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ORCIDKatherine A. Yelick
- > Home > Persons > Katherine A. Yelick
Publications
- 2025
[c135]Alok Tripathy, Alina Lazar, Xiangyang Ju, Paolo Calafiura, Katherine A. Yelick, Aydin Buluç:
Scaling Graph Neural Networks for Particle Track Reconstruction. IPDPS (Workshops) 2025: 772-776- [i27]Alok Tripathy, Alina Lazar, Xiangyang Ju, Paolo Calafiura, Katherine A. Yelick, Aydin Buluç:
Scaling Graph Neural Networks for Particle Track Reconstruction. CoRR abs/2504.04670 (2025) - [i26]Ujjaini Mukhopadhyay, Alok Tripathy, Oguz Selvitopi, Katherine A. Yelick, Aydin Buluç:
Sparsity-Aware Communication for Distributed Graph Neural Network Training. CoRR abs/2504.04673 (2025) - [i25]Gabriel Raulet, Dmitriy Morozov, Aydin Buluç, Katherine A. Yelick:
Distributed-Memory Parallel Algorithms for Fixed-Radius Near Neighbor Graph Construction. CoRR abs/2510.14147 (2025) - 2024
- [j33]Steven A. Hofmeyr
, Aydin Buluç, Robert Riley, Rob Egan, Oguz Selvitopi, Leonid Oliker, Katherine A. Yelick, Migun Shakya, Brett Youtsey, Ariful Azad:
Exabiome: Advancing Microbial Science through Exascale Computing. Comput. Sci. Eng. 26(2): 8-15 (2024) - [c134]Ujjaini Mukhopadhyay, Alok Tripathy, Oguz Selvitopi, Katherine A. Yelick, Aydin Buluç:
Sparsity-Aware Communication for Distributed Graph Neural Network Training. ICPP 2024: 117-126 - [c133]Benjamin Brock, Aydin Buluç, Katherine A. Yelick:
RDMA-Based Algorithms for Sparse Matrix Multiplication on GPUs. ICS 2024: 225-235 - [c132]Alok Tripathy, Katherine A. Yelick, Aydin Buluç:
Distributed Matrix-Based Sampling for Graph Neural Network Training. MLSys 2024 - [c131]Yuxin Chen, Aydin Buluç, Katherine A. Yelick, John D. Owens:
Accelerating Multi-GPU Embedding Retrieval with PGAS-Style Communication for Deep Learning Recommendation Systems. SC Workshops 2024: 1262-1273 - 2023
- [i24]Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi, Muaaz G. Awan, Georgios A. Pavlopoulos, Ariful Azad, Nikos Kyrpides, Leonid Oliker, Katherine A. Yelick, Aydin Buluç:
Extreme-scale many-against-many protein similarity search. CoRR abs/2303.01845 (2023) - [i23]Alok Tripathy, Katherine A. Yelick, Aydin Buluç:
Distributed Matrix-Based Sampling for Graph Neural Network Training. CoRR abs/2311.02909 (2023) - [i22]Benjamin Brock, Aydin Buluç, Katherine A. Yelick:
RDMA-Based Algorithms for Sparse Matrix Multiplication on GPUs. CoRR abs/2311.18141 (2023) - 2022
- [c127]Yuxin Chen, Benjamin Brock, Serban D. Porumbescu, Aydin Buluç, Katherine A. Yelick, John D. Owens:
Atos: A Task-Parallel GPU Scheduler for Graph Analytics. ICPP 2022: 50:1-50:11 - [c126]Giulia Guidi, Gabriel Raulet, Daniel Rokhsar, Leonid Oliker, Katherine A. Yelick, Aydin Buluç:
Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly. ICPP 2022: 82:1-82:11 - [c125]Oguz Selvitopi, Saliya Ekanayake, Giulia Guidi, Muaaz G. Awan, Georgios A. Pavlopoulos, Ariful Azad, Nikos Kyrpides, Leonid Oliker, Katherine A. Yelick, Aydin Buluç:
Extreme-Scale Many-against-Many Protein Similarity Search. SC 2022: 1:1-1:12 - [c124]Yuxin Chen, Benjamin Brock, Serban D. Porumbescu, Aydin Buluç, Katherine A. Yelick, John D. Owens:
Scalable Irregular Parallelism with GPUs: Getting CPUs Out of the Way. SC 2022: 50:1-50:16 - [i21]Giulia Guidi, Gabriel Raulet, Daniel Rokhsar, Leonid Oliker, Katherine A. Yelick, Aydin Buluç:
Distributed-Memory Parallel Contig Generation for De Novo Long-Read Genome Assembly. CoRR abs/2207.04350 (2022) - 2021
- [c123]Giulia Guidi, Marquita Ellis, Daniel Rokhsar, Katherine A. Yelick, Aydin Buluç:
BELLA: Berkeley Efficient Long-Read to Long-Read Aligner and Overlapper. ACDA 2021: 123-134 - [c122]Marquita Ellis, Aydin Buluç, Katherine A. Yelick:
Scaling Generalized N-Body Problems, A Case Study from Genomics. ICPP 2021: 64:1-64:9 - [c121]Oguz Selvitopi, Benjamin Brock, Israt Nisa, Alok Tripathy, Katherine A. Yelick, Aydin Buluç:
Distributed-memory parallel algorithms for sparse times tall-skinny-dense matrix multiplication. ICS 2021: 431-442 - [c120]Giulia Guidi, Oguz Selvitopi, Marquita Ellis, Leonid Oliker, Katherine A. Yelick, Aydin Buluç:
Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly. IPDPS 2021: 517-526 - [c119]Israt Nisa, Prashant Pandey, Marquita Ellis, Leonid Oliker, Aydin Buluç, Katherine A. Yelick:
Distributed-Memory k-mer Counting on GPUs. IPDPS 2021: 527-536 - [c118]Marquita Ellis, Aydin Buluç, Katherine A. Yelick:
Asynchrony versus bulk-synchrony for a generalized N-body problem from genomics. PPoPP 2021: 465-466 - [c116]Muaaz Gul Awan, Steven A. Hofmeyr, Rob Egan, Nan Ding, Aydin Buluç, Jack Deslippe, Leonid Oliker, Katherine A. Yelick:
Accelerating large scale de novo metagenome assembly using GPUs. SC 2021: 7 - [c114]Giulia Guidi, Marquita Ellis, Aydin Buluç, Katherine A. Yelick, David E. Culler:
10 Years Later: Cloud Computing is Closing the Performance Gap. ICPE (Companion) 2021: 41-48 - [i19]Yuxin Chen, Benjamin Brock, Serban D. Porumbescu, Aydin Buluç, Katherine A. Yelick, John D. Owens:
Atos: A Task-Parallel GPU Dynamic Scheduling Framework for Dynamic Irregular Computations. CoRR abs/2112.00132 (2021) - 2020
- [j31]Muaaz G. Awan, Jack Deslippe, Aydin Buluç, Oguz Selvitopi, Steven A. Hofmeyr, Leonid Oliker, Katherine A. Yelick:
ADEPT: a domain independent sequence alignment strategy for gpu architectures. BMC Bioinform. 21(1): 406 (2020) - [c111]Francesco Peverelli, Lorenzo Di Tucci, Marco D. Santambrogio, Nan Ding, Steven A. Hofmeyr, Aydin Buluç, Leonid Oliker, Katherine A. Yelick:
GPU accelerated partial order multiple sequence alignment for long reads self-correction. IPDPS Workshops 2020: 174-182 - [c110]Alberto Zeni, Giulia Guidi, Marquita Ellis, Nan Ding, Marco D. Santambrogio, Steven A. Hofmeyr, Aydin Buluç, Leonid Oliker, Katherine A. Yelick:
LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment. IPDPS 2020: 462-471 - [c108]Alok Tripathy, Katherine A. Yelick, Aydin Buluç:
Reducing communication in graph neural network training. SC 2020: 70 - [i18]Katherine A. Yelick, Aydin Buluç, Muaaz G. Awan, Ariful Azad, Benjamin Brock, Rob Egan, Saliya Ekanayake, Marquita Ellis, Evangelos Georganas, Giulia Guidi, Steven A. Hofmeyr, Oguz Selvitopi, Cristina Teodoropol, Leonid Oliker:
The Parallelism Motifs of Genomic Data Analysis. CoRR abs/2001.06989 (2020) - [i17]Marquita Ellis, Giulia Guidi, Aydin Buluç, Leonid Oliker, Katherine A. Yelick:
diBELLA: Distributed Long Read to Long Read Alignment. CoRR abs/2001.10049 (2020) - [i16]Alberto Zeni, Giulia Guidi, Marquita Ellis, Nan Ding, Marco D. Santambrogio, Steven A. Hofmeyr, Aydin Buluç, Leonid Oliker, Katherine A. Yelick:
LOGAN: High-Performance GPU-Based X-Drop Long-Read Alignment. CoRR abs/2002.05200 (2020) - [i15]Alok Tripathy, Katherine A. Yelick, Aydin Buluç:
Reducing Communication in Graph Neural Network Training. CoRR abs/2005.03300 (2020) - [i13]Giulia Guidi, Oguz Selvitopi, Marquita Ellis, Leonid Oliker, Katherine A. Yelick, Aydin Buluç:
Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly. CoRR abs/2010.10055 (2020) - [i12]Nicolas Swenson, Aditi S. Krishnapriyan, Aydin Buluç, Dmitriy Morozov, Katherine A. Yelick:
PersGNN: Applying Topological Data Analysis and Geometric Deep Learning to Structure-Based Protein Function Prediction. CoRR abs/2010.16027 (2020) - [i11]Giulia Guidi, Marquita Ellis, Aydin Buluç, Katherine A. Yelick, David E. Culler:
10 Years Later: Cloud Computing is Closing the Performance Gap. CoRR abs/2011.00656 (2020) - 2019
- [c107]Marquita Ellis, Giulia Guidi, Aydin Buluç, Leonid Oliker, Katherine A. Yelick:
diBELLA: Distributed Long Read to Long Read Alignment. ICPP 2019: 70:1-70:11 - [c106]Benjamin Brock, Aydin Buluç, Katherine A. Yelick:
BCL: A Cross-Platform Distributed Data Structures Library. ICPP 2019: 102:1-102:10 - [c105]Benjamin A. Brock, Yuxin Chen, Jiakun Yan, John D. Owens, Aydin Buluç, Katherine A. Yelick:
RDMA vs. RPC for Implementing Distributed Data Structures. IA3@SC 2019: 17-22 - [i10]Benjamin Brock, Yuxin Chen, Jiakun Yan, John D. Owens, Aydin Buluç, Katherine A. Yelick:
RDMA vs. RPC for Implementing Distributed Data Structures. CoRR abs/1910.02158 (2019) - 2018
- [c104]Penporn Koanantakool, Alnur Ali, Ariful Azad, Aydin Buluç, Dmitriy Morozov, Leonid Oliker, Katherine A. Yelick, Sang-Yun Oh:
Communication-Avoiding Optimization Methods for Distributed Massive-Scale Sparse Inverse Covariance Estimation. AISTATS 2018: 1376-1386 - [c101]Evangelos Georganas, Rob Egan, Steven A. Hofmeyr, Eugene Goltsman, Bill Arndt, Andrew Tritt, Aydin Buluç, Leonid Oliker, Katherine A. Yelick:
Extreme scale de novo metagenome assembly. SC 2018: 10:1-10:13 - [i9]Evangelos Georganas, Rob Egan, Steven A. Hofmeyr, Eugene Goltsman, Bill Arndt, Andrew Tritt, Aydin Buluç, Leonid Oliker, Katherine A. Yelick:
Extreme Scale De Novo Metagenome Assembly. CoRR abs/1809.07014 (2018) - [i8]Benjamin Brock, Aydin Buluç, Katherine A. Yelick:
BCL: A Cross-Platform Distributed Container Library. CoRR abs/1810.13029 (2018) - 2017
- [c100]Marquita Ellis, Evangelos Georganas, Rob Egan, Steven A. Hofmeyr, Aydin Buluç, Brandon Cook, Leonid Oliker, Katherine A. Yelick:
Performance Characterization of De Novo Genome Assembly on Leading Parallel Systems. Euro-Par 2017: 79-91 - [c99]Evangelos Georganas, Marquita Ellis, Rob Egan, Steven A. Hofmeyr, Aydin Buluç, Brandon Cook, Leonid Oliker, Katherine A. Yelick:
MerBench: PGAS Benchmarks for High Performance Genome Assembly. PAW@SC 2017: 5:1-5:4 - [i7]Evangelos Georganas, Steven A. Hofmeyr, Rob Egan, Aydin Buluç, Leonid Oliker, Daniel Rokhsar, Katherine A. Yelick:
Extreme-Scale De Novo Genome Assembly. CoRR abs/1705.11147 (2017) - [i5]Penporn Koanantakool, Alnur Ali, Ariful Azad, Aydin Buluç, Dmitriy Morozov, Sang-Yun Oh, Leonid Oliker, Katherine A. Yelick:
Communication-Avoiding Optimization Methods for Massive-Scale Graphical Model Structure Learning. CoRR abs/1710.10769 (2017) - 2016
- [c97]Penporn Koanantakool, Ariful Azad, Aydin Buluç, Dmitriy Morozov, Sang-Yun Oh, Leonid Oliker, Katherine A. Yelick:
Communication-Avoiding Parallel Sparse-Dense Matrix-Matrix Multiplication. IPDPS 2016: 842-853 - 2015
- [c95]Evangelos Georganas, Aydin Buluç, Jarrod Chapman, Leonid Oliker, Daniel Rokhsar, Katherine A. Yelick:
merAligner: A Fully Parallel Sequence Aligner. IPDPS 2015: 561-570 - [c93]Evangelos Georganas, Aydin Buluç, Jarrod Chapman, Steven A. Hofmeyr, Chaitanya Aluru, Rob Egan, Leonid Oliker, Daniel Rokhsar, Katherine A. Yelick:
HipMer: an extreme-scale de novo genome assembler. SC 2015: 14:1-14:11 - 2014
- [c86]Evangelos Georganas, Aydin Buluç, Jarrod Chapman, Leonid Oliker, Daniel Rokhsar, Katherine A. Yelick:
Parallel De Bruijn Graph Construction and Traversal for De Novo Genome Assembly. SC 2014: 437-448
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