{"id":"https://openalex.org/W4403862485","doi":"https://doi.org/10.1145/3702234","title":"How Do Large Language Models Understand Genes and Cells","display_name":"How Do Large Language Models Understand Genes and Cells","publication_year":2024,"publication_date":"2024-10-29","ids":{"openalex":"https://openalex.org/W4403862485","doi":"https://doi.org/10.1145/3702234"},"language":"en","primary_location":{"id":"doi:10.1145/3702234","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3702234","pdf_url":null,"source":{"id":"https://openalex.org/S2492086750","display_name":"ACM Transactions on Intelligent Systems and Technology","issn_l":"2157-6904","issn":["2157-6904","2157-6912"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Intelligent Systems and Technology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://doi.org/10.1145/3702234","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5090644161","display_name":"Chen Fang","orcid":"https://orcid.org/0009-0001-6382-1960"},"institutions":[{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]},{"id":"https://openalex.org/I4210167311","display_name":"Institute of Zoology","ror":"https://ror.org/05skxkv18","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210167311"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Chen Fang","raw_affiliation_strings":["State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China and Computer Network Information Center, Chinese Academy of Sciences, Beijing, China and University of Chinese Academy of Sciences, Beijing, China","State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences; Computer Network Information Center, Chinese Academy of Sciences; University of Chinese Academy of Sciences, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China and Computer Network Information Center, Chinese Academy of Sciences, Beijing, China and University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210167311"]},{"raw_affiliation_string":"State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences; Computer Network Information Center, Chinese Academy of Sciences; University of Chinese Academy of Sciences, China","institution_ids":["https://openalex.org/I4210167311","https://openalex.org/I4210165038","https://openalex.org/I4210108629"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100685716","display_name":"Yidong Wang","orcid":"https://orcid.org/0009-0007-9969-8259"},"institutions":[{"id":"https://openalex.org/I20231570","display_name":"Peking University","ror":"https://ror.org/02v51f717","country_code":"CN","type":"education","lineage":["https://openalex.org/I20231570"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yidong Wang","raw_affiliation_strings":["Peking University, Beijing, China","Peking University, China"],"affiliations":[{"raw_affiliation_string":"Peking University, Beijing, China","institution_ids":["https://openalex.org/I20231570"]},{"raw_affiliation_string":"Peking University, China","institution_ids":["https://openalex.org/I20231570"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5034940599","display_name":"Yunze Song","orcid":null},"institutions":[{"id":"https://openalex.org/I146655781","display_name":"University of Liverpool","ror":"https://ror.org/04xs57h96","country_code":"GB","type":"education","lineage":["https://openalex.org/I146655781"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Yunze Song","raw_affiliation_strings":["University of Liverpool, Liverpool, UK","University of Liverpool, UK"],"affiliations":[{"raw_affiliation_string":"University of Liverpool, Liverpool, UK","institution_ids":["https://openalex.org/I146655781"]},{"raw_affiliation_string":"University of Liverpool, UK","institution_ids":["https://openalex.org/I146655781"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027022795","display_name":"Qingqing Long","orcid":"https://orcid.org/0009-0003-7105-361X"},"institutions":[{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qingqing Long","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences, Beijing, China and University of Chinese Academy of Sciences, Beijing, China","Computer Network Information Center, Chinese Academy of Sciences; University of Chinese Academy of Sciences, China"],"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences, Beijing, China and University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I4210165038"]},{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences; University of Chinese Academy of Sciences, China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100774978","display_name":"Lu Wang","orcid":"https://orcid.org/0000-0003-4035-0737"},"institutions":[{"id":"https://openalex.org/I99065089","display_name":"Tsinghua University","ror":"https://ror.org/03cve4549","country_code":"CN","type":"education","lineage":["https://openalex.org/I99065089"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wang Lu","raw_affiliation_strings":["Tsinghua University, Beijing, China","Tsinghua University, China"],"affiliations":[{"raw_affiliation_string":"Tsinghua University, Beijing, China","institution_ids":["https://openalex.org/I99065089"]},{"raw_affiliation_string":"Tsinghua University, China","institution_ids":["https://openalex.org/I99065089"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101593418","display_name":"Ling-Hui Chen","orcid":"https://orcid.org/0009-0009-4247-4128"},"institutions":[{"id":"https://openalex.org/I39774598","display_name":"Hefei University","ror":"https://ror.org/01f5rdf64","country_code":"CN","type":"education","lineage":["https://openalex.org/I39774598"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Linghui Chen","raw_affiliation_strings":["iFLYTEK Research, Hefei, China and Oristruct Biotech Co., Ltd, Hefei, China","iFLYTEK Research; Oristruct Biotech Co., Ltd, China"],"affiliations":[{"raw_affiliation_string":"iFLYTEK Research, Hefei, China and Oristruct Biotech Co., Ltd, Hefei, China","institution_ids":["https://openalex.org/I39774598"]},{"raw_affiliation_string":"iFLYTEK Research; Oristruct Biotech Co., Ltd, China","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055004688","display_name":"Guihai Feng","orcid":"https://orcid.org/0000-0002-8726-1734"},"institutions":[{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]},{"id":"https://openalex.org/I4210167311","display_name":"Institute of Zoology","ror":"https://ror.org/05skxkv18","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210167311"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Guihai Feng","raw_affiliation_strings":["State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China and University of Chinese Academy of Sciences, Beijing, China","State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Chin"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China and University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210167311"]},{"raw_affiliation_string":"State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, Chin","institution_ids":["https://openalex.org/I4210165038"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065865669","display_name":"Yuanchun Zhou","orcid":"https://orcid.org/0000-0003-2144-1131"},"institutions":[{"id":"https://openalex.org/I4210108629","display_name":"Computer Network Information Center","ror":"https://ror.org/01s0wyf50","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210108629"]},{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanchun Zhou","raw_affiliation_strings":["Computer Network Information Center, Chinese Academy of Sciences, Beijing, China and University of Chinese Academy of Sciences, Beijing, China","Computer Network Information Center, Chinese Academy of Sciences; University of Chinese Academy of Sciences, China"],"affiliations":[{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences, Beijing, China and University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I4210165038"]},{"raw_affiliation_string":"Computer Network Information Center, Chinese Academy of Sciences; University of Chinese Academy of Sciences, China","institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I4210165038"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5108148511","display_name":"Xin Li","orcid":"https://orcid.org/0009-0003-2751-1169"},"institutions":[{"id":"https://openalex.org/I4210165038","display_name":"University of Chinese Academy of Sciences","ror":"https://ror.org/05qbk4x57","country_code":"CN","type":"education","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210165038"]},{"id":"https://openalex.org/I4210167311","display_name":"Institute of Zoology","ror":"https://ror.org/05skxkv18","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210167311"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xin Li","raw_affiliation_strings":["State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China and University of Chinese Academy of Sciences, Beijing, China","State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, China"],"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, China and University of Chinese Academy of Sciences, Beijing, China","institution_ids":["https://openalex.org/I4210167311"]},{"raw_affiliation_string":"State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences; University of Chinese Academy of Sciences, China","institution_ids":["https://openalex.org/I4210167311","https://openalex.org/I4210165038"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5090644161"],"corresponding_institution_ids":["https://openalex.org/I4210108629","https://openalex.org/I4210165038","https://openalex.org/I4210167311"],"apc_list":null,"apc_paid":null,"fwci":0.4679,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.65614965,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":95},"biblio":{"volume":"16","issue":"6","first_page":"1","last_page":"16"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9940999746322632,"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"}},"topics":[{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9940999746322632,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9909999966621399,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9891999959945679,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.8854662179946899},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.5071725845336914},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4172343909740448},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.40207913517951965}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8854662179946899},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.5071725845336914},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4172343909740448},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.40207913517951965}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1145/3702234","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3702234","pdf_url":null,"source":{"id":"https://openalex.org/S2492086750","display_name":"ACM Transactions on Intelligent Systems and Technology","issn_l":"2157-6904","issn":["2157-6904","2157-6912"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Intelligent Systems and Technology","raw_type":"journal-article"}],"best_oa_location":{"id":"doi:10.1145/3702234","is_oa":true,"landing_page_url":"https://doi.org/10.1145/3702234","pdf_url":null,"source":{"id":"https://openalex.org/S2492086750","display_name":"ACM Transactions on Intelligent Systems and Technology","issn_l":"2157-6904","issn":["2157-6904","2157-6912"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319798","host_organization_name":"Association for Computing Machinery","host_organization_lineage":["https://openalex.org/P4310319798"],"host_organization_lineage_names":["Association for Computing Machinery"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"ACM Transactions on Intelligent Systems and Technology","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.46000000834465027,"display_name":"Quality Education"}],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":33,"referenced_works":["https://openalex.org/W1532325895","https://openalex.org/W1965115186","https://openalex.org/W1968931043","https://openalex.org/W2118258530","https://openalex.org/W2256016639","https://openalex.org/W2950257119","https://openalex.org/W2951560273","https://openalex.org/W2952631022","https://openalex.org/W2992387300","https://openalex.org/W3112652901","https://openalex.org/W4213069590","https://openalex.org/W4220837089","https://openalex.org/W4221166199","https://openalex.org/W4224309748","https://openalex.org/W4233452865","https://openalex.org/W4289262011","https://openalex.org/W4296783454","https://openalex.org/W4297243391","https://openalex.org/W4367046738","https://openalex.org/W4367602258","https://openalex.org/W4367627405","https://openalex.org/W4378806473","https://openalex.org/W4378838672","https://openalex.org/W4385572162","https://openalex.org/W4386220752","https://openalex.org/W4386791134","https://openalex.org/W4387122971","https://openalex.org/W4387819650","https://openalex.org/W4393153069","https://openalex.org/W4399380363","https://openalex.org/W4400064739","https://openalex.org/W6948966457","https://openalex.org/W6959643953"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W3204019825"],"abstract_inverted_index":{"Researching":[0],"genes":[1,93],"and":[2,20,31,51,72,94,149],"their":[3,27,44,56,74],"interactions":[4],"is":[5,58],"crucial":[6],"for":[7,136],"deciphering":[8],"the":[9,111,120,142],"fundamental":[10],"laws":[11],"of":[12,55,90,92,114,117,141],"cellular":[13],"activity,":[14],"advancing":[15],"disease":[16],"treatment,":[17],"drug":[18],"discovery,":[19],"more.":[21],"Large":[22],"language":[23],"Models":[24],"(LLMs),":[25],"with":[26],"profound":[28],"text":[29],"comprehension":[30],"generation":[32],"capabilities,":[33],"have":[34,109],"made":[35],"significant":[36],"strides":[37],"across":[38,76],"various":[39],"natural":[40],"science":[41],"fields.":[42],"However,":[43],"application":[45],"in":[46,64,102],"cell":[47,125,130],"biology":[48,131],"remains":[49],"limited":[50],"a":[52,87],"systematic":[53],"evaluation":[54],"performance":[57,75],"lacking.":[59],"To":[60],"address":[61],"this":[62,65],"gap,":[63],"article,":[66],"we":[67,108],"select":[68],"seven":[69],"mainstream":[70],"LLMs":[71,85,135],"evaluate":[73],"nine":[77],"gene-related":[78],"problem":[79],"scenarios.":[80],"Our":[81],"findings":[82],"indicate":[83],"that":[84],"possess":[86],"certain":[88],"level":[89],"understanding":[91],"cells,":[95,118],"but":[96],"still":[97],"lag":[98],"behind":[99],"domain-specific":[100],"models":[101],"comprehending":[103],"transcriptional":[104],"expression":[105],"profiles.":[106],"Moreover,":[107],"improved":[110],"current":[112],"method":[113],"textual":[115],"representation":[116],"enhancing":[119],"LLMs\u2019":[121],"ability":[122],"to":[123,133],"tackle":[124],"annotation":[126],"tasks.":[127],"We":[128,145],"encourage":[129],"researchers":[132],"leverage":[134],"problem-solving":[137],"while":[138],"being":[139],"mindful":[140],"associated":[143],"challenges.":[144],"release":[146],"our":[147],"code":[148],"data":[150],"at":[151],"https://github.com/epang-ucas/Evaluate_LLMs_to_Genes":[152],".":[153]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1}],"updated_date":"2026-03-27T05:58:40.876381","created_date":"2025-10-10T00:00:00"}
