{"id":"https://openalex.org/W4392089985","doi":"https://doi.org/10.48550/arxiv.2402.13653","title":"PQA: Zero-shot Protein Question Answering for Free-form Scientific Enquiry with Large Language Models","display_name":"PQA: Zero-shot Protein Question Answering for Free-form Scientific Enquiry with Large Language Models","publication_year":2024,"publication_date":"2024-02-21","ids":{"openalex":"https://openalex.org/W4392089985","doi":"https://doi.org/10.48550/arxiv.2402.13653"},"language":"en","primary_location":{"id":"pmh:oai:arXiv.org:2402.13653","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2402.13653","pdf_url":"https://arxiv.org/pdf/2402.13653","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"type":"preprint","indexed_in":["arxiv","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2402.13653","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069185541","display_name":"Eli M. Carrami","orcid":"https://orcid.org/0000-0002-7770-2065"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Carrami, Eli M","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5039442998","display_name":"Sahand Sharifzadeh","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sharifzadeh, Sahand","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5069185541"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T10028","display_name":"Topic Modeling","score":0.9987999796867371,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9825000166893005,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10181","display_name":"Natural Language Processing Techniques","score":0.9670000076293945,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/zero","display_name":"Zero (linguistics)","score":0.8030003309249878},{"id":"https://openalex.org/keywords/question-answering","display_name":"Question answering","score":0.5865825414657593},{"id":"https://openalex.org/keywords/shot","display_name":"Shot (pellet)","score":0.5465287566184998},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4168001413345337},{"id":"https://openalex.org/keywords/linguistics","display_name":"Linguistics","score":0.3428215980529785},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3372195363044739},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.2146865725517273},{"id":"https://openalex.org/keywords/philosophy","display_name":"Philosophy","score":0.20797023177146912}],"concepts":[{"id":"https://openalex.org/C2780813799","wikidata":"https://www.wikidata.org/wiki/Q3274237","display_name":"Zero (linguistics)","level":2,"score":0.8030003309249878},{"id":"https://openalex.org/C44291984","wikidata":"https://www.wikidata.org/wiki/Q1074173","display_name":"Question answering","level":2,"score":0.5865825414657593},{"id":"https://openalex.org/C2778344882","wikidata":"https://www.wikidata.org/wiki/Q278938","display_name":"Shot (pellet)","level":2,"score":0.5465287566184998},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4168001413345337},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.3428215980529785},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3372195363044739},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.2146865725517273},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.20797023177146912},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:arXiv.org:2402.13653","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2402.13653","pdf_url":"https://arxiv.org/pdf/2402.13653","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},{"id":"doi:10.48550/arxiv.2402.13653","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2402.13653","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2402.13653","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2402.13653","pdf_url":"https://arxiv.org/pdf/2402.13653","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4392089985.pdf","grobid_xml":"https://content.openalex.org/works/W4392089985.grobid-xml"},"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2074502265","https://openalex.org/W4214877189","https://openalex.org/W2773965352","https://openalex.org/W2381179799","https://openalex.org/W2384605597","https://openalex.org/W2980279061","https://openalex.org/W2334685461","https://openalex.org/W2387743295","https://openalex.org/W2366718574","https://openalex.org/W2359774528"],"abstract_inverted_index":{"Understanding":[0],"protein":[1,138,141],"structure":[2],"and":[3,16,50,68,101,125,133,151],"function":[4],"is":[5,154],"crucial":[6],"in":[7,59,162],"biology.":[8],"However,":[9],"current":[10,60,74],"computational":[11],"methods":[12,76],"are":[13,57],"often":[14],"task-specific":[15,40],"resource-intensive.":[17],"To":[18],"address":[19],"this,":[20],"we":[21],"propose":[22,109],"zero-shot":[23],"Protein":[24],"Question":[25],"Answering":[26],"(PQA),":[27],"a":[28,33,94,102,115,130],"task":[29],"designed":[30],"to":[31,78,88,136],"answer":[32],"wide":[34],"range":[35],"of":[36,44,55,70],"protein-related":[37],"queries":[38],"without":[39],"training.":[41],"The":[42],"success":[43],"PQA":[45,100,145],"hinges":[46],"on":[47,157],"high-quality":[48],"datasets":[49,63],"robust":[51],"evaluation":[52,75],"strategies,":[53],"both":[54],"which":[56],"lacking":[58],"research.":[61,142],"Existing":[62],"suffer":[64],"from":[65],"biases,":[66],"noise,":[67],"lack":[69],"evolutionary":[71],"context,":[72],"while":[73],"fail":[77],"accurately":[79],"assess":[80],"model":[81,152],"performance.":[82],"We":[83,107],"introduce":[84],"the":[85,163],"Pika":[86,92],"framework":[87],"overcome":[89],"these":[90],"limitations.":[91],"comprises":[93],"curated,":[95],"debiased":[96],"dataset":[97],"tailored":[98],"for":[99,118],"biochemically":[103],"relevant":[104],"benchmarking":[105],"strategy.":[106],"also":[108],"multimodal":[110],"large":[111],"language":[112,123],"models":[113],"as":[114],"strong":[116],"baseline":[117],"PQA,":[119],"leveraging":[120],"their":[121],"natural":[122],"processing":[124],"knowledge.":[126],"This":[127],"approach":[128],"promises":[129],"more":[131],"flexible":[132],"efficient":[134],"way":[135],"explore":[137],"properties,":[139],"advancing":[140],"Our":[143],"comprehensive":[144],"framework,":[146],"Pika,":[147],"including":[148],"dataset,":[149],"code,":[150],"checkpoints,":[153],"openly":[155],"accessible":[156],"github.com/EMCarrami/Pika,":[158],"promoting":[159],"wider":[160],"research":[161],"field.":[164]},"counts_by_year":[],"updated_date":"2026-03-09T08:58:05.943551","created_date":"2025-10-10T00:00:00"}
