{"id":"https://openalex.org/W7126120663","doi":"https://doi.org/10.1109/bibm66473.2025.11356816","title":"CoTox: Chain-of-Thought-Based Molecular Toxicity Reasoning and Prediction","display_name":"CoTox: Chain-of-Thought-Based Molecular Toxicity Reasoning and Prediction","publication_year":2025,"publication_date":"2025-12-15","ids":{"openalex":"https://openalex.org/W7126120663","doi":"https://doi.org/10.1109/bibm66473.2025.11356816"},"language":null,"primary_location":{"id":"doi:10.1109/bibm66473.2025.11356816","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356816","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5124254704","display_name":"Jueon Park","orcid":null},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":true,"raw_author_name":"Jueon Park","raw_affiliation_strings":["Korea University,Department of Computer Science and Engineering,Seoul,Republic of Korea,17035"],"affiliations":[{"raw_affiliation_string":"Korea University,Department of Computer Science and Engineering,Seoul,Republic of Korea,17035","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124154311","display_name":"Yein Park","orcid":null},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":false,"raw_author_name":"Yein Park","raw_affiliation_strings":["Korea University,Department of Computer Science and Engineering,Seoul,Republic of Korea,17035"],"affiliations":[{"raw_affiliation_string":"Korea University,Department of Computer Science and Engineering,Seoul,Republic of Korea,17035","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112308940","display_name":"Minju Song","orcid":null},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":false,"raw_author_name":"Minju Song","raw_affiliation_strings":["Korea University,Department of Computer Science and Engineering,Seoul,Republic of Korea,17035"],"affiliations":[{"raw_affiliation_string":"Korea University,Department of Computer Science and Engineering,Seoul,Republic of Korea,17035","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085901626","display_name":"Soyon Park","orcid":null},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":false,"raw_author_name":"Soyon Park","raw_affiliation_strings":["Korea University,Department of Computer Science and Engineering,Seoul,Republic of Korea,17035"],"affiliations":[{"raw_affiliation_string":"Korea University,Department of Computer Science and Engineering,Seoul,Republic of Korea,17035","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100436324","display_name":"Dong Hyeon Lee","orcid":"https://orcid.org/0000-0003-2044-6854"},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":false,"raw_author_name":"Donghyeon Lee","raw_affiliation_strings":["Korea University,Department of Computer Science and Engineering,Seoul,Republic of Korea,17035"],"affiliations":[{"raw_affiliation_string":"Korea University,Department of Computer Science and Engineering,Seoul,Republic of Korea,17035","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103230242","display_name":"Seungheun Baek","orcid":"https://orcid.org/0000-0002-3231-478X"},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":false,"raw_author_name":"Seungheun Baek","raw_affiliation_strings":["Korea University,Department of Computer Science and Engineering,Seoul,Republic of Korea,17035"],"affiliations":[{"raw_affiliation_string":"Korea University,Department of Computer Science and Engineering,Seoul,Republic of Korea,17035","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5113149933","display_name":"Jaewoo Kang","orcid":null},"institutions":[{"id":"https://openalex.org/I197347611","display_name":"Korea University","ror":"https://ror.org/047dqcg40","country_code":"KR","type":"education","lineage":["https://openalex.org/I197347611"]},{"id":"https://openalex.org/I4210161052","display_name":"Korea University","ror":"https://ror.org/05m1gnk07","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210161052"]}],"countries":["JP","KR"],"is_corresponding":false,"raw_author_name":"Jaewoo Kang","raw_affiliation_strings":["Korea University,Department of Computer Science and Engineering,Seoul,Republic of Korea,17035"],"affiliations":[{"raw_affiliation_string":"Korea University,Department of Computer Science and Engineering,Seoul,Republic of Korea,17035","institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5124254704"],"corresponding_institution_ids":["https://openalex.org/I197347611","https://openalex.org/I4210161052"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.7568313,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"4002","last_page":"4007"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.6065000295639038,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.6065000295639038,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"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":0.1665000021457672,"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":0.02879999950528145,"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/interpretability","display_name":"Interpretability","score":0.9437000155448914},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6241000294685364},{"id":"https://openalex.org/keywords/in-silico","display_name":"In silico","score":0.46070000529289246},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.424699991941452},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.38499999046325684},{"id":"https://openalex.org/keywords/liver-toxicity","display_name":"Liver toxicity","score":0.3698999881744385},{"id":"https://openalex.org/keywords/training-set","display_name":"Training set","score":0.3684999942779541}],"concepts":[{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.9437000155448914},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6241000294685364},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6159999966621399},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5361999869346619},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5095999836921692},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.46070000529289246},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.424699991941452},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.38499999046325684},{"id":"https://openalex.org/C2993709057","wikidata":"https://www.wikidata.org/wiki/Q1349821","display_name":"Liver toxicity","level":3,"score":0.3698999881744385},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.3684999942779541},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.35929998755455017},{"id":"https://openalex.org/C2992092908","wikidata":"https://www.wikidata.org/wiki/Q45959","display_name":"Drug toxicity","level":3,"score":0.33820000290870667},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3077999949455261},{"id":"https://openalex.org/C29730261","wikidata":"https://www.wikidata.org/wiki/Q274160","display_name":"Toxicity","level":2,"score":0.302700012922287},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.2888999879360199},{"id":"https://openalex.org/C2776760102","wikidata":"https://www.wikidata.org/wiki/Q5139990","display_name":"Code (set theory)","level":3,"score":0.2865000069141388},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.26100000739097595},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.2574999928474426}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm66473.2025.11356816","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm66473.2025.11356816","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2025 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/4","score":0.6342192888259888,"display_name":"Quality Education"}],"awards":[{"id":"https://openalex.org/G2127363765","display_name":null,"funder_award_id":"NRF2023RIA2C3004176","funder_id":"https://openalex.org/F4320322120","funder_display_name":"National Research Foundation of Korea"},{"id":"https://openalex.org/G2196686709","display_name":null,"funder_award_id":"RS-2023-00262002","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G7401429048","display_name":null,"funder_award_id":"KSC-2024-CRE-0391","funder_id":"https://openalex.org/F4320337144","funder_display_name":"National Supercomputing Center, Korea Institute of Science and Technology Information"}],"funders":[{"id":"https://openalex.org/F4320322120","display_name":"National Research Foundation of Korea","ror":"https://ror.org/013aysd81"},{"id":"https://openalex.org/F4320322557","display_name":"Seoul National University Hospital","ror":"https://ror.org/01z4nnt86"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"},{"id":"https://openalex.org/F4320337144","display_name":"National Supercomputing Center, Korea Institute of Science and Technology Information","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":21,"referenced_works":["https://openalex.org/W2064148898","https://openalex.org/W2113524447","https://openalex.org/W2116859321","https://openalex.org/W2147243352","https://openalex.org/W2295598076","https://openalex.org/W2398766679","https://openalex.org/W2793838702","https://openalex.org/W2801555904","https://openalex.org/W2897256745","https://openalex.org/W2973039076","https://openalex.org/W3048843500","https://openalex.org/W4211238337","https://openalex.org/W4367050536","https://openalex.org/W4390221451","https://openalex.org/W4403284571","https://openalex.org/W4405185373","https://openalex.org/W4407802602","https://openalex.org/W4408681177","https://openalex.org/W4413911708","https://openalex.org/W4415798795","https://openalex.org/W4416036334"],"related_works":[],"abstract_inverted_index":{"Drug":[0],"toxicity":[1,17,89,106,150],"remains":[2],"a":[3,50,77],"major":[4],"challenge":[5],"in":[6,15,158,163,168,194],"phar-maceutical":[7],"development.":[8],"Recent":[9],"machine":[10,120],"learning":[11,121,124],"models":[12],"have":[13],"improved":[14],"silico":[16],"prediction,":[18],"but":[19],"their":[20,30,34],"reliance":[21],"on":[22],"annotated":[23],"data":[24],"and":[25,56,67,98,122,183,191],"lack":[26,64],"of":[27,58,177],"interpretability":[28,182],"limit":[29],"applica-bility.":[31],"This":[32,172],"limits":[33],"ability":[35],"to":[36,103,134,180],"capture":[37],"organ-specific":[38,149],"toxicities":[39],"driven":[40],"by":[41],"complex":[42],"biological":[43,65,96],"mechanisms.":[44],"Large":[45],"language":[46],"mod-els":[47],"(LLMs)":[48],"offer":[49],"promising":[51],"alternative":[52],"through":[53,108],"step-by-step":[54,109],"reasoning":[55,86,153],"integration":[57],"textual":[59],"data,":[60,95],"yet":[61],"prior":[62],"approaches":[63],"context":[66],"transparent":[68],"rationale.":[69],"To":[70],"address":[71],"this":[72,195],"issue,":[73],"we":[74,113],"propose":[75],"CoTox,":[76],"novel":[78],"framework":[79],"that":[80,115],"integrates":[81],"LLM":[82],"with":[83],"chain-of-thought":[84],"(CoT)":[85],"for":[87],"multi-organ":[88],"prediction.":[90],"CoTox":[91,116,137],"combines":[92],"chemical":[93],"structure":[94],"pathways,":[97],"Gene":[99],"Ontology":[100],"(GO)":[101],"terms":[102],"generate":[104],"interpretable":[105],"predictions":[107],"reasoning.":[110],"Using":[111],"GPT-40,":[112],"show":[114],"outperforms":[117],"both":[118],"traditional":[119],"deep":[123],"models.":[125],"We":[126],"further":[127],"examine":[128],"its":[129],"performance":[130,146],"across":[131,147],"various":[132],"LLMs":[133],"identify":[135],"where":[136],"is":[138],"most":[139],"effective.":[140],"In":[141],"particular,":[142],"Gemini-2.5-Pro":[143],"demonstrates":[144],"strong":[145],"multiple":[148],"tasks.":[151],"Its":[152],"outputs":[154],"are":[155,197],"consistently":[156],"grounded":[157],"biologically":[159],"validated":[160],"mechanisms":[161],"documented":[162],"the":[164,169,175],"literature,":[165],"as":[166],"shown":[167],"case":[170],"study.":[171],"result":[173],"highlights":[174],"potential":[176],"LLM-based":[178],"frameworks":[179],"improve":[181],"support":[184],"early-stage":[185],"drug":[186],"safety":[187],"assessment.":[188],"The":[189],"code":[190],"prompt":[192],"used":[193],"work":[196],"available":[198],"at":[199],"https://github.comJdmis-lab/CoTox.":[200]},"counts_by_year":[],"updated_date":"2026-04-09T08:11:56.329763","created_date":"2026-01-30T00:00:00"}
