tao and
Zhiyong Lu},
title = {ML-Net: multi-label classification of biomedical texts with deep neural
networks},
journal = {CoRR},
volume = {abs/1811.05475},
year = {2018},
url = {http://arxiv.org/abs/1811.05475},
eprinttype = {arXiv},
eprint = {1811.05475},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1811-05475.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1811-07492,
author = {Yifan Peng and
Shazia Dharssi and
Qingyu Chen and
Tiarnan D. Keenan and
Elvira Agr{\'{o}}n and
Wai T. Wong and
Emily Y. Chew and
Zhiyong Lu},
title = {DeepSeeNet: {A} deep learning model for automated classification of
patient-based age-related macular degeneration severity from color
fundus photographs},
journal = {CoRR},
volume = {abs/1811.07492},
year = {2018},
url = {http://arxiv.org/abs/1811.07492},
eprinttype = {arXiv},
eprint = {1811.07492},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1811-07492.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1812-00422,
author = {Qingyu Chen and
Yifan Peng and
Tiarnan D. Keenan and
Shazia Dharssi and
Elvira Agr{\'{o}}n and
Wai T. Wong and
Emily Y. Chew and
Zhiyong Lu},
title = {A multi-task deep learning model for the classification of Age-related
Macular Degeneration},
journal = {CoRR},
volume = {abs/1812.00422},
year = {2018},
url = {http://arxiv.org/abs/1812.00422},
eprinttype = {arXiv},
eprint = {1812.00422},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1812-00422.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/PouxAMBWLBBFRC17,
author = {Sylvain Poux and
Cecilia N. Arighi and
Michele Magrane and
Alex Bateman and
Chih{-}Hsuan Wei and
Zhiyong Lu and
Emmanuel Boutet and
Hema Bye{-}A{-}Jee and
Maria Livia Famiglietti and
Bernd Roechert and
UniProt Consortium},
title = {On expert curation and scalability: UniProtKB/Swiss-Prot as a case
study},
journal = {Bioinform.},
volume = {33},
number = {21},
pages = {3454--3460},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx439},
doi = {10.1093/BIOINFORMATICS/BTX439},
timestamp = {Mon, 30 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/PouxAMBWLBBFRC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/MaoL17,
author = {Yuqing Mao and
Zhiyong Lu},
title = {MeSH Now: automatic MeSH indexing at PubMed scale via learning to
rank},
journal = {J. Biomed. Semant.},
volume = {8},
number = {1},
pages = {15:1--15:9},
year = {2017},
url = {https://doi.org/10.1186/s13326-017-0123-3},
doi = {10.1186/S13326-017-0123-3},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/MaoL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/LiuYLSL17,
author = {Xiaoxia Liu and
Zhihao Yang and
Hongfei Lin and
Michael Simmons and
Zhiyong Lu},
title = {DIGNiFI: Discovering causative genes for orphan diseases using protein-protein
interaction networks},
journal = {{BMC} Syst. Biol.},
volume = {11},
number = {3},
pages = {23:1--23:11},
year = {2017},
url = {https://doi.org/10.1186/s12918-017-0402-8},
doi = {10.1186/S12918-017-0402-8},
timestamp = {Wed, 25 Feb 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcsb/LiuYLSL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/KimFWL17,
author = {Sun Kim and
Nicolas Fiorini and
W. John Wilbur and
Zhiyong Lu},
title = {Bridging the gap: Incorporating a semantic similarity measure for
effectively mapping PubMed queries to documents},
journal = {J. Biomed. Informatics},
volume = {75},
pages = {122--127},
year = {2017},
url = {https://doi.org/10.1016/j.jbi.2017.09.014},
doi = {10.1016/J.JBI.2017.09.014},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/KimFWL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jdis/MaoL17,
author = {Yuqing Mao and
Zhiyong Lu},
title = {Mining Related Articles for Automatic Journal Cataloging},
journal = {J. Data Inf. Sci.},
volume = {1},
number = {2},
pages = {45--59},
year = {2017},
url = {https://doi.org/10.20309/jdis.201613},
doi = {10.20309/JDIS.201613},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jdis/MaoL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/FioriniL17,
author = {Nicolas Fiorini and
Zhiyong Lu},
title = {New Relevance Search Algorithm for PubMed},
booktitle = {{AMIA} 2017, American Medical Informatics Association Annual Symposium,
Washington, DC, USA, November 4-8, 2017},
publisher = {{AMIA}},
year = {2017},
url = {https://knowledge.amia.org/65881-amiab-1.4254737/t001-1.4259018/f001-1.4259019/2732046-1.4259290/2730604-1.4259287},
timestamp = {Wed, 17 Apr 2024 11:47:24 +0200},
biburl = {https://dblp.org/rec/conf/amia/FioriniL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/PengWLBSL17,
author = {Yifan Peng and
Xiaosong Wang and
Le Lu and
Mohammadhadi Bagheri and
Ronald M. Summers and
Zhiyong Lu},
title = {Text Mining Radiology Reports for Deep Learning Radiology Images},
booktitle = {{AMIA} 2017, American Medical Informatics Association Annual Symposium,
Washington, DC, USA, November 4-8, 2017},
publisher = {{AMIA}},
year = {2017},
url = {https://knowledge.amia.org/65881-amiab-1.4254737/t001-1.4259018/f001-1.4259019/2730974-1.4259149/2730753-1.4259146},
timestamp = {Mon, 30 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/PengWLBSL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/PengL17,
author = {Yifan Peng and
Zhiyong Lu},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
Junichi Tsujii},
title = {Deep learning for extracting protein-protein interactions from biomedical
literature},
booktitle = {BioNLP 2017, Vancouver, Canada, August 4, 2017},
pages = {29--38},
publisher = {Association for Computational Linguistics},
year = {2017},
url = {https://doi.org/10.18653/v1/W17-2304},
doi = {10.18653/V1/W17-2304},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/PengL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/DoganCKWPCL17,
author = {Rezarta Islamaj Dogan and
Andrew Chatr{-}aryamontri and
Sun Kim and
Chih{-}Hsuan Wei and
Yifan Peng and
Donald C. Comeau and
Zhiyong Lu},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
Junichi Tsujii},
title = {BioCreative {VI} Precision Medicine Track: creating a training corpus
for mining protein-protein interactions affected by mutations},
booktitle = {BioNLP 2017, Vancouver, Canada, August 4, 2017},
pages = {171--175},
publisher = {Association for Computational Linguistics},
year = {2017},
url = {https://doi.org/10.18653/v1/W17-2321},
doi = {10.18653/V1/W17-2321},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/DoganCKWPCL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/MohanFKL17,
author = {Sunil Mohan and
Nicolas Fiorini and
Sun Kim and
Zhiyong Lu},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
Junichi Tsujii},
title = {Deep Learning for Biomedical Information Retrieval: Learning Textual
Relevance from Click Logs},
booktitle = {BioNLP 2017, Vancouver, Canada, August 4, 2017},
pages = {222--231},
publisher = {Association for Computational Linguistics},
year = {2017},
url = {https://doi.org/10.18653/v1/W17-2328},
doi = {10.18653/V1/W17-2328},
timestamp = {Tue, 20 Aug 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/MohanFKL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cvpr/WangPLLBS17,
author = {Xiaosong Wang and
Yifan Peng and
Le Lu and
Zhiyong Lu and
Mohammadhadi Bagheri and
Ronald M. Summers},
title = {ChestX-Ray8: Hospital-Scale Chest X-Ray Database and Benchmarks on
Weakly-Supervised Classification and Localization of Common Thorax
Diseases},
booktitle = {2017 {IEEE} Conference on Computer Vision and Pattern Recognition,
{CVPR} 2017, Honolulu, HI, USA, July 21-26, 2017},
pages = {3462--3471},
publisher = {{IEEE} Computer Society},
year = {2017},
url = {https://doi.org/10.1109/CVPR.2017.369},
doi = {10.1109/CVPR.2017.369},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/cvpr/WangPLLBS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/nas/ZhuangQLWX17,
author = {Xiaozhao Zhuang and
Xiaoyang Qu and
Zhiyong Lu and
Jiguang Wan and
Changsheng Xie},
title = {Exploiting Virtual Metadata Servers to Provide Multi-Level Consistency
for Key-Value Object-Based Data Store},
booktitle = {2017 International Conference on Networking, Architecture, and Storage,
{NAS} 2017, Shenzhen, China, August 7-9, 2017},
pages = {1--6},
publisher = {{IEEE} Computer Society},
year = {2017},
url = {https://doi.org/10.1109/NAS.2017.8026857},
doi = {10.1109/NAS.2017.8026857},
timestamp = {Sat, 14 Mar 2026 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/nas/ZhuangQLWX17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/WangPLLBS17,
author = {Xiaosong Wang and
Yifan Peng and
Le Lu and
Zhiyong Lu and
Mohammadhadi Bagheri and
Ronald M. Summers},
title = {ChestX-ray8: Hospital-scale Chest X-ray Database and Benchmarks on
Weakly-Supervised Classification and Localization of Common Thorax
Diseases},
journal = {CoRR},
volume = {abs/1705.02315},
year = {2017},
url = {http://arxiv.org/abs/1705.02315},
eprinttype = {arXiv},
eprint = {1705.02315},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/WangPLLBS17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/PengL17,
author = {Yifan Peng and
Zhiyong Lu},
title = {Deep learning for extracting protein-protein interactions from biomedical
literature},
journal = {CoRR},
volume = {abs/1706.01556},
year = {2017},
url = {http://arxiv.org/abs/1706.01556},
eprinttype = {arXiv},
eprint = {1706.01556},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/PengL17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1712-05898,
author = {Yifan Peng and
Xiaosong Wang and
Le Lu and
Mohammadhadi Bagheri and
Ronald M. Summers and
Zhiyong Lu},
title = {NegBio: a high-performance tool for negation and uncertainty detection
in radiology reports},
journal = {CoRR},
volume = {abs/1712.05898},
year = {2017},
url = {http://arxiv.org/abs/1712.05898},
eprinttype = {arXiv},
eprint = {1712.05898},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1712-05898.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/LiZCBSL16,
author = {Jiao Li and
Si Zheng and
Bin Chen and
Atul J. Butte and
S. Joshua Swamidass and
Zhiyong Lu},
title = {A survey of current trends in computational drug repositioning},
journal = {Briefings Bioinform.},
volume = {17},
number = {1},
pages = {2--12},
year = {2016},
url = {https://doi.org/10.1093/bib/bbv020},
doi = {10.1093/BIB/BBV020},
timestamp = {Tue, 16 Dec 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/LiZCBSL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KhareGLSL16,
author = {Ritu Khare and
Benjamin M. Good and
Robert Leaman and
Andrew I. Su and
Zhiyong Lu},
title = {Crowdsourcing in biomedicine: challenges and opportunities},
journal = {Briefings Bioinform.},
volume = {17},
number = {1},
pages = {23--32},
year = {2016},
url = {https://doi.org/10.1093/bib/bbv021},
doi = {10.1093/BIB/BBV021},
timestamp = {Tue, 16 Dec 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/KhareGLSL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/HuangL16,
author = {Chung{-}Chi Huang and
Zhiyong Lu},
title = {Community challenges in biomedical text mining over 10 years: success,
failure and the future},
journal = {Briefings Bioinform.},
volume = {17},
number = {1},
pages = {132--144},
year = {2016},
url = {https://doi.org/10.1093/bib/bbv024},
doi = {10.1093/BIB/BBV024},
timestamp = {Tue, 16 Dec 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bib/HuangL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/HuangL16,
author = {Chung{-}Chi Huang and
Zhiyong Lu},
title = {Discovering biomedical semantic relations in PubMed queries for information
retrieval and database curation},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016},
url = {https://doi.org/10.1093/database/baw025},
doi = {10.1093/DATABASE/BAW025},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/HuangL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/LeamanWZL16,
author = {Robert Leaman and
Chih{-}Hsuan Wei and
Cherry Zou and
Zhiyong Lu},
title = {Mining chemical patents with an ensemble of open systems},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016},
url = {https://doi.org/10.1093/database/baw065},
doi = {10.1093/DATABASE/BAW065},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/LeamanWZL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/LiSJSWLDMWL16,
author = {Jiao Li and
Yueping Sun and
Robin J. Johnson and
Daniela Sciaky and
Chih{-}Hsuan Wei and
Robert Leaman and
Allan Peter Davis and
Carolyn J. Mattingly and
Thomas C. Wiegers and
Zhiyong Lu},
title = {BioCreative {V} {CDR} task corpus: a resource for chemical disease
relation extraction},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016},
url = {https://doi.org/10.1093/database/baw068},
doi = {10.1093/DATABASE/BAW068},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/LiSJSWLDMWL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/SinghalLCLMPXAL16,
author = {Ayush Singhal and
Robert Leaman and
Natalie L. Catlett and
Thomas Lemberger and
Johanna R. McEntyre and
Shawn W. Polson and
Ioannis Xenarios and
Cecilia N. Arighi and
Zhiyong Lu},
title = {Pressing needs of biomedical text mining in biocuration and beyond:
opportunities and challenges},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016},
url = {https://doi.org/10.1093/database/baw161},
doi = {10.1093/DATABASE/BAW161},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/SinghalLCLMPXAL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/WangAAABBCCCCCD16,
author = {Qinghua Wang and
Shabbir Syed{-}Abdul and
Lara Almeida and
Sophia Ananiadou and
Yalbi I. Balderas{-}Mart{\'{\i}}nez and
Riza Batista{-}Navarro and
David Campos and
Lucy Chilton and
Hui{-}Jou Chou and
Gabriela Contreras and
Laurel Cooper and
Hong{-}Jie Dai and
Barbra Ferrell and
Juliane Fluck and
Socorro Gama{-}Castro and
Nancy George and
Georgios V. Gkoutos and
Afroza Khanam Irin and
Lars Juhl Jensen and
Silvia Jimenez and
Toni Rose Jue and
Ingrid M. Keseler and
Sumit Madan and
S{\'{e}}rgio Matos and
Peter McQuilton and
Marija Milacic and
Matthew E. Mort and
Jeyakumar Natarajan and
Evangelos Pafilis and
Emiliano Pereira and
Shruti Rao and
Fabio Rinaldi and
Karen Rothfels and
David Salgado and
Raquel M. Silva and
Onkar Singh and
Raymund Stefancsik and
Chu{-}Hsien Su and
Suresh Subramani and
Hamsa D. Tadepally and
Loukia Tsaprouni and
Nicole A. Vasilevsky and
Xiaodong Wang and
Andrew Chatr{-}aryamontri and
Stanley J. F. Laulederkind and
Sherri Matis{-}Mitchell and
Johanna R. McEntyre and
Sandra E. Orchard and
Sangya Pundir and
Raul Rodriguez{-}Esteban and
Kimberly Van Auken and
Zhiyong Lu and
Mary L. Schaeffer and
Cathy H. Wu and
Lynette Hirschman and
Cecilia N. Arighi},
title = {Overview of the interactive task in BioCreative {V}},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016},
url = {https://doi.org/10.1093/database/baw119},
doi = {10.1093/DATABASE/BAW119},
timestamp = {Sat, 15 Nov 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/WangAAABBCCCCCD16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/WeiPLDMLWL16,
author = {Chih{-}Hsuan Wei and
Yifan Peng and
Robert Leaman and
Allan Peter Davis and
Carolyn J. Mattingly and
Jiao Li and
Thomas C. Wiegers and
Zhiyong Lu},
title = {Assessing the state of the art in biomedical relation extraction:
overview of the BioCreative {V} chemical-disease relation {(CDR)}
task},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016},
url = {https://doi.org/10.1093/database/baw032},
doi = {10.1093/DATABASE/BAW032},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/WeiPLDMLWL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeiLL16,
author = {Chih{-}Hsuan Wei and
Robert Leaman and
Zhiyong Lu},
title = {Beyond accuracy: creating interoperable and scalable text-mining web
services},
journal = {Bioinform.},
volume = {32},
number = {12},
pages = {1907--1910},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btv760},
doi = {10.1093/BIOINFORMATICS/BTV760},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeiLL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LeamanL16,
author = {Robert Leaman and
Zhiyong Lu},
title = {TaggerOne: joint named entity recognition and normalization with semi-Markov
Models},
journal = {Bioinform.},
volume = {32},
number = {18},
pages = {2839--2846},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btw343},
doi = {10.1093/BIOINFORMATICS/BTW343},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LeamanL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jamia/SinghalSL16,
author = {Ayush Singhal and
Michael Simmons and
Zhiyong Lu},
title = {Text mining for precision medicine: automating disease-mutation relationship
extraction from biomedical literature},
journal = {J. Am. Medical Informatics Assoc.},
volume = {23},
number = {4},
pages = {766--772},
year = {2016},
url = {https://doi.org/10.1093/jamia/ocw041},
doi = {10.1093/JAMIA/OCW041},
timestamp = {Mon, 11 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jamia/SinghalSL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/PengWL16,
author = {Yifan Peng and
Chih{-}Hsuan Wei and
Zhiyong Lu},
title = {Improving chemical disease relation extraction with rich features
and weakly labeled data},
journal = {J. Cheminformatics},
volume = {8},
number = {1},
pages = {53:1--53:12},
year = {2016},
url = {https://doi.org/10.1186/s13321-016-0165-z},
doi = {10.1186/S13321-016-0165-Z},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcheminf/PengWL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/SinghalSL16,
author = {Ayush Singhal and
Michael Simmons and
Zhiyong Lu},
title = {Text Mining Genotype-Phenotype Relationships from Biomedical Literature
for Database Curation and Precision Medicine},
journal = {PLoS Comput. Biol.},
volume = {12},
number = {11},
year = {2016},
url = {https://doi.org/10.1371/journal.pcbi.1005017},
doi = {10.1371/JOURNAL.PCBI.1005017},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/SinghalSL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/acl-louhi/HuangL16,
author = {Chung{-}Chi Huang and
Zhiyong Lu},
editor = {Cyril Grouin and
Thierry Hamon and
Aur{\'{e}}lie N{\'{e}}v{\'{e}}ol and
Pierre Zweigenbaum},
title = {Exploring Query Expansion for Entity Searches in PubMed},
booktitle = {Proceedings of the Seventh International Workshop on Health Text Mining
and Information Analysis, Louhi@EMNLP 2016, Austin, TX, USA, November
5, 2016},
pages = {106--112},
publisher = {Association for Computational Linguistics},
year = {2016},
url = {https://doi.org/10.18653/v1/W16-6114},
doi = {10.18653/V1/W16-6114},
timestamp = {Fri, 06 Aug 2021 00:41:34 +0200},
biburl = {https://dblp.org/rec/conf/acl-louhi/HuangL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/LiuYLSL16,
author = {Xiaoxia Liu and
Zhihao Yang and
Hongfei Lin and
Michael Simmons and
Zhiyong Lu},
title = {DIGNiFI: Discovering causative genes for orphan diseases using protein-protein
interaction networks},
booktitle = {Proceedings of the 7th {ACM} International Conference on Bioinformatics,
Computational Biology, and Health Informatics, {BCB} 2016, Seattle,
WA, USA, October 2-5, 2016},
pages = {527},
publisher = {{ACM}},
year = {2016},
url = {https://doi.org/10.1145/2975167.2985669},
doi = {10.1145/2975167.2985669},
timestamp = {Tue, 06 Nov 2018 16:59:10 +0100},
biburl = {https://dblp.org/rec/conf/bcb/LiuYLSL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/YeganovaKKDLCLW16,
author = {Lana Yeganova and
Won Kim and
Sun Kim and
Rezarta Islamaj Dogan and
Wanli Liu and
Donald C. Comeau and
Zhiyong Lu and
W. John Wilbur},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
Jun'ichi Tsujii},
title = {PubTermVariants: biomedical term variants and their use for PubMed
search},
booktitle = {Proceedings of the 15th Workshop on Biomedical Natural Language Processing,
BioNLP@ACL 2016, Berlin, Germany, August 12, 2016},
pages = {141--145},
publisher = {Association for Computational Linguistics},
year = {2016},
url = {https://doi.org/10.18653/v1/W16-2919},
doi = {10.18653/V1/W16-2919},
timestamp = {Fri, 06 Aug 2021 00:41:22 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/YeganovaKKDLCLW16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/ComeauDKWWL16,
author = {Donald C. Comeau and
Rezarta Islamaj Dogan and
Sun Kim and
Chih{-}Hsuan Wei and
W. John Wilbur and
Zhiyong Lu},
editor = {Pankaj Jaiswal and
Robert Hoehndorf and
Cecilia N. Arighi and
Austin Meier},
title = {BioCconvert: {A} Conversion Tool Between BioC and PubAnnotation},
booktitle = {Proceedings of the Joint International Conference on Biological Ontology
and BioCreative, Corvallis, Oregon, United States, August 1-4, 2016},
series = {{CEUR} Workshop Proceedings},
volume = {1747},
publisher = {CEUR-WS.org},
year = {2016},
url = {https://ceur-ws.org/Vol-1747/BT304\_ICBO2016.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:23 +0100},
biburl = {https://dblp.org/rec/conf/icbo/ComeauDKWWL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/WeiLL16,
author = {Chih{-}Hsuan Wei and
Robert Leaman and
Zhiyong Lu},
editor = {Pankaj Jaiswal and
Robert Hoehndorf and
Cecilia N. Arighi and
Austin Meier},
title = {Large-scale Semantic Indexing with Biomedical Ontologies},
booktitle = {Proceedings of the Joint International Conference on Biological Ontology
and BioCreative, Corvallis, Oregon, United States, August 1-4, 2016},
series = {{CEUR} Workshop Proceedings},
volume = {1747},
publisher = {CEUR-WS.org},
year = {2016},
url = {https://ceur-ws.org/Vol-1747/BIT101-D204\_ICBO2016.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/WeiLL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/KimWL16,
author = {Sun Kim and
W. John Wilbur and
Zhiyong Lu},
title = {Bridging the Gap: a Semantic Similarity Measure between Queries and
Documents},
journal = {CoRR},
volume = {abs/1608.01972},
year = {2016},
url = {http://arxiv.org/abs/1608.01972},
eprinttype = {arXiv},
eprint = {1608.01972},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/KimWL16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/advcs/JiaoLS15,
author = {Bo Jiao and
Zhiyong Lu and
Jianmai Shi},
title = {The Application of Semidefinite Integer Programming Model for the
Simulation of Complex Networks},
journal = {Adv. Complex Syst.},
volume = {18},
number = {3-4},
pages = {1550015:1--1550015:25},
year = {2015},
url = {https://doi.org/10.1142/S0219525915500150},
doi = {10.1142/S0219525915500150},
timestamp = {Sat, 13 Dec 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/advcs/JiaoLS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/KhareBATCHL15,
author = {Ritu Khare and
John D. Burger and
John S. Aberdeen and
David Tresner{-}Kirsch and
Theodore J. Corrales and
Lynette Hirschman and
Zhiyong Lu},
title = {Scaling drug indication curation through crowdsourcing},
journal = {Database J. Biol. Databases Curation},
volume = {2015},
year = {2015},
url = {https://doi.org/10.1093/database/bav016},
doi = {10.1093/DATABASE/BAV016},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/KhareBATCHL15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KimLW15,
author = {Sun Kim and
Zhiyong Lu and
W. John Wilbur},
title = {Identifying named entities from PubMed{\textregistered}; for enriching
semantic categories},
journal = {{BMC} Bioinform.},
volume = {16},
pages = {57:1--57:10},
year = {2015},
url = {https://doi.org/10.1186/s12859-015-0487-2},
doi = {10.1186/S12859-015-0487-2},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KimLW15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/datascience/LiL15,
author = {Jiao Li and
Zhiyong Lu},
title = {An Integrative Approach for Discovery of New Uses of Existing Drugs},
journal = {Data Sci. J.},
volume = {14},
pages = {9},
year = {2015},
url = {https://doi.org/10.5334/dsj-2015-009},
doi = {10.5334/DSJ-2015-009},
timestamp = {Wed, 02 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/datascience/LiL15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/LeamanKL15,
author = {Robert Leaman and
Ritu Khare and
Zhiyong Lu},
title = {Challenges in clinical natural language processing for automated disorder
normalization},
journal = {J. Biomed. Informatics},
volume = {57},
pages = {28--37},
year = {2015},
url = {https://doi.org/10.1016/j.jbi.2015.07.010},
doi = {10.1016/J.JBI.2015.07.010},
timestamp = {Fri, 21 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/LeamanKL15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/KrallingerRL15,
author = {Martin Krallinger and
Obdulia Rabal and
Florian Leitner and
Miguel Vazquez and
David Salgado and
Zhiyong Lu and
Robert Leaman and
Yanan Lu and
Donghong Ji and
Daniel M. Lowe and
Roger A. Sayle and
Riza Theresa Batista{-}Navarro and
Rafal Rak and
Torsten Huber and
Tim Rockt{\"{a}}schel and
S{\'{e}}rgio Matos and
David Campos and
Buzhou Tang and
Hua Xu and
Tsendsuren Munkhdalai and
Keun Ho Ryu and
S. V. Ramanan and
P. Senthil Nathan and
Slavko Zitnik and
Marko Bajec and
Lutz Weber and
Matthias Irmer and
Saber A. Akhondi and
Jan A. Kors and
Shuo Xu and
Xin An and
Utpal Kumar Sikdar and
Asif Ekbal and
Masaharu Yoshioka and
Thaer M. Dieb and
Miji Choi and
Karin Verspoor and
Madian Khabsa and
C. Lee Giles and
Hongfang Liu and
Ravikumar Komandur Elayavilli and
Andre Lamurias and
Francisco M. Couto and
Hong{-}Jie Dai and
Richard Tzong{-}Han Tsai and
Caglar Ata and
Tolga Can and
Anabel Usie and
Rui Alves and
Isabel Segura{-}Bedmar and
Paloma Mart{\'{\i}}nez and
Julen Oyarzabal and
Alfonso Valencia},
title = {The {CHEMDNER} corpus of chemicals and drugs and its annotation principles},
journal = {J. Cheminformatics},
volume = {7},
number = {{S-1}},
pages = {S2},
year = {2015},
url = {https://doi.org/10.1186/1758-2946-7-S1-S2},
doi = {10.1186/1758-2946-7-S1-S2},
timestamp = {Wed, 12 Mar 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/KrallingerRL15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcheminf/LeamanWL15,
author = {Robert Leaman and
Chih{-}Hsuan Wei and
Zhiyong Lu},
title = {tmChem: a high performance approach for chemical named entity recognition
and normalization},
journal = {J. Cheminformatics},
volume = {7},
number = {{S-1}},
pages = {S3},
year = {2015},
url = {https://doi.org/10.1186/1758-2946-7-S1-S3},
doi = {10.1186/1758-2946-7-S1-S3},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcheminf/LeamanWL15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/titb/WeiLL15,
author = {Chih{-}Hsuan Wei and
Robert Leaman and
Zhiyong Lu},
title = {SimConcept: {A} Hybrid Approach for Simplifying Composite Named Entities
in Biomedical Text},
journal = {{IEEE} J. Biomed. Health Informatics},
volume = {19},
number = {4},
pages = {1385--1391},
year = {2015},
url = {https://doi.org/10.1109/JBHI.2015.2422651},
doi = {10.1109/JBHI.2015.2422651},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/titb/WeiLL15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/clef/MaoL15,
author = {Yuqing Mao and
Zhiyong Lu},
editor = {Linda Cappellato and
Nicola Ferro and
Gareth J. F. Jones and
Eric SanJuan},
title = {{NCBI} at the 2015 BioASQ Challenge Task: Baseline Results from MeSH
Now},
booktitle = {Working Notes of {CLEF} 2015 - Conference and Labs of the Evaluation
forum, Toulouse, France, September 8-11, 2015},
series = {{CEUR} Workshop Proceedings},
volume = {1391},
publisher = {CEUR-WS.org},
year = {2015},
url = {https://ceur-ws.org/Vol-1391/168-CR.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:42 +0100},
biburl = {https://dblp.org/rec/conf/clef/MaoL15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/LeamanGSL15,
author = {Robert Leaman and
Benjamin M. Good and
Andrew I. Su and
Zhiyong Lu},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein and
Marylyn D. Ritchie},
title = {Session Introduction},
booktitle = {Biocomputing 2015: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 4-8, 2015},
pages = {267--269},
year = {2015},
url = {http://psb.stanford.edu/psb-online/proceedings/psb15/intro-crowdsourcing.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/LeamanGSL15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/ArighiWCHKVLWW14,
author = {Cecilia N. Arighi and
Cathy H. Wu and
Kevin Bretonnel Cohen and
Lynette Hirschman and
Martin Krallinger and
Alfonso Valencia and
Zhiyong Lu and
W. John Wilbur and
Thomas C. Wiegers},
title = {BioCreative-IV virtual issue},
journal = {Database J. Biol. Databases Curation},
volume = {2014},
year = {2014},
url = {https://doi.org/10.1093/database/bau039},
doi = {10.1093/DATABASE/BAU039},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/ArighiWCHKVLWW14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/AukenSMLLWHTADMSMWL14,
author = {Kimberly Van Auken and
Mary L. Schaeffer and
Peter McQuilton and
Stanley J. F. Laulederkind and
Donghui Li and
Shur{-}Jen Wang and
G. Thomas Hayman and
Susan Tweedie and
Cecilia N. Arighi and
James Done and
Hans{-}Michael M{\"{u}}ller and
Paul W. Sternberg and
Yuqing Mao and
Chih{-}Hsuan Wei and
Zhiyong Lu},
title = {{BC4GO:} a full-text corpus for the BioCreative {IV} {GO} task},
journal = {Database J. Biol. Databases Curation},
volume = {2014},
year = {2014},
url = {https://doi.org/10.1093/database/bau074},
doi = {10.1093/DATABASE/BAU074},
timestamp = {Sat, 15 Nov 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/AukenSMLLWHTADMSMWL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/BurgerDKWMATWKLH14,
author = {John D. Burger and
Emily Doughty and
Ritu Khare and
Chih{-}Hsuan Wei and
Rajashree Mishra and
John S. Aberdeen and
David Tresner{-}Kirsch and
Ben Wellner and
Maricel G. Kann and
Zhiyong Lu and
Lynette Hirschman},
title = {Hybrid curation of gene-mutation relations combining automated extraction
and crowdsourcing},
journal = {Database J. Biol. Databases Curation},
volume = {2014},
year = {2014},
url = {https://doi.org/10.1093/database/bau094},
doi = {10.1093/DATABASE/BAU094},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/BurgerDKWMATWKLH14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/ComeauBDDJKLMMNPRRTVWWW14,
author = {Donald C. Comeau and
Riza Theresa Batista{-}Navarro and
Hong{-}Jie Dai and
Rezarta Islamaj Dogan and
Antonio Jimeno{-}Yepes and
Ritu Khare and
Zhiyong Lu and
Hernani Marques and
Carolyn J. Mattingly and
Mariana L. Neves and
Yifan Peng and
Rafal Rak and
Fabio Rinaldi and
Richard Tzong{-}Han Tsai and
Karin Verspoor and
Thomas C. Wiegers and
Cathy H. Wu and
W. John Wilbur},
title = {BioC interoperability track overview},
journal = {Database J. Biol. Databases Curation},
volume = {2014},
year = {2014},
url = {https://doi.org/10.1093/database/bau053},
doi = {10.1093/DATABASE/BAU053},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/ComeauBDDJKLMMNPRRTVWWW14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/KhareWMLL14,
author = {Ritu Khare and
Chih{-}Hsuan Wei and
Yuqing Mao and
Robert Leaman and
Zhiyong Lu},
title = {\emph{tmBioC}: improving interoperability of text-mining tools with
BioC},
journal = {Database J. Biol. Databases Curation},
volume = {2014},
year = {2014},
url = {https://doi.org/10.1093/database/bau073},
doi = {10.1093/DATABASE/BAU073},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/KhareWMLL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/MaoALAMHTSLWGRLKCCYLZLYEGCDL14,
author = {Yuqing Mao and
Kimberly Van Auken and
Donghui Li and
Cecilia N. Arighi and
Peter McQuilton and
G. Thomas Hayman and
Susan Tweedie and
Mary L. Schaeffer and
Stanley J. F. Laulederkind and
Shur{-}Jen Wang and
Julien Gobeill and
Patrick Ruch and
Anh Tuan Luu and
Jung{-}Jae Kim and
Jung{-}Hsien Chiang and
Yu{-}De Chen and
Chia{-}Jung Yang and
Hongfang Liu and
Dongqing Zhu and
Yanpeng Li and
Hong Yu and
Ehsan Emadzadeh and
Graciela Gonzalez and
Jian{-}Ming Chen and
Hong{-}Jie Dai and
Zhiyong Lu},
title = {Overview of the gene ontology task at BioCreative {IV}},
journal = {Database J. Biol. Databases Curation},
volume = {2014},
year = {2014},
url = {https://doi.org/10.1093/database/bau086},
doi = {10.1093/DATABASE/BAU086},
timestamp = {Sun, 06 Oct 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/MaoALAMHTSLWGRLKCCYLZLYEGCDL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/iet-com/JiaoZDHLL14,
author = {Bo Jiao and
Ying Zhou and
Jing Du and
Chengdong Huang and
Zhiyong Lu and
Yinglong Liu},
title = {Study on the stability of the topology interactive growth mechanism
using graph spectra},
journal = {{IET} Commun.},
volume = {8},
number = {16},
pages = {2845--2857},
year = {2014},
url = {https://doi.org/10.1049/iet-com.2014.0183},
doi = {10.1049/IET-COM.2014.0183},
timestamp = {Sat, 13 Dec 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/iet-com/JiaoZDHLL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jasis/LiuDKCKYLW14,
author = {Wanli Liu and
Rezarta Islamaj Dogan and
Sun Kim and
Donald C. Comeau and
Won Kim and
Lana Yeganova and
Zhiyong Lu and
W. John Wilbur},
title = {Author name disambiguation for PubMed},
journal = {J. Assoc. Inf. Sci. Technol.},
volume = {65},
number = {4},
pages = {765--781},
year = {2014},
url = {https://doi.org/10.1002/asi.23063},
doi = {10.1002/ASI.23063},
timestamp = {Fri, 13 May 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jasis/LiuDKCKYLW14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/DoganLL14,
author = {Rezarta Islamaj Dogan and
Robert Leaman and
Zhiyong Lu},
title = {{NCBI} disease corpus: {A} resource for disease name recognition and
concept normalization},
journal = {J. Biomed. Informatics},
volume = {47},
pages = {1--10},
year = {2014},
url = {https://doi.org/10.1016/j.jbi.2013.12.006},
doi = {10.1016/J.JBI.2013.12.006},
timestamp = {Mon, 26 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbi/DoganLL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/KhareLL14,
author = {Ritu Khare and
Jiao Li and
Zhiyong Lu},
title = {LabeledIn: Cataloging labeled indications for human drugs},
journal = {J. Biomed. Informatics},
volume = {52},
pages = {448--456},
year = {2014},
url = {https://doi.org/10.1016/j.jbi.2014.08.004},
doi = {10.1016/J.JBI.2014.08.004},
timestamp = {Wed, 02 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/KhareLL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/KhareWL14,
author = {Ritu Khare and
Chih{-}Hsuan Wei and
Zhiyong Lu},
title = {Automatic Extraction of Drug Indications from {FDA} Drug Labels},
booktitle = {{AMIA} 2014, American Medical Informatics Association Annual Symposium,
Washington, DC, USA, November 15-19, 2014},
publisher = {{AMIA}},
year = {2014},
url = {https://knowledge.amia.org/56638-amia-1.1540970/t-004-1.1544972/f-004-1.1544973/a-176-1.1545145/a-177-1.1545142},
timestamp = {Wed, 17 Apr 2024 11:47:48 +0200},
biburl = {https://dblp.org/rec/conf/amia/KhareWL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/WeiLL14,
author = {Chih{-}Hsuan Wei and
Robert Leaman and
Zhiyong Lu},
editor = {Pierre Baldi and
Wei Wang},
title = {SimConcept: a hybrid approach for simplifying composite named entities
in biomedicine},
booktitle = {Proceedings of the 5th {ACM} Conference on Bioinformatics, Computational
Biology, and Health Informatics, {BCB} '14, Newport Beach, California,
USA, September 20-23, 2014},
pages = {138--146},
publisher = {{ACM}},
year = {2014},
url = {https://doi.org/10.1145/2649387.2649420},
doi = {10.1145/2649387.2649420},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/WeiLL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/LeamanL14,
author = {Robert Leaman and
Zhiyong Lu},
editor = {Pierre Baldi and
Wei Wang},
title = {Disease named entity recognition and normalization with DNorm},
booktitle = {Proceedings of the 5th {ACM} Conference on Bioinformatics, Computational
Biology, and Health Informatics, {BCB} '14, Newport Beach, California,
USA, September 20-23, 2014},
pages = {587},
publisher = {{ACM}},
year = {2014},
url = {https://doi.org/10.1145/2649387.2660780},
doi = {10.1145/2649387.2660780},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/LeamanL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/WeiKL14,
author = {Chih{-}Hsuan Wei and
Hung{-}Yu Kao and
Zhiyong Lu},
editor = {Pierre Baldi and
Wei Wang},
title = {Text mining tools for assisting literature curation},
booktitle = {Proceedings of the 5th {ACM} Conference on Bioinformatics, Computational
Biology, and Health Informatics, {BCB} '14, Newport Beach, California,
USA, September 20-23, 2014},
pages = {590--591},
publisher = {{ACM}},
year = {2014},
url = {https://doi.org/10.1145/2649387.2660786},
doi = {10.1145/2649387.2660786},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bcb/WeiKL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/LeamanL14,
author = {Robert Leaman and
Zhiyong Lu},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
Jun'ichi Tsujii},
title = {Automated Disease Normalization with Low Rank Approximations},
booktitle = {Proceedings of BioNLP, Baltimore, Maryland, USA, BioNLP@ACL 2014,
June 27-28, 2014},
pages = {24--28},
publisher = {Association for Computational Linguistics},
year = {2014},
url = {https://doi.org/10.3115/v1/W14-3404},
doi = {10.3115/V1/W14-3404},
timestamp = {Fri, 06 Aug 2021 00:41:22 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/LeamanL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/clef/MaoWL14,
author = {Yuqing Mao and
Chih{-}Hsuan Wei and
Zhiyong Lu},
editor = {Linda Cappellato and
Nicola Ferro and
Martin Halvey and
Wessel Kraaij},
title = {{NCBI} at the 2014 BioASQ Challenge Task: Large-scale Biomedical Semantic
Indexing and Question Answering},
booktitle = {Working Notes for {CLEF} 2014 Conference, Sheffield, UK, September
15-18, 2014},
series = {{CEUR} Workshop Proceedings},
volume = {1180},
pages = {1319--1327},
publisher = {CEUR-WS.org},
year = {2014},
url = {https://ceur-ws.org/Vol-1180/CLEF2014wn-QA-MaoEt2014.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:41 +0100},
biburl = {https://dblp.org/rec/conf/clef/MaoWL14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/SwamidassLAB14,
author = {S. Joshua Swamidass and
Zhiyong Lu and
Pankaj Agarwal and
Atul J. Butte},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein and
Marylyn D. Ritchie},
title = {Session Introduction},
booktitle = {Biocomputing 2014: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 3-7, 2014},
pages = {110--113},
year = {2014},
url = {http://psb.stanford.edu/psb-online/proceedings/psb14/intro-cdr.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/SwamidassLAB14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/ArighiCCKWFDCSDMLHGJRMBDBLCSPHALCMCBWLWTRSNCDW13,
author = {Cecilia N. Arighi and
Ben Carterette and
K. Bretonnel Cohen and
Martin Krallinger and
W. John Wilbur and
Petra Fey and
Robert J. Dodson and
Laurel Cooper and
Ceri E. Van Slyke and
Wasila M. Dahdul and
Paula M. Mabee and
Donghui Li and
Bethany R. Harris and
Marc Gillespie and
Silvia Jimenez and
Phoebe M. Roberts and
Lisa Matthews and
Kevin G. Becker and
Harold J. Drabkin and
Susan M. Bello and
Luana Licata and
Andrew Chatr{-}aryamontri and
Mary L. Schaeffer and
Julie Park and
Melissa A. Haendel and
Kimberly Van Auken and
Yuling Li and
Juancarlos Chan and
Hans{-}Michael M{\"{u}}ller and
Hong Cui and
James P. Balhoff and
Chi{-}Yang Wu and
Zhiyong Lu and
Chih{-}Hsuan Wei and
Catalina O. Tudor and
Kalpana Raja and
Suresh Subramani and
Jeyakumar Natarajan and
Juan Miguel Cejuela and
Pratibha Dubey and
Cathy H. Wu},
title = {An overview of the BioCreative 2012 Workshop Track {III:} interactive
text mining task},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013},
url = {https://doi.org/10.1093/database/bas056},
doi = {10.1093/DATABASE/BAS056},
timestamp = {Sat, 15 Nov 2025 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/ArighiCCKWFDCSDMLHGJRMBDBLCSPHALCMCBWLWTRSNCDW13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/ComeauDCCKLLPRTVVWWW13,
author = {Donald C. Comeau and
Rezarta Islamaj Dogan and
Paolo Ciccarese and
Kevin Bretonnel Cohen and
Martin Krallinger and
Florian Leitner and
Zhiyong Lu and
Yifan Peng and
Fabio Rinaldi and
Manabu Torii and
Alfonso Valencia and
Karin Verspoor and
Thomas C. Wiegers and
Cathy H. Wu and
W. John Wilbur},
title = {BioC: a minimalist approach to interoperability for biomedical text
processing},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013},
url = {https://doi.org/10.1093/database/bat064},
doi = {10.1093/DATABASE/BAT064},
timestamp = {Fri, 27 Jun 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/ComeauDCCKLLPRTVVWWW13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WeiHKL13,
author = {Chih{-}Hsuan Wei and
Bethany R. Harris and
Hung{-}Yu Kao and
Zhiyong Lu},
title = {tmVar: a text mining approach for extracting sequence variants in
biomedical literature},
journal = {Bioinform.},
volume = {29},
number = {11},
pages = {1433--1439},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt156},
doi = {10.1093/BIOINFORMATICS/BTT156},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/WeiHKL13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LeamanDL13,
author = {Robert Leaman and
Rezarta Islamaj Dogan and
Zhiyong Lu},
title = {DNorm: disease name normalization with pairwise learning to rank},
journal = {Bioinform.},
volume = {29},
number = {22},
pages = {2909--2917},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt474},
doi = {10.1093/BIOINFORMATICS/BTT474},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LeamanDL13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LiL13,
author = {Jiao Li and
Zhiyong Lu},
title = {Pathway-based drug repositioning using causal inference},
journal = {{BMC} Bioinform.},
volume = {14},
number = {{S-16}},
pages = {S3},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-S16-S3},
doi = {10.1186/1471-2105-14-S16-S3},
timestamp = {Wed, 02 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/LiL13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/WeiKL13,
author = {Chih{-}Hsuan Wei and
Hung{-}Yu Kao and
Zhiyong Lu},
title = {PubTator: a web-based text mining tool for assisting biocuration},
journal = {Nucleic Acids Res.},
volume = {41},
number = {Webserver-Issue},
pages = {518--522},
year = {2013},
url = {https://doi.org/10.1093/nar/gkt441},
doi = {10.1093/NAR/GKT441},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/WeiKL13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/DoganLL13,
author = {Rezarta Islamaj Dogan and
Robert Leaman and
Zhiyong Lu},
title = {{NCBI} Disease Corpus: {A} Valuable Resource for Disease Name Recognition
and Normalization},
booktitle = {{AMIA} 2013, American Medical Informatics Association Annual Symposium,
Washington, DC, USA, November 16-20, 2013},
publisher = {{AMIA}},
year = {2013},
url = {https://knowledge.amia.org/amia-55142-a2013e-1.580047/t-06-1.582200/f-006-1.582201/a-218-1.583361/a-220-1.583355},
timestamp = {Wed, 17 Apr 2024 11:47:55 +0200},
biburl = {https://dblp.org/rec/conf/amia/DoganLL13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/LeamanDWL13,
author = {Robert Leaman and
Rezarta Islamaj Dogan and
Chih{-}Hsuan Wei and
Zhiyong Lu},
title = {DNorm: {A} New Method and Online Tool for Disease Name Normalization},
booktitle = {{AMIA} 2013, American Medical Informatics Association Annual Symposium,
Washington, DC, USA, November 16-20, 2013},
publisher = {{AMIA}},
year = {2013},
url = {https://knowledge.amia.org/amia-55142-a2013e-1.580047/t-06-1.582200/f-006-1.582201/a-284-1.583148/a-285-1.583142},
timestamp = {Wed, 17 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/LeamanDWL13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/MaoL13,
author = {Yuqing Mao and
Zhiyong Lu},
title = {Predicting clicks of PubMed articles},
booktitle = {{AMIA} 2013, American Medical Informatics Association Annual Symposium,
Washington, DC, USA, November 16-20, 2013},
publisher = {{AMIA}},
year = {2013},
url = {https://knowledge.amia.org/amia-55142-a2013e-1.580047/t-05-1.583941/f-005-1.583942/a-329-1.584089/a-331-1.584086},
timestamp = {Wed, 17 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/MaoL13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/NeveolRL13,
author = {Aur{\'{e}}lie N{\'{e}}v{\'{e}}ol and
Bastien Rance and
Zhiyong Lu},
title = {A systematic comparison of current sources of disease knowledge},
booktitle = {{AMIA} 2013, American Medical Informatics Association Annual Symposium,
Washington, DC, USA, November 16-20, 2013},
publisher = {{AMIA}},
year = {2013},
url = {https://knowledge.amia.org/amia-55142-a2013e-1.580047/t-06-1.582200/f-006-1.582201/a-379-1.582854/a-381-1.582851},
timestamp = {Wed, 17 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/amia/NeveolRL13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/clef/LeamanKL13,
author = {Robert Leaman and
Ritu Khare and
Zhiyong Lu},
editor = {Pamela Forner and
Roberto Navigli and
Dan Tufis and
Nicola Ferro},
title = {{NCBI} at 2013 ShARe/CLEF eHealth Shared Task: Disorder Normalization
in Clinical Notes with Dnorm},
booktitle = {Working Notes for {CLEF} 2013 Conference , Valencia, Spain, September
23-26, 2013},
series = {{CEUR} Workshop Proceedings},
volume = {1179},
publisher = {CEUR-WS.org},
year = {2013},
url = {https://ceur-ws.org/Vol-1179/CLEF2013wn-CLEFeHealth-LeamanEt2013.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:37 +0100},
biburl = {https://dblp.org/rec/conf/clef/LeamanKL13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ichi/KhareLL13,
author = {Ritu Khare and
Jiao Li and
Zhiyong Lu},
title = {Toward Creating a Gold Standard of Drug Indications from {FDA} Drug
Labels},
booktitle = {{IEEE} International Conference on Healthcare Informatics, {ICHI}
2013, 9-11 September, 2013, Philadelphia, PA, {USA}},
pages = {30--35},
publisher = {{IEEE} Computer Society},
year = {2013},
url = {https://doi.org/10.1109/ICHI.2013.11},
doi = {10.1109/ICHI.2013.11},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ichi/KhareLL13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/LuAB13,
author = {Zhiyong Lu and
Pankaj Agarwal and
Atul J. Butte},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Session Introduction},
booktitle = {Biocomputing 2013: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 3-7, 2013},
pages = {1--4},
publisher = {World Scientific Publishing},
year = {2013},
url = {http://psb.stanford.edu/psb-online/proceedings/psb13/intro-cdr.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/LuAB13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/KimKWLW12,
author = {Sun Kim and
Won Kim and
Chih{-}Hsuan Wei and
Zhiyong Lu and
W. John Wilbur},
title = {Prioritizing PubMed articles for the Comparative Toxicogenomic Database
utilizing semantic information},
journal = {Database J. Biol. Databases Curation},
volume = {2012},
year = {2012},
url = {https://doi.org/10.1093/database/bas042},
doi = {10.1093/DATABASE/BAS042},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/KimKWLW12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/LuH12,
author = {Zhiyong Lu and
Lynette Hirschman},
title = {Biocuration workflows and text mining: overview of the BioCreative
2012 Workshop Track {II}},
journal = {Database J. Biol. Databases Curation},
volume = {2012},
year = {2012},
url = {https://doi.org/10.1093/database/bas043},
doi = {10.1093/DATABASE/BAS043},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/LuH12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/NeveolWL12,
author = {Aur{\'{e}}lie N{\'{e}}v{\'{e}}ol and
W. John Wilbur and
Zhiyong Lu},
title = {Improving links between literature and biological data with text mining:
a case study with GEO, {PDB} and {MEDLINE}},
journal = {Database J. Biol. Databases Curation},
volume = {2012},
year = {2012},
url = {https://doi.org/10.1093/database/bas026},
doi = {10.1093/DATABASE/BAS026},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/NeveolWL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/WeiHLBHKL12,
author = {Chih{-}Hsuan Wei and
Bethany R. Harris and
Donghui Li and
Tanya Z. Berardini and
Eva Huala and
Hung{-}Yu Kao and
Zhiyong Lu},
title = {Accelerating literature curation with text-mining tools: a case study
of using PubTator to curate genes in PubMed abstracts},
journal = {Database J. Biol. Databases Curation},
volume = {2012},
year = {2012},
url = {https://doi.org/10.1093/database/bas041},
doi = {10.1093/DATABASE/BAS041},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biodb/WeiHLBHKL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/WuACHKLMVWW12,
author = {Cathy H. Wu and
Cecilia N. Arighi and
Kevin Bretonnel Cohen and
Lynette Hirschman and
Martin Krallinger and
Zhiyong Lu and
Carolyn J. Mattingly and
Alfonso Valencia and
Thomas C. Wiegers and
W. John Wilbur},
title = {BioCreative-2012 Virtual Issue},
journal = {Database J. Biol. Databases Curation},
volume = {2012},
year = {2012},
url = {https://doi.org/10.1093/database/bas049},
doi = {10.1093/DATABASE/BAS049},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/WuACHKLMVWW12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/LiL12,
author = {Jiao Li and
Zhiyong Lu},
title = {Systematic identification of pharmacogenomics information from clinical
trials},
journal = {J. Biomed. Informatics},
volume = {45},
number = {5},
pages = {870--878},
year = {2012},
url = {https://doi.org/10.1016/j.jbi.2012.04.005},
doi = {10.1016/J.JBI.2012.04.005},
timestamp = {Wed, 02 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/LiL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/midm/LiL12,
author = {Jiao Li and
Zhiyong Lu},
title = {Automatic identification and normalization of dosage forms in drug
monographs},
journal = {{BMC} Medical Informatics Decis. Mak.},
volume = {12},
pages = {9},
year = {2012},
url = {https://doi.org/10.1186/1472-6947-12-9},
doi = {10.1186/1472-6947-12-9},
timestamp = {Wed, 02 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/midm/LiL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SayersBBBBCCCDFFFGHKKLLLMMMMMKOPPPSSSSSSSSTWWWYY12,
author = {Eric W. Sayers and
Tanya Barrett and
Dennis A. Benson and
Evan Bolton and
Stephen H. Bryant and
Kathi Canese and
Vyacheslav Chetvernin and
Deanna M. Church and
Michael DiCuccio and
Scott Federhen and
Michael Feolo and
Ian M. Fingerman and
Lewis Y. Geer and
Wolfgang Helmberg and
Yuri Kapustin and
Sergey Krasnov and
David Landsman and
David J. Lipman and
Zhiyong Lu and
Thomas L. Madden and
Tom Madej and
Donna R. Maglott and
Aron Marchler{-}Bauer and
Vadim Miller and
Ilene Karsch{-}Mizrachi and
James Ostell and
Anna R. Panchenko and
Lon Phan and
Kim D. Pruitt and
Gregory D. Schuler and
Edwin Sequeira and
Stephen T. Sherry and
Martin Shumway and
Karl Sirotkin and
Douglas J. Slotta and
Alexandre Souvorov and
Grigory Starchenko and
Tatiana A. Tatusova and
Lukas Wagner and
Yanli Wang and
W. John Wilbur and
Eugene Yaschenko and
Jian Ye},
title = {Database resources of the National Center for Biotechnology Information},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {13--25},
year = {2012},
url = {https://doi.org/10.1093/nar/gkr1184},
doi = {10.1093/NAR/GKR1184},
timestamp = {Tue, 18 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SayersBBBBCCCDFFFGHKKLLLMMMMMKOPPPSSSSSSSSTWWWYY12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/aaaifs/DoganL12,
author = {Rezarta Islamaj Dogan and
Zhiyong Lu},
title = {An Inference Method for Disease Name Normalization},
booktitle = {Information Retrieval and Knowledge Discovery in Biomedical Text,
Papers from the 2012 {AAAI} Fall Symposium, Arlington, Virginia, USA,
November 2-4, 2012},
series = {{AAAI} Technical Report},
volume = {{FS-12-05}},
publisher = {{AAAI}},
year = {2012},
url = {http://www.aaai.org/ocs/index.php/FSS/FSS12/paper/view/5604},
timestamp = {Tue, 08 Mar 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/aaaifs/DoganL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibm/LiL12,
author = {Jiao Li and
Zhiyong Lu},
title = {A new method for computational drug repositioning using drug pairwise
similarity},
booktitle = {2012 {IEEE} International Conference on Bioinformatics and Biomedicine,
{BIBM} 2012, Philadelphia, PA, USA, October 4-7, 2012},
pages = {1--4},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/BIBM.2012.6392722},
doi = {10.1109/BIBM.2012.6392722},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibm/LiL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/DoganL12,
author = {Rezarta Islamaj Dogan and
Zhiyong Lu},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
Bonnie L. Webber and
Jun'ichi Tsujii and
John Pestian},
title = {An improved corpus of disease mentions in PubMed citations},
booktitle = {Proceedings of the 2012 Workshop on Biomedical Natural Language Processing,
BioNLP@HLT-NAACL Montr{\`{e}}al, Canada, June 8, 2012},
pages = {91--99},
publisher = {Association for Computational Linguistics},
year = {2012},
url = {https://aclanthology.org/W12-2411/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/DoganL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hisb/LiL12,
author = {Jiao Li and
Zhiyong Lu},
title = {A Network Approach for Computational Drug Repositioning},
booktitle = {2012 {IEEE} Second International Conference on Healthcare Informatics,
Imaging and Systems Biology, {HISB} 2012, La Jolla, CA, USA, September
27-28, 2012},
pages = {83},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/HISB.2012.26},
doi = {10.1109/HISB.2012.26},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/hisb/LiL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hisb/LiKL12,
author = {Jiao Li and
Ritu Khare and
Zhiyong Lu},
title = {Improving Online Access to Drug-Related Information},
booktitle = {2012 {IEEE} Second International Conference on Healthcare Informatics,
Imaging and Systems Biology, {HISB} 2012, La Jolla, CA, USA, September
27-28, 2012},
pages = {148},
publisher = {{IEEE} Computer Society},
year = {2012},
url = {https://doi.org/10.1109/HISB.2012.73},
doi = {10.1109/HISB.2012.73},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/hisb/LiKL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ihi/NeveolLL12,
author = {Aur{\'{e}}lie N{\'{e}}v{\'{e}}ol and
Jiao Li and
Zhiyong Lu},
editor = {Gang Luo and
Jiming Liu and
Christopher C. Yang},
title = {Linking multiple disease-related resources through {UMLS}},
booktitle = {{ACM} International Health Informatics Symposium, {IHI} '12, Miami,
FL, USA, January 28-30, 2012},
pages = {767--772},
publisher = {{ACM}},
year = {2012},
url = {https://doi.org/10.1145/2110363.2110455},
doi = {10.1145/2110363.2110455},
timestamp = {Wed, 02 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ihi/NeveolLL12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/Lu11,
author = {Zhiyong Lu},
title = {PubMed and beyond: a survey of web tools for searching biomedical
literature},
journal = {Database J. Biol. Databases Curation},
volume = {2011},
year = {2011},
url = {https://doi.org/10.1093/database/baq036},
doi = {10.1093/DATABASE/BAQ036},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/Lu11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NeveolWL11,
author = {Aur{\'{e}}lie N{\'{e}}v{\'{e}}ol and
W. John Wilbur and
Zhiyong Lu},
title = {Extraction of data deposition statements from the literature: a method
for automatically tracking research results},
journal = {Bioinform.},
volume = {27},
number = {23},
pages = {3306--3312},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr573},
doi = {10.1093/BIOINFORMATICS/BTR573},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/NeveolWL11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/DoganNL11,
author = {Rezarta Islamaj Dogan and
Aur{\'{e}}lie N{\'{e}}v{\'{e}}ol and
Zhiyong Lu},
title = {A context-blocks model for identifying clinical relationships in patient
records},
journal = {{BMC} Bioinform.},
volume = {12},
number = {{S-3}},
pages = {S3},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-S3-S3},
doi = {10.1186/1471-2105-12-S3-S3},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/DoganNL11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ArighiLKCWVHW11,
author = {Cecilia N. Arighi and
Zhiyong Lu and
Martin Krallinger and
Kevin Bretonnel Cohen and
W. John Wilbur and
Alfonso Valencia and
Lynette Hirschman and
Cathy H. Wu},
title = {Overview of the BioCreative {III} Workshop},
journal = {{BMC} Bioinform.},
volume = {12},
number = {{S-8}},
pages = {S1},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-S8-S1},
doi = {10.1186/1471-2105-12-S8-S1},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ArighiLKCWVHW11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/LuKWHLKHTDOCGSALVRRRBSLTMCVLW11,
author = {Zhiyong Lu and
Hung{-}Yu Kao and
Chih{-}Hsuan Wei and
Minlie Huang and
Jingchen Liu and
Cheng{-}Ju Kuo and
Chun{-}Nan Hsu and
Richard Tzong{-}Han Tsai and
Hong{-}Jie Dai and
Naoaki Okazaki and
Han{-}Cheol Cho and
Martin Gerner and
Ill{\'{e}}s Solt and
Shashank Agarwal and
Feifan Liu and
Dina Vishnyakova and
Patrick Ruch and
Martin Romacker and
Fabio Rinaldi and
Sanmitra Bhattacharya and
Padmini Srinivasan and
Hongfang Liu and
Manabu Torii and
S{\'{e}}rgio Matos and
David Campos and
Karin Verspoor and
Kevin M. Livingston and
W. John Wilbur},
title = {The gene normalization task in BioCreative {III}},
journal = {{BMC} Bioinform.},
volume = {12},
number = {{S-8}},
pages = {S2},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-S8-S2},
doi = {10.1186/1471-2105-12-S8-S2},
timestamp = {Thu, 25 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/LuKWHLKHTDOCGSALVRRRBSLTMCVLW11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KrallingerVLSCWPBLICCTSRLGMKWRSTALWRNEL11,
author = {Martin Krallinger and
Miguel Vazquez and
Florian Leitner and
David Salgado and
Andrew Chatr{-}aryamontri and
Andrew G. Winter and
Livia Perfetto and
Leonardo Briganti and
Luana Licata and
Marta Iannuccelli and
Luisa Castagnoli and
Gianni Cesareni and
Mike Tyers and
Gerold Schneider and
Fabio Rinaldi and
Robert Leaman and
Graciela Gonzalez and
S{\'{e}}rgio Matos and
Sun Kim and
W. John Wilbur and
Luis M. Rocha and
Hagit Shatkay and
Ashish V. Tendulkar and
Shashank Agarwal and
Feifan Liu and
Xinglong Wang and
Rafal Rak and
Keith Noto and
Charles Elkan and
Zhiyong Lu},
title = {The Protein-Protein Interaction tasks of BioCreative {III:} classification/ranking
of articles and linking bio-ontology concepts to full text},
journal = {{BMC} Bioinform.},
volume = {12},
number = {{S-8}},
pages = {S3},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-S8-S3},
doi = {10.1186/1471-2105-12-S8-S3},
timestamp = {Tue, 05 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/KrallingerVLSCWPBLICCTSRLGMKWRSTALWRNEL11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ArighiRABCCCGGHHKLLLLMOPRSSSTTHW11,
author = {Cecilia N. Arighi and
Phoebe M. Roberts and
Shashank Agarwal and
Sanmitra Bhattacharya and
Gianni Cesareni and
Andrew Chatr{-}aryamontri and
Simon Clematide and
Pascale Gaudet and
Michelle G. Giglio and
Ian Harrow and
Eva Huala and
Martin Krallinger and
Ulf Leser and
Donghui Li and
Feifan Liu and
Zhiyong Lu and
Lois J. Maltais and
Naoaki Okazaki and
Livia Perfetto and
Fabio Rinaldi and
Rune S{\ae}tre and
David Salgado and
Padmini Srinivasan and
Philippe E. Thomas and
Luca Toldo and
Lynette Hirschman and
Cathy H. Wu},
title = {BioCreative {III} interactive task: an overview},
journal = {{BMC} Bioinform.},
volume = {12},
number = {{S-8}},
pages = {S4},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-S8-S4},
doi = {10.1186/1471-2105-12-S8-S4},
timestamp = {Tue, 05 Aug 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ArighiRABCCCGGHHKLLLLMOPRSSSTTHW11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jamia/HuangNL11,
author = {Minlie Huang and
Aur{\'{e}}lie N{\'{e}}v{\'{e}}ol and
Zhiyong Lu},
title = {Recommending MeSH terms for annotating biomedical articles},
journal = {J. Am. Medical Informatics Assoc.},
volume = {18},
number = {5},
pages = {660--667},
year = {2011},
url = {https://doi.org/10.1136/amiajnl-2010-000055},
doi = {10.1136/AMIAJNL-2010-000055},
timestamp = {Mon, 11 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jamia/HuangNL11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/NeveolDL11,
author = {Aur{\'{e}}lie N{\'{e}}v{\'{e}}ol and
Rezarta Islamaj Dogan and
Zhiyong Lu},
title = {Semi-automatic semantic annotation of PubMed queries: {A} study on
quality, efficiency, satisfaction},
journal = {J. Biomed. Informatics},
volume = {44},
number = {2},
pages = {310--318},
year = {2011},
url = {https://doi.org/10.1016/j.jbi.2010.11.001},
doi = {10.1016/J.JBI.2010.11.001},
timestamp = {Mon, 26 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jbi/NeveolDL11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SayersBBBBCCCDFFFGHKLLLMMMMMMOPPPSSSSSSSSTWWWYY11,
author = {Eric W. Sayers and
Tanya Barrett and
Dennis A. Benson and
Evan Bolton and
Stephen H. Bryant and
Kathi Canese and
Vyacheslav Chetvernin and
Deanna M. Church and
Michael DiCuccio and
Scott Federhen and
Michael Feolo and
Ian M. Fingerman and
Lewis Y. Geer and
Wolfgang Helmberg and
Yuri Kapustin and
David Landsman and
David J. Lipman and
Zhiyong Lu and
Thomas L. Madden and
Tom Madej and
Donna R. Maglott and
Aron Marchler{-}Bauer and
Vadim Miller and
Ilene Mizrachi and
James Ostell and
Anna R. Panchenko and
Lon Phan and
Kim D. Pruitt and
Gregory D. Schuler and
Edwin Sequeira and
Stephen T. Sherry and
Martin Shumway and
Karl Sirotkin and
Douglas J. Slotta and
Alexandre Souvorov and
Grigory Starchenko and
Tatiana A. Tatusova and
Lukas Wagner and
Yanli Wang and
W. John Wilbur and
Eugene Yaschenko and
Jian Ye},
title = {Database resources of the National Center for Biotechnology Information},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Database-Issue},
pages = {38--51},
year = {2011},
url = {https://doi.org/10.1093/nar/gkq1172},
doi = {10.1093/NAR/GKQ1172},
timestamp = {Tue, 01 Apr 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SayersBBBBCCCDFFFGHKLLLMMMMMMOPPPSSSSSSSSTWWWYY11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/NeveolWL11,
author = {Aur{\'{e}}lie N{\'{e}}v{\'{e}}ol and
W. John Wilbur and
Zhiyong Lu},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
John Pestian and
Jun'ichi Tsujii and
Bonnie L. Webber},
title = {Automatic extraction of data deposition statements: where do the research
results go?},
booktitle = {Proceedings of the 2011 Workshop on Biomedical Natural Language Processing,
BioNLP@ACL, Portland, Oregon, USA, June 23-24, 2011},
pages = {103--104},
publisher = {Association for Computational Linguistics},
year = {2011},
url = {https://aclanthology.org/W11-0213/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/NeveolWL11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/DoganL10,
author = {Rezarta Islamaj Dogan and
Zhiyong Lu},
title = {Click-words: learning to predict document keywords from a user perspective},
journal = {Bioinform.},
volume = {26},
number = {21},
pages = {2767--2775},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq459},
doi = {10.1093/BIOINFORMATICS/BTQ459},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/DoganL10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jamia/MorkBDDLLNPSA10,
author = {James G. Mork and
Olivier Bodenreider and
Dina Demner{-}Fushman and
Rezarta Islamaj Dogan and
Fran{\c{c}}ois{-}Michel Lang and
Zhiyong Lu and
Aur{\'{e}}lie N{\'{e}}v{\'{e}}ol and
Lee B. Peters and
Sonya E. Shooshan and
Alan R. Aronson},
title = {Extracting Rx information from clinical narrative},
journal = {J. Am. Medical Informatics Assoc.},
volume = {17},
number = {5},
pages = {536--539},
year = {2010},
url = {https://doi.org/10.1136/jamia.2010.003970},
doi = {10.1136/JAMIA.2010.003970},
timestamp = {Mon, 11 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jamia/MorkBDDLLNPSA10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SayersBBBBCCCDFFGHKLLLMMMMMMOPPSSSSSSSSTWWWYY10,
author = {Eric W. Sayers and
Tanya Barrett and
Dennis A. Benson and
Evan Bolton and
Stephen H. Bryant and
Kathi Canese and
Vyacheslav Chetvernin and
Deanna M. Church and
Michael DiCuccio and
Scott Federhen and
Michael Feolo and
Lewis Y. Geer and
Wolfgang Helmberg and
Yuri Kapustin and
David Landsman and
David J. Lipman and
Zhiyong Lu and
Thomas L. Madden and
Tom Madej and
Donna R. Maglott and
Aron Marchler{-}Bauer and
Vadim Miller and
Ilene Mizrachi and
James Ostell and
Anna R. Panchenko and
Kim D. Pruitt and
Gregory D. Schuler and
Edwin Sequeira and
Stephen T. Sherry and
Martin Shumway and
Karl Sirotkin and
Douglas J. Slotta and
Alexandre Souvorov and
Grigory Starchenko and
Tatiana A. Tatusova and
Lukas Wagner and
Yanli Wang and
W. John Wilbur and
Eugene Yaschenko and
Jian Ye},
title = {Database resources of the National Center for Biotechnology Information},
journal = {Nucleic Acids Res.},
volume = {38},
number = {Database-Issue},
pages = {5--16},
year = {2010},
url = {https://doi.org/10.1093/nar/gkp967},
doi = {10.1093/NAR/GKP967},
timestamp = {Tue, 18 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SayersBBBBCCCDFFGHKLLLMMMMMMOPPSSSSSSSSTWWWYY10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/coling/HuangL10,
author = {Minlie Huang and
Zhiyong Lu},
editor = {Chu{-}Ren Huang and
Dan Jurafsky},
title = {Learning to Annotate Scientific Publications},
booktitle = {{COLING} 2010, 23rd International Conference on Computational Linguistics,
Posters Volume, 23-27 August 2010, Beijing, China},
pages = {463--471},
publisher = {Chinese Information Processing Society of China},
year = {2010},
url = {https://aclanthology.org/C10-2053/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/coling/HuangL10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icmla/DoganNL10,
author = {Rezarta Islamaj Dogan and
Aur{\'{e}}lie N{\'{e}}v{\'{e}}ol and
Zhiyong Lu},
editor = {Sorin Draghici and
Taghi M. Khoshgoftaar and
Vasile Palade and
Witold Pedrycz and
M. Arif Wani and
Xingquan Zhu},
title = {A Textual Representation Scheme for Identifying Clinical Relationships
in Patient Records},
booktitle = {The Ninth International Conference on Machine Learning and Applications,
{ICMLA} 2010, Washington, DC, USA, 12-14 December 2010},
pages = {995--998},
publisher = {{IEEE} Computer Society},
year = {2010},
url = {https://doi.org/10.1109/ICMLA.2010.164},
doi = {10.1109/ICMLA.2010.164},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icmla/DoganNL10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ihi/NeveolL10,
author = {Aur{\'{e}}lie N{\'{e}}v{\'{e}}ol and
Zhiyong Lu},
editor = {Tiffany C. Veinot and
{\"{U}}mit V. {\c{C}}ataly{\"{u}}rek and
Gang Luo and
Henrique Andrade and
Neil R. Smalheiser},
title = {Automatic integration of drug indications from multiple health resources},
booktitle = {{ACM} International Health Informatics Symposium, {IHI} 2010, Arlington,
VA, USA, November 11 - 12, 2010, Proceedings},
pages = {666--673},
publisher = {{ACM}},
year = {2010},
url = {https://doi.org/10.1145/1882992.1883096},
doi = {10.1145/1882992.1883096},
timestamp = {Tue, 06 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ihi/NeveolL10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/DoganMNL09,
author = {Rezarta Islamaj Dogan and
G. Craig Murray and
Aur{\'{e}}lie N{\'{e}}v{\'{e}}ol and
Zhiyong Lu},
title = {Understanding PubMed\({}^{\mbox{{\textregistered}}}\) user search
behavior through log analysis},
journal = {Database J. Biol. Databases Curation},
volume = {2009},
year = {2009},
url = {https://doi.org/10.1093/database/bap018},
doi = {10.1093/DATABASE/BAP018},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/DoganMNL09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuXW09,
author = {Zhiyong Lu and
Natalie Xie and
W. John Wilbur},
title = {Identifying related journals through log analysis},
journal = {Bioinform.},
volume = {25},
number = {22},
pages = {3038--3039},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp529},
doi = {10.1093/BIOINFORMATICS/BTP529},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuXW09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ir/LuKW09,
author = {Zhiyong Lu and
Won Kim and
W. John Wilbur},
title = {Evaluation of query expansion using MeSH in PubMed},
journal = {Inf. Retr.},
volume = {12},
number = {1},
pages = {69--80},
year = {2009},
url = {https://doi.org/10.1007/s10791-008-9074-8},
doi = {10.1007/S10791-008-9074-8},
timestamp = {Wed, 14 Nov 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ir/LuKW09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jamia/LuKW09,
author = {Zhiyong Lu and
Won Kim and
W. John Wilbur},
title = {Viewpoint Paper: Evaluating Relevance Ranking Strategies for {MEDLINE}
Retrieval},
journal = {J. Am. Medical Informatics Assoc.},
volume = {16},
number = {1},
pages = {32--36},
year = {2009},
url = {https://doi.org/10.1197/jamia.M2935},
doi = {10.1197/JAMIA.M2935},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jamia/LuKW09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/LuW09,
author = {Zhiyong Lu and
W. John Wilbur},
title = {Improving accuracy for identifying related PubMed queries by an integrated
approach},
journal = {J. Biomed. Informatics},
volume = {42},
number = {5},
pages = {831--838},
year = {2009},
url = {https://doi.org/10.1016/j.jbi.2008.12.006},
doi = {10.1016/J.JBI.2008.12.006},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/LuW09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/LuWMIS09,
author = {Zhiyong Lu and
W. John Wilbur and
Johanna R. McEntyre and
Alexey Iskhakov and
Lee Szilagyi},
title = {Finding Query Suggestions for PubMed},
booktitle = {{AMIA} 2009, American Medical Informatics Association Annual Symposium,
San Francisco, CA, USA, November 14-18, 2009},
publisher = {{AMIA}},
year = {2009},
url = {https://knowledge.amia.org/amia-55142-a2009a-1.626575/t-001-1.627318/f-001-1.627319/a-077-1.627521/a-078-1.627518},
timestamp = {Wed, 17 Apr 2024 11:48:10 +0200},
biburl = {https://dblp.org/rec/conf/amia/LuWMIS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/JinHLZ09,
author = {Feng Jin and
Minlie Huang and
Zhiyong Lu and
Xiaoyan Zhu},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
John Pestian and
Jun'ichi Tsujii and
Bonnie L. Webber},
title = {Towards Automatic Generation of Gene Summary},
booktitle = {Proceedings of the BioNLP Workshop, BioNLP@HLT-NAACL 2009, Boulder,
Colorado, USA, June 4-5, 2009},
pages = {97--105},
publisher = {Association for Computational Linguistics},
year = {2009},
url = {https://aclanthology.org/W09-1312/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/JinHLZ09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bionlp/NeveolKWL09,
author = {Aur{\'{e}}lie N{\'{e}}v{\'{e}}ol and
Won Kim and
W. John Wilbur and
Zhiyong Lu},
editor = {Kevin Bretonnel Cohen and
Dina Demner{-}Fushman and
Sophia Ananiadou and
John Pestian and
Jun'ichi Tsujii and
Bonnie L. Webber},
title = {Exploring Two Biomedical Text Genres for Disease Recognition},
booktitle = {Proceedings of the BioNLP Workshop, BioNLP@HLT-NAACL 2009, Boulder,
Colorado, USA, June 4-5, 2009},
pages = {144--152},
publisher = {Association for Computational Linguistics},
year = {2009},
url = {https://aclanthology.org/W09-1319/},
timestamp = {Fri, 06 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/bionlp/NeveolKWL09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/jcdl/MurrayLWL09,
author = {G. Craig Murray and
Jimmy Lin and
W. John Wilbur and
Zhiyong Lu},
editor = {Fred Heath and
Mary Lynn Rice{-}Lively and
Richard Furuta},
title = {Users' adjustments to unsuccessful queries in biomedical search},
booktitle = {Proceedings of the 2009 Joint International Conference on Digital
Libraries, {JCDL} 2009, Austin, TX, USA, June 15-19, 2009},
pages = {433--434},
publisher = {{ACM}},
year = {2009},
url = {https://doi.org/10.1145/1555400.1555499},
doi = {10.1145/1555400.1555499},
timestamp = {Fri, 27 Aug 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/jcdl/MurrayLWL09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/webi/ChenHL09,
author = {Shouyuan Chen and
Minlie Huang and
Zhiyong Lu},
title = {Summarizing Documents by Measuring the Importance of a Subset of Vertices
within a Graph},
booktitle = {2009 {IEEE/WIC/ACM} International Conference on Web Intelligence,
{WI} 2009, Milan, Italy, 15-18 September 2009, Main Conference Proceedings},
pages = {269--272},
publisher = {{IEEE} Computer Society},
year = {2009},
url = {https://doi.org/10.1109/WI-IAT.2009.46},
doi = {10.1109/WI-IAT.2009.46},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/webi/ChenHL09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/BethardLMH08,
author = {Steven Bethard and
Zhiyong Lu and
James H. Martin and
Lawrence Hunter},
title = {Semantic role labeling for protein transport predicates},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-277},
doi = {10.1186/1471-2105-9-277},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/BethardLMH08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HunterLFBJOC08,
author = {Lawrence Hunter and
Zhiyong Lu and
James Firby and
William A. Baumgartner Jr. and
Helen L. Johnson and
Philip V. Ogren and
K. Bretonnel Cohen},
title = {OpenDMAP: An open source, ontology-driven concept analysis engine,
with applications to capturing knowledge regarding protein transport,
protein interactions and cell-type-specific gene expression},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-78},
doi = {10.1186/1471-2105-9-78},
timestamp = {Tue, 26 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/HunterLFBJOC08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/amia/LuKW08,
author = {Zhiyong Lu and
Won Kim and
W. John Wilbur},
title = {Evaluating Relevance Ranking Strategies for {MEDLINE} Retrieval},
booktitle = {{AMIA} 2008, American Medical Informatics Association Annual Symposium,
Washington, DC, USA, November 8-12, 2008},
publisher = {{AMIA}},
year = {2008},
url = {https://knowledge.amia.org/amia-55142-a2008a-1.625176/t-001-1.626020/f-001-1.626021/a-090-1.626294/a-091-1.626291},
timestamp = {Wed, 17 Apr 2024 11:48:12 +0200},
biburl = {https://dblp.org/rec/conf/amia/LuKW08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/LuCH07,
author = {Zhiyong Lu and
K. Bretonnel Cohen and
Lawrence Hunter},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Generif Quality Assurance as Summary Revision},
booktitle = {Biocomputing 2007, Proceedings of the Pacific Symposium, Maui, Hawaii,
USA, 3-7 January 2007},
pages = {269--280},
publisher = {World Scientific},
year = {2007},
url = {http://psb.stanford.edu/psb-online/proceedings/psb07/lu\_z.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/LuCH07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-0710-2083,
author = {Oliver Schulte and
Flavia Moser and
Martin Ester and
Zhiyong Lu},
title = {Association Rules in the Relational Calculus},
journal = {CoRR},
volume = {abs/0710.2083},
year = {2007},
url = {http://arxiv.org/abs/0710.2083},
eprinttype = {arXiv},
eprint = {0710.2083},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-0710-2083.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/JohnsonCBLBKKH06,
author = {Helen L. Johnson and
K. Bretonnel Cohen and
William A. Baumgartner Jr. and
Zhiyong Lu and
Michael Bada and
Todd Kester and
Hyunmin Kim and
Lawrence Hunter},
editor = {Russ B. Altman and
Tiffany Murray and
Teri E. Klein and
A. Keith Dunker and
Lawrence Hunter},
title = {Evaluation of Lexical Methods for Detecting Relationships Between
Concepts from Multiple Ontologies},
booktitle = {Biocomputing 2006, Proceedings of the Pacific Symposium, Maui, Hawaii,
USA, 3-7 January 2006},
pages = {28--39},
publisher = {World Scientific},
year = {2006},
url = {http://psb.stanford.edu/psb-online/proceedings/psb06/johnson.pdf},
timestamp = {Tue, 26 Jan 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/JohnsonCBLBKKH06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/LuCH06,
author = {Zhiyong Lu and
K. Bretonnel Cohen and
Lawrence Hunter},
editor = {Russ B. Altman and
Tiffany Murray and
Teri E. Klein and
A. Keith Dunker and
Lawrence Hunter},
title = {Finding GeneRIFs via Gene Ontology Annotations},
booktitle = {Biocomputing 2006, Proceedings of the Pacific Symposium, Maui, Hawaii,
USA, 3-7 January 2006},
pages = {52--63},
publisher = {World Scientific},
year = {2006},
url = {http://psb.stanford.edu/psb-online/proceedings/psb06/lu.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/LuCH06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/trec/CaporasoBKLJMLFWCH06,
author = {J. Gregory Caporaso and
William A. Baumgartner Jr. and
Hyunmin Kim and
Zhiyong Lu and
Helen L. Johnson and
Olga Medvedeva and
Anna Lindemann and
Lynne M. Fox and
Elizabeth K. White and
K. Bretonnel Cohen and
Lawrence Hunter},
editor = {Ellen M. Voorhees and
Lori P. Buckland},
title = {Concept Recognition, Information Retrieval, and Machine Learning in
Genomics Question-Answering},
booktitle = {Proceedings of the Fifteenth Text REtrieval Conference, {TREC} 2006,
Gaithersburg, Maryland, USA, November 14-17, 2006},
series = {{NIST} Special Publication},
volume = {500-272},
publisher = {National Institute of Standards and Technology {(NIST)}},
year = {2006},
url = {http://trec.nist.gov/pubs/trec15/papers/ucolorado.geo.final.pdf},
timestamp = {Wed, 07 Jul 2021 16:44:22 +0200},
biburl = {https://dblp.org/rec/conf/trec/CaporasoBKLJMLFWCH06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/LuH05,
author = {Zhiyong Lu and
Lawrence Hunter},
editor = {Russ B. Altman and
Tiffany A. Jung and
Teri E. Klein and
A. Keith Dunker and
Lawrence Hunter},
title = {{GO} Molecular Function Terms Are Predictive of Subcellular Localization},
booktitle = {Biocomputing 2005, Proceedings of the Pacific Symposium, Hawaii, USA,
4-8 January 2005},
publisher = {World Scientific},
year = {2005},
url = {http://psb.stanford.edu/psb-online/proceedings/psb05/lu.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/LuH05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LuSGLWPAME04,
author = {Zhiyong Lu and
Duane Szafron and
Russell Greiner and
Paul Lu and
David S. Wishart and
Brett Poulin and
John Anvik and
Cam Macdonell and
Roman Eisner},
title = {Predicting subcellular localization of proteins using machine-learned
classifiers},
journal = {Bioinform.},
volume = {20},
number = {4},
pages = {547--556},
year = {2004},
url = {https://doi.org/10.1093/bioinformatics/btg447},
doi = {10.1093/BIOINFORMATICS/BTG447},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/LuSGLWPAME04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SzafronLGWPELAMFM04,
author = {Duane Szafron and
Paul Lu and
Russell Greiner and
David S. Wishart and
Brett Poulin and
Roman Eisner and
Zhiyong Lu and
John Anvik and
Cam Macdonell and
Alona Fyshe and
David Meeuwis},
title = {Proteome Analyst: custom predictions with explanations in a web-based
tool for high-throughput proteome annotations},
journal = {Nucleic Acids Res.},
volume = {32},
number = {Web-Server-Issue},
pages = {365--371},
year = {2004},
url = {https://doi.org/10.1093/nar/gkh485},
doi = {10.1093/NAR/GKH485},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/SzafronLGWPELAMFM04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/pakdd/SanderQLNK03,
author = {J{\"{o}}rg Sander and
Xuejie Qin and
Zhiyong Lu and
Nan Niu and
Alex Kovarsky},
editor = {Kyu{-}Young Whang and
Jongwoo Jeon and
Kyuseok Shim and
Jaideep Srivastava},
title = {Automatic Extraction of Clusters from Hierarchical Clustering Representations},
booktitle = {Advances in Knowledge Discovery and Data Mining, 7th Pacific-Asia
Conference, {PAKDD} 2003, Seoul, Korea, April 30 - May 2, 2003, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2637},
pages = {75--87},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/3-540-36175-8\_8},
doi = {10.1007/3-540-36175-8\_8},
timestamp = {Tue, 14 May 2019 10:00:51 +0200},
biburl = {https://dblp.org/rec/conf/pakdd/SanderQLNK03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/amc/PingZZ99,
author = {Ping He and
Zheng Chen and
Zhiyong Lu},
title = {Artificial neural networks model of share analysis specialist system},
journal = {Appl. Math. Comput.},
volume = {106},
number = {2-3},
pages = {277--283},
year = {1999},
url = {https://doi.org/10.1016/S0096-3003(98)10129-7},
doi = {10.1016/S0096-3003(98)10129-7},
timestamp = {Wed, 21 May 2025 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/amc/PingZZ99.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
manage site settings
To protect your privacy, all features that rely on external API calls from your browser are turned off by default. You need to opt-in for them to become active. All settings here will be stored as cookies with your web browser. For more information see our F.A.Q.
last updated on 2026-03-17 23:41 CET by the dblp team
all metadata released as open data under CC0 1.0 license
see also: Terms of Use | Privacy Policy | Imprint
dblp was originally created in 1993 at:
since 2018, dblp has been operated and maintained by:
the dblp computer science bibliography is funded and supported by:
