{"id":"https://openalex.org/W4413028691","doi":"https://doi.org/10.1186/s13321-025-01048-7","title":"VitroBert: modeling DILI by pretraining BERT on in vitro data","display_name":"VitroBert: modeling DILI by pretraining BERT on in vitro data","publication_year":2025,"publication_date":"2025-08-06","ids":{"openalex":"https://openalex.org/W4413028691","doi":"https://doi.org/10.1186/s13321-025-01048-7","pmid":"https://pubmed.ncbi.nlm.nih.gov/40770816"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-025-01048-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01048-7","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01048-7","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/s13321-025-01048-7","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5030874161","display_name":"Muhammad Arslan Masood","orcid":"https://orcid.org/0000-0002-9190-3023"},"institutions":[{"id":"https://openalex.org/I1330063522","display_name":"Johnson & Johnson (United States)","ror":"https://ror.org/03qd7mz70","country_code":"US","type":"company","lineage":["https://openalex.org/I1330063522"]},{"id":"https://openalex.org/I4210160666","display_name":"Johnson & Johnson (Brazil)","ror":"https://ror.org/04f89zf73","country_code":"BR","type":"company","lineage":["https://openalex.org/I1330063522","https://openalex.org/I4210160666"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["BR","FI","US"],"is_corresponding":true,"raw_author_name":"Muhammad Arslan Masood","raw_affiliation_strings":["Aalto University, Espoo, Finland. arslan.masood@aalto.fi","Johnson & Johnson, Beerse, Belgium. arslan.masood@aalto.fi"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aalto University, Espoo, Finland. arslan.masood@aalto.fi","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"Johnson & Johnson, Beerse, Belgium. arslan.masood@aalto.fi","institution_ids":["https://openalex.org/I1330063522","https://openalex.org/I4210160666"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5119236575","display_name":"Anamya Ajjolli Nagaraja","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Anamya Ajjolli Nagaraja","raw_affiliation_strings":["Johnson & Johnson, Beerse, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Johnson & Johnson, Beerse, Belgium","institution_ids":[]}]},{"author_position":"middle","author":{"id":null,"display_name":"Katia Belaid","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Katia Belaid","raw_affiliation_strings":["Johnson & Johnson, Beerse, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Johnson & Johnson, Beerse, Belgium","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5080731813","display_name":"Natalie Mesens","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Natalie Mesens","raw_affiliation_strings":["Johnson & Johnson, Beerse, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Johnson & Johnson, Beerse, Belgium","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019296124","display_name":"Hugo Ceulemans","orcid":"https://orcid.org/0000-0002-7059-4399"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hugo Ceulemans","raw_affiliation_strings":["Johnson & Johnson, Beerse, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Johnson & Johnson, Beerse, Belgium","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018305257","display_name":"Samuel Kaski","orcid":"https://orcid.org/0000-0003-1925-9154"},"institutions":[{"id":"https://openalex.org/I28407311","display_name":"University of Manchester","ror":"https://ror.org/027m9bs27","country_code":"GB","type":"education","lineage":["https://openalex.org/I28407311"]},{"id":"https://openalex.org/I4210102091","display_name":"Espoo Music Institute","ror":"https://ror.org/017zq4f19","country_code":"FI","type":"education","lineage":["https://openalex.org/I4210102091"]},{"id":"https://openalex.org/I4210124774","display_name":"ElFys (Finland)","ror":"https://ror.org/0277khs39","country_code":"FI","type":"company","lineage":["https://openalex.org/I4210124774"]},{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI","GB"],"is_corresponding":false,"raw_author_name":"Samuel Kaski","raw_affiliation_strings":["Aalto University, Espoo, Finland","ELLIS Institute, Espoo, Finland","University of Manchester, Manchester, United Kingdom"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aalto University, Espoo, Finland","institution_ids":["https://openalex.org/I9927081"]},{"raw_affiliation_string":"ELLIS Institute, Espoo, Finland","institution_ids":["https://openalex.org/I4210124774","https://openalex.org/I4210102091"]},{"raw_affiliation_string":"University of Manchester, Manchester, United Kingdom","institution_ids":["https://openalex.org/I28407311"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5003314826","display_name":"Dorota Herman","orcid":"https://orcid.org/0000-0001-7836-8989"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Dorota Herman","raw_affiliation_strings":["Johnson & Johnson, Beerse, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Johnson & Johnson, Beerse, Belgium","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5101444999","display_name":"Markus Heinonen","orcid":"https://orcid.org/0000-0002-7741-2279"},"institutions":[{"id":"https://openalex.org/I9927081","display_name":"Aalto University","ror":"https://ror.org/020hwjq30","country_code":"FI","type":"education","lineage":["https://openalex.org/I9927081"]}],"countries":["FI"],"is_corresponding":false,"raw_author_name":"Markus Heinonen","raw_affiliation_strings":["Aalto University, Espoo, Finland"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Aalto University, Espoo, Finland","institution_ids":["https://openalex.org/I9927081"]}]}],"institutions":[],"countries_distinct_count":4,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5030874161"],"corresponding_institution_ids":["https://openalex.org/I1330063522","https://openalex.org/I4210160666","https://openalex.org/I9927081"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":0.9002,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.73788139,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":98},"biblio":{"volume":"17","issue":"1","first_page":"119","last_page":"119"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9911999702453613,"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"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.9911999702453613,"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/T12535","display_name":"Machine Learning and Data Classification","score":0.9873999953269958,"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/T10876","display_name":"Fault Detection and Control Systems","score":0.9625999927520752,"subfield":{"id":"https://openalex.org/subfields/2207","display_name":"Control and Systems Engineering"},"field":{"id":"https://openalex.org/fields/22","display_name":"Engineering"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7292221784591675},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.6663451790809631},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.5624293088912964},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4723984897136688},{"id":"https://openalex.org/keywords/transformer","display_name":"Transformer","score":0.46911361813545227},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4532918632030487},{"id":"https://openalex.org/keywords/class","display_name":"Class (philosophy)","score":0.4325670599937439},{"id":"https://openalex.org/keywords/labeled-data","display_name":"Labeled data","score":0.4145606756210327},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.4108804762363434},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.38305380940437317},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.25109708309173584},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.13906341791152954}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7292221784591675},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.6663451790809631},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5624293088912964},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4723984897136688},{"id":"https://openalex.org/C66322947","wikidata":"https://www.wikidata.org/wiki/Q11658","display_name":"Transformer","level":3,"score":0.46911361813545227},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4532918632030487},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.4325670599937439},{"id":"https://openalex.org/C2776145971","wikidata":"https://www.wikidata.org/wiki/Q30673951","display_name":"Labeled data","level":2,"score":0.4145606756210327},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.4108804762363434},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.38305380940437317},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.25109708309173584},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.13906341791152954},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.0},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C165801399","wikidata":"https://www.wikidata.org/wiki/Q25428","display_name":"Voltage","level":2,"score":0.0}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/s13321-025-01048-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01048-7","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01048-7","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:40770816","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40770816","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:pure.atira.dk:publications/369d5b13-5a16-47d1-996a-79837d36e234","is_oa":false,"landing_page_url":"https://research.manchester.ac.uk/en/publications/369d5b13-5a16-47d1-996a-79837d36e234","pdf_url":null,"source":{"id":"https://openalex.org/S4306400662","display_name":"Research Explorer (The University of Manchester)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I28407311","host_organization_name":"University of Manchester","host_organization_lineage":["https://openalex.org/I28407311"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Masood, M A, Nagaraja, A A, Belaid, K, Mesens, N, Ceulemans, H, Kaski, S, Herman, D & Heinonen, M 2025, 'VitroBert: modeling DILI by pretraining BERT on in vitro data', Journal of Cheminformatics, vol. 17, no. 1, 119. https://doi.org/10.1186/s13321-025-01048-7","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:oai:aaltodoc.aalto.fi:123456789/138824","is_oa":true,"landing_page_url":"https://research.aalto.fi/en/publications/3951a14a-4f10-4ccc-8977-8d1b50c7db6f","pdf_url":null,"source":{"id":"https://openalex.org/S4306401663","display_name":"Aaltodoc (Aalto University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I9927081","host_organization_name":"Aalto University","host_organization_lineage":["https://openalex.org/I9927081"],"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":null,"raw_type":"publishedVersion"},{"id":"pmh:oai:doaj.org/article:101a86803fb440a485e4952a65441fed","is_oa":true,"landing_page_url":"https://doaj.org/article/101a86803fb440a485e4952a65441fed","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 1-12 (2025)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12326598","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12326598","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/s13321-025-01048-7","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-025-01048-7","pdf_url":"https://jcheminf.biomedcentral.com/counter/pdf/10.1186/s13321-025-01048-7","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":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.4699999988079071}],"awards":[{"id":"https://openalex.org/G223242278","display_name":null,"funder_award_id":"956832","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"},{"id":"https://openalex.org/G2914985473","display_name":null,"funder_award_id":"EP-W002973-1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"},{"id":"https://openalex.org/G448529986","display_name":null,"funder_award_id":"EP/W002973/1","funder_id":"https://openalex.org/F4320314731","funder_display_name":"UK Research and Innovation"},{"id":"https://openalex.org/G7842005466","display_name":null,"funder_award_id":"Horizon 2020","funder_id":"https://openalex.org/F4320320300","funder_display_name":"European Commission"}],"funders":[{"id":"https://openalex.org/F4320314731","display_name":"UK Research and Innovation","ror":"https://ror.org/001aqnf71"},{"id":"https://openalex.org/F4320320300","display_name":"European Commission","ror":"https://ror.org/00k4n6c32"},{"id":"https://openalex.org/F4320332050","display_name":"Finnish Center for Artificial Intelligence","ror":null},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320335254","display_name":"Horizon 2020","ror":null}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4413028691.pdf","grobid_xml":"https://content.openalex.org/works/W4413028691.grobid-xml"},"referenced_works_count":48,"referenced_works":["https://openalex.org/W114962175","https://openalex.org/W1500036797","https://openalex.org/W1975147762","https://openalex.org/W1976526581","https://openalex.org/W1979392432","https://openalex.org/W1988037271","https://openalex.org/W2007396202","https://openalex.org/W2011257176","https://openalex.org/W2089901490","https://openalex.org/W2092126505","https://openalex.org/W2099536383","https://openalex.org/W2110820547","https://openalex.org/W2145578524","https://openalex.org/W2565367159","https://openalex.org/W2565684601","https://openalex.org/W2806547269","https://openalex.org/W2884561390","https://openalex.org/W2900694120","https://openalex.org/W2901476322","https://openalex.org/W2914415092","https://openalex.org/W2953128081","https://openalex.org/W2963351448","https://openalex.org/W2966357564","https://openalex.org/W2973114758","https://openalex.org/W2974029770","https://openalex.org/W2983879675","https://openalex.org/W3022069365","https://openalex.org/W3030834496","https://openalex.org/W3032781902","https://openalex.org/W3033752684","https://openalex.org/W3080112347","https://openalex.org/W3092036475","https://openalex.org/W3125345344","https://openalex.org/W3207106422","https://openalex.org/W4226159083","https://openalex.org/W4292738946","https://openalex.org/W4297179162","https://openalex.org/W4298009900","https://openalex.org/W4313485929","https://openalex.org/W4321096990","https://openalex.org/W4367042867","https://openalex.org/W4379197245","https://openalex.org/W4385690438","https://openalex.org/W4386408107","https://openalex.org/W4387451180","https://openalex.org/W4388425414","https://openalex.org/W4393169482","https://openalex.org/W4400446175"],"related_works":["https://openalex.org/W4390516098","https://openalex.org/W2181948922","https://openalex.org/W2384362569","https://openalex.org/W2142795561","https://openalex.org/W4205302943","https://openalex.org/W2561132942","https://openalex.org/W2480711475","https://openalex.org/W3155418658","https://openalex.org/W4243199227","https://openalex.org/W4389518428"],"abstract_inverted_index":{"Drug-induced":[0],"liver":[1],"injury":[2],"(DILI)":[3],"presents":[4],"a":[5,22,47,81,88],"significant":[6,101],"challenge":[7],"due":[8],"to":[9,25,62,70,80,95,109],"its":[10],"complexity,":[11],"small":[12],"datasets,":[13],"and":[14,87,127,151],"severe":[15],"class":[16,115],"imbalance.":[17],"While":[18],"unsupervised":[19,96],"pretraining":[20,97],"is":[21],"common":[23],"approach":[24],"learn":[26],"molecular":[27,66,149],"representations":[28,50],"for":[29],"downstream":[30],"tasks,":[31],"it":[32],"often":[33],"lacks":[34],"insights":[35],"into":[36,148],"how":[37],"molecules":[38],"interact":[39],"with":[40],"biological":[41,146],"systems.":[42],"We":[43],"therefore":[44],"introduce":[45],"VitroBERT,":[46],"bidirectional":[48],"encoder":[49],"from":[51],"transformers":[52],"(BERT)":[53],"model":[54,162],"pretrained":[55],"on":[56],"large-scale":[57],"in":[58,72,84,91,105,160],"vitro":[59],"assay":[60],"profiles":[61],"generate":[63],"biologically":[64],"informed":[65],"embeddings.":[67],"When":[68],"leveraged":[69],"predict":[71],"vivo":[73],"DILI":[74],"endpoints,":[75],"these":[76],"embeddings":[77],"delivered":[78],"up":[79],"29%":[82],"improvement":[83,102],"biochemistry-related":[85],"tasks":[86],"16%":[89],"gain":[90],"histopathology":[92],"endpoints":[93],"compared":[94],"(MolBERT).":[98],"However,":[99],"no":[100],"was":[103],"observed":[104],"clinical":[106],"tasks.":[107,168],"Furthermore,":[108],"address":[110],"the":[111,136,142,153],"critical":[112],"issue":[113],"of":[114,144,155,164],"imbalance,":[116],"we":[117],"evaluated":[118],"multiple":[119],"loss":[120,134,158],"functions-including":[121],"BCE,":[122,124],"weighted":[123,128,132],"Focal":[125,129,133],"loss,":[126],"loss-and":[130],"identified":[131],"as":[135],"most":[137],"effective.":[138],"Our":[139],"findings":[140],"demonstrate":[141],"potential":[143],"integrating":[145],"context":[147],"models":[150],"highlight":[152],"importance":[154],"selecting":[156],"appropriate":[157],"functions":[159],"improving":[161],"performance":[163],"highly":[165],"imbalanced":[166],"DILI-related":[167]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-02T08:42:23.175194","created_date":"2025-10-10T00:00:00"}