{"id":"https://openalex.org/W4410369053","doi":"https://doi.org/10.1186/s13321-025-01012-5","title":"Fate-tox: fragment attention transformer for E(3)-equivariant multi-organ toxicity prediction","display_name":"Fate-tox: fragment attention transformer for E(3)-equivariant multi-organ toxicity prediction","publication_year":2025,"publication_date":"2025-05-14","ids":{"openalex":"https://openalex.org/W4410369053","doi":"https://doi.org/10.1186/s13321-025-01012-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/40369624"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-01012-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01012-5","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01012-5","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01012-5","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038930904","display_name":"Sy Ha","orcid":"https://orcid.org/0000-0002-9191-8743"},"institutions":[{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["KR"],"is_corresponding":true,"raw_author_name":"Sumin Ha","raw_affiliation_strings":["Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, 08826, Republic of Korea"],"affiliations":[{"raw_affiliation_string":"Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, 08826, Republic of Korea","institution_ids":["https://openalex.org/I139264467"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5057875428","display_name":"Dongmin Bang","orcid":"https://orcid.org/0000-0001-9217-8380"},"institutions":[{"id":"https://openalex.org/I4210151723","display_name":"Institute of Refrigeration","ror":"https://ror.org/046jmy298","country_code":"GB","type":"nonprofit","lineage":["https://openalex.org/I4210151723"]},{"id":"https://openalex.org/I139264467","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542","country_code":"KR","type":"education","lineage":["https://openalex.org/I139264467"]}],"countries":["GB","KR"],"is_corresponding":false,"raw_author_name":"Dongmin Bang","raw_affiliation_strings":["AIGENDRUG Co., Ltd., Seoul, 08758, Republic of Korea","Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea"],"affiliations":[{"raw_affiliation_string":"AIGENDRUG Co., Ltd., Seoul, 08758, Republic of Korea","institution_ids":["https://openalex.org/I4210151723"]},{"raw_affiliation_string":"Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea","institution_ids":["https://openalex.org/I139264467"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012503420","display_name":"Sun Yeou Kim","orcid":"https://orcid.org/0000-0001-8044-5613"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Sun Kim","raw_affiliation_strings":["AIGENDRUG Co., Ltd., Seoul, 08758, Republic of Korea. sunkim.bioinfo@snu.ac.kr","Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea. sunkim.bioinfo@snu.ac.kr","Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, 08826, Republic of Korea. sunkim.bioinfo@snu.ac.kr","Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea. sunkim.bioinfo@snu.ac.kr"],"affiliations":[{"raw_affiliation_string":"AIGENDRUG Co., Ltd., Seoul, 08758, Republic of Korea. sunkim.bioinfo@snu.ac.kr","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science and Engineering, Seoul National University, Seoul, 08826, Republic of Korea. sunkim.bioinfo@snu.ac.kr","institution_ids":[]},{"raw_affiliation_string":"Interdisciplinary Program in Artificial Intelligence, Seoul National University, Seoul, 08826, Republic of Korea. sunkim.bioinfo@snu.ac.kr","institution_ids":[]},{"raw_affiliation_string":"Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea. sunkim.bioinfo@snu.ac.kr","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5038930904"],"corresponding_institution_ids":["https://openalex.org/I139264467"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":6.7399,"has_fulltext":true,"cited_by_count":5,"citation_normalized_percentile":{"value":0.96792193,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"17","issue":"1","first_page":"74","last_page":"74"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998000264167786,"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":0.9998000264167786,"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/T11948","display_name":"Machine Learning in Materials Science","score":0.9950000047683716,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10836","display_name":"Metabolomics and Mass Spectrometry Studies","score":0.9506999850273132,"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":0.6690046191215515},{"id":"https://openalex.org/keywords/toxicity","display_name":"Toxicity","score":0.6547263860702515},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.39190107583999634},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.36683160066604614},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3439773917198181},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.20919141173362732},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.18223217129707336}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6690046191215515},{"id":"https://openalex.org/C29730261","wikidata":"https://www.wikidata.org/wiki/Q274160","display_name":"Toxicity","level":2,"score":0.6547263860702515},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.39190107583999634},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.36683160066604614},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3439773917198181},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.20919141173362732},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.18223217129707336},{"id":"https://openalex.org/C178790620","wikidata":"https://www.wikidata.org/wiki/Q11351","display_name":"Organic chemistry","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/s13321-025-01012-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01012-5","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01012-5","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:40369624","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40369624","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of cheminformatics","raw_type":null},{"id":"pmh:oai:doaj.org/article:d8e67cd7148b43cb96dba9b14910b896","is_oa":true,"landing_page_url":"https://doaj.org/article/d8e67cd7148b43cb96dba9b14910b896","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 17, Iss 1, Pp 1-16 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12080013","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12080013","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"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":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-025-01012-5","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01012-5","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01012-5","source":{"id":"https://openalex.org/S180838163","display_name":"Journal of Cheminformatics","issn_l":"1758-2946","issn":["1758-2946"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/3","display_name":"Good health and well-being","score":0.6899999976158142}],"awards":[{"id":"https://openalex.org/G3553684906","display_name":null,"funder_award_id":"RS-2023-00257479","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G3598079552","display_name":null,"funder_award_id":"RS-2021-II211343","funder_id":"https://openalex.org/F4320335489","funder_display_name":"Institute for Information and Communications Technology Promotion"},{"id":"https://openalex.org/G4700831490","display_name":null,"funder_award_id":"2022-","funder_id":"https://openalex.org/F4320335489","funder_display_name":"Institute for Information and Communications Technology Promotion"},{"id":"https://openalex.org/G7288789209","display_name":null,"funder_award_id":"RS-2021-II211343","funder_id":"https://openalex.org/F4320328359","funder_display_name":"Ministry of Science and ICT, South Korea"},{"id":"https://openalex.org/G7798134731","display_name":null,"funder_award_id":"RS-2021-II211343","funder_id":"https://openalex.org/F4320321292","funder_display_name":"Seoul National University"}],"funders":[{"id":"https://openalex.org/F2467035380","display_name":"AIGENDRUG","ror":null},{"id":"https://openalex.org/F4320320671","display_name":"National Research Foundation","ror":"https://ror.org/05s0g1g46"},{"id":"https://openalex.org/F4320321292","display_name":"Seoul National University","ror":"https://ror.org/04h9pn542"},{"id":"https://openalex.org/F4320328359","display_name":"Ministry of Science and ICT, South Korea","ror":"https://ror.org/01wpjm123"},{"id":"https://openalex.org/F4320335489","display_name":"Institute for Information and Communications Technology Promotion","ror":"https://ror.org/01g0hqq23"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4410369053.pdf","grobid_xml":"https://content.openalex.org/works/W4410369053.grobid-xml"},"referenced_works_count":64,"referenced_works":["https://openalex.org/W1133957130","https://openalex.org/W1498436455","https://openalex.org/W1868158647","https://openalex.org/W1977340881","https://openalex.org/W1995013024","https://openalex.org/W2010769998","https://openalex.org/W2010956035","https://openalex.org/W2012513486","https://openalex.org/W2022476850","https://openalex.org/W2024899621","https://openalex.org/W2027689756","https://openalex.org/W2031301975","https://openalex.org/W2043509228","https://openalex.org/W2046208342","https://openalex.org/W2048709650","https://openalex.org/W2049060014","https://openalex.org/W2050273205","https://openalex.org/W2054203041","https://openalex.org/W2066532920","https://openalex.org/W2084087750","https://openalex.org/W2085925007","https://openalex.org/W2096793782","https://openalex.org/W2155060282","https://openalex.org/W2158131645","https://openalex.org/W2268755124","https://openalex.org/W2321102680","https://openalex.org/W2594183968","https://openalex.org/W2778051509","https://openalex.org/W2801088198","https://openalex.org/W2888936354","https://openalex.org/W2911964244","https://openalex.org/W2962858109","https://openalex.org/W3042394400","https://openalex.org/W3094640617","https://openalex.org/W3104644561","https://openalex.org/W3157427301","https://openalex.org/W3199532305","https://openalex.org/W3207161423","https://openalex.org/W3208039415","https://openalex.org/W4213077304","https://openalex.org/W4214868967","https://openalex.org/W4220982113","https://openalex.org/W4239510810","https://openalex.org/W4283066927","https://openalex.org/W4312221417","https://openalex.org/W4323304388","https://openalex.org/W4366822094","https://openalex.org/W4372330430","https://openalex.org/W4378070318","https://openalex.org/W4386212964","https://openalex.org/W4386508152","https://openalex.org/W4386587901","https://openalex.org/W4386878844","https://openalex.org/W4391440627","https://openalex.org/W4393936599","https://openalex.org/W4396514423","https://openalex.org/W4397001794","https://openalex.org/W4398765742","https://openalex.org/W4401782114","https://openalex.org/W4404396704","https://openalex.org/W4406808496","https://openalex.org/W4407319372","https://openalex.org/W6600194071","https://openalex.org/W6604545811"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W4387369504","https://openalex.org/W4394896187","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W3107602296","https://openalex.org/W4364306694","https://openalex.org/W4312192474","https://openalex.org/W4283697347"],"abstract_inverted_index":{"Toxicity":[0],"is":[1,67],"a":[2,68,122,280],"critical":[3],"hurdle":[4],"in":[5,42,47,95,105,177,203,266],"drug":[6,297],"development,":[7],"often":[8,20],"causing":[9],"the":[10,48,78,233,246,272],"late-stage":[11],"failure":[12],"of":[13,28,51,64,80,86,92,101,107,134,170],"promising":[14],"compounds.":[15],"Existing":[16],"computational":[17],"prediction":[18,63,102,204],"models":[19],"focus":[21],"on":[22,215],"single-organ":[23],"toxicity.":[24],"However,":[25],"avoiding":[26],"toxicity":[27,41,66,85,130,163,216],"an":[29],"organ,":[30,44],"such":[31,141],"as":[32,45,142],"reducing":[33],"gastrointestinal":[34],"side":[35],"effects,":[36],"may":[37],"inadvertently":[38],"lead":[39],"to":[40,57,84,150,161,208,242,245,263,274,287],"another":[43],"seen":[46],"real":[49],"case":[50],"rofecoxib,":[52],"which":[53],"was":[54],"withdrawn":[55],"due":[56],"increased":[58],"cardiovascular":[59],"risks.":[60],"Thus,":[61],"simultaneous":[62],"multi-organ":[65,129],"desirable":[69],"but":[70],"challenging":[71],"task.":[72],"The":[73],"main":[74],"challenges":[75,115],"are":[76],"(1)":[77],"variability":[79,133],"substructures":[81,108,157],"that":[82,155,250],"contribute":[83],"different":[87,165],"organs,":[88],"(2)":[89],"insufficient":[90,168],"power":[91,169],"molecular":[93,171,175],"representations":[94,176],"diverse":[96,156],"perspectives,":[97],"and":[98,146,180,224,230,277,283,294],"(3)":[99],"explainability":[100],"results":[103],"especially":[104],"terms":[106],"or":[109],"potential":[110,190,273],"toxicophores.":[111],"To":[112],"address":[113],"these":[114,254],"with":[116,206,260,279],"multiple":[117],"strategies,":[118],"we":[119,136,173],"developed":[120],"FATE-Tox,":[121],"novel":[123],"multi-view":[124],"deep":[125],"learning":[126,235,248],"framework":[127,199,249],"for":[128,164],"prediction.":[131],"For":[132,167,183],"substructures,":[135],"used":[137,160,174],"three":[138],"fragmentation":[139],"methods":[140,214],"BRICS,":[143],"Bemis-Murcko":[144],"scaffolds,":[145],"RDKit":[147],"Functional":[148],"Groups":[149],"formulate":[151],"fragment-level":[152],"graphs":[153],"so":[154],"can":[158],"be":[159],"identify":[162],"organs.":[166],"representations,":[172],"both":[178],"2D":[179],"3D":[181,191],"perspectives.":[182],"explainability,":[184],"our":[185],"fragment":[186],"attention":[187,194,257],"transformer":[188],"identifies":[189],"toxicophores":[192],"using":[193],"coefficients.":[195],"Scientific":[196],"contribution:":[197],"Our":[198,269],"achieved":[200],"significant":[201],"improvements":[202],"performance,":[205],"up":[207,241],"3.01%":[209],"gains":[210],"over":[211],"prior":[212],"baseline":[213],"benchmark":[217],"datasets":[218],"from":[219],"MoleculeNet":[220],"(BBBP,":[221],"SIDER,":[222],"ClinTox)":[223],"TDC":[225],"(DILI,":[226],"Skin":[227],"Reaction,":[228],"Carcinogens,":[229],"hERG),":[231],"while":[232],"multi-task":[234],"approach":[236,270],"further":[237],"enhanced":[238],"performance":[239],"by":[240],"1.44%":[243],"compared":[244],"single-task":[247],"had":[251],"already":[252],"surpassed":[253],"baselines.":[255],"Additionally,":[256],"visualization":[258],"aligning":[259],"literature":[261],"contributes":[262],"greater":[264],"transparency":[265],"predictive":[267],"modeling.":[268],"has":[271],"provide":[275],"scientists":[276],"clinicians":[278],"more":[281,295],"interpretable":[282],"clinically":[284],"meaningful":[285],"tool":[286],"assess":[288],"systemic":[289],"toxicity,":[290],"ultimately":[291],"supporting":[292],"safer":[293],"informed":[296],"development":[298],"processes.":[299]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":2}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
