{"id":"https://openalex.org/W7126238826","doi":"https://doi.org/10.1186/s13321-026-01155-z","title":"Chemical genomics language model toward reliable and explainable compound-protein interaction exploration","display_name":"Chemical genomics language model toward reliable and explainable compound-protein interaction exploration","publication_year":2026,"publication_date":"2026-01-30","ids":{"openalex":"https://openalex.org/W7126238826","doi":"https://doi.org/10.1186/s13321-026-01155-z","pmid":"https://pubmed.ncbi.nlm.nih.gov/41618385"},"language":"en","primary_location":{"id":"doi:10.1186/s13321-026-01155-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-026-01155-z","pdf_url":null,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","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://doi.org/10.1186/s13321-026-01155-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027799892","display_name":"Takuto Koyama","orcid":"https://orcid.org/0000-0002-9569-8370"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takuto Koyama","raw_affiliation_strings":["Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018854552","display_name":"Hayato Tsumura","orcid":null},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hayato Tsumura","raw_affiliation_strings":["Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124440166","display_name":"Ryunosuke Okita","orcid":null},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ryunosuke Okita","raw_affiliation_strings":["Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto, 606-8501, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Pharmaceutical Sciences, Kyoto University, 46-29 Yoshida-Shimo-Adachi-cho, Sakyo-ku, Kyoto, 606-8501, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004701153","display_name":"Kimihiro Yamazaki","orcid":"https://orcid.org/0000-0003-4827-9488"},"institutions":[{"id":"https://openalex.org/I2252096349","display_name":"Fujitsu (Japan)","ror":"https://ror.org/038e2g226","country_code":"JP","type":"company","lineage":["https://openalex.org/I2252096349"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Kimihiro Yamazaki","raw_affiliation_strings":["Fujitsu Limited, 4-1-1 Kamikodanaka, Nakahara-ku, Kawasaki, Kanagawa, 211-8588, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fujitsu Limited, 4-1-1 Kamikodanaka, Nakahara-ku, Kawasaki, Kanagawa, 211-8588, Japan","institution_ids":["https://openalex.org/I2252096349"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124417672","display_name":"Aki Hasegawa","orcid":null},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Aki Hasegawa","raw_affiliation_strings":["Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124328072","display_name":"Keiko Imamura","orcid":null},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4210096362","display_name":"RIKEN BioResource Research Center","ror":"https://ror.org/00s05em53","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210096362","https://openalex.org/I4210110652"]},{"id":"https://openalex.org/I4210126580","display_name":"RIKEN Center for Advanced Intelligence Project","ror":"https://ror.org/03ckxwf91","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210126580"]},{"id":"https://openalex.org/I4210150196","display_name":"Kyoto University Hospital","ror":"https://ror.org/04k6gr834","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210150196"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Keiko Imamura","raw_affiliation_strings":["Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan","Medical\u2011Risk Avoidance Based On iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Tokyo, Japan","iPSC\u2011Based Drug Discovery and Development Team, RIKEN BioResource Research Center (BRC), Kyoto, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan","institution_ids":["https://openalex.org/I4210150196","https://openalex.org/I22299242"]},{"raw_affiliation_string":"Medical\u2011Risk Avoidance Based On iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Tokyo, Japan","institution_ids":["https://openalex.org/I4210126580"]},{"raw_affiliation_string":"iPSC\u2011Based Drug Discovery and Development Team, RIKEN BioResource Research Center (BRC), Kyoto, Japan","institution_ids":["https://openalex.org/I4210096362"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5103511759","display_name":"Takashi Kato","orcid":"https://orcid.org/0009-0007-0097-5923"},"institutions":[{"id":"https://openalex.org/I2252096349","display_name":"Fujitsu (Japan)","ror":"https://ror.org/038e2g226","country_code":"JP","type":"company","lineage":["https://openalex.org/I2252096349"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Takashi Kato","raw_affiliation_strings":["Fujitsu Limited, 4-1-1 Kamikodanaka, Nakahara-ku, Kawasaki, Kanagawa, 211-8588, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Fujitsu Limited, 4-1-1 Kamikodanaka, Nakahara-ku, Kawasaki, Kanagawa, 211-8588, Japan","institution_ids":["https://openalex.org/I2252096349"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124405408","display_name":"Hiroaki Iwata","orcid":null},"institutions":[{"id":"https://openalex.org/I4588055","display_name":"Tottori University","ror":"https://ror.org/024yc3q36","country_code":"JP","type":"education","lineage":["https://openalex.org/I4588055"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Hiroaki Iwata","raw_affiliation_strings":["Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Faculty of Medicine, Tottori University, 86 Nishi-cho, Yonago, Tottori, 683-8503, Japan","institution_ids":["https://openalex.org/I4588055"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5124456440","display_name":"Ryosuke Kojima","orcid":null},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4210116810","display_name":"RIKEN Center for Biosystems Dynamics Research","ror":"https://ror.org/023rffy11","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210116810"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Ryosuke Kojima","raw_affiliation_strings":["Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan","RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan","institution_ids":["https://openalex.org/I22299242"]},{"raw_affiliation_string":"RIKEN Center for Biosystems Dynamics Research, 2-2-3 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan","institution_ids":["https://openalex.org/I4210116810"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5041828364","display_name":"H. Inoue","orcid":null},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4210096362","display_name":"RIKEN BioResource Research Center","ror":"https://ror.org/00s05em53","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210096362","https://openalex.org/I4210110652"]},{"id":"https://openalex.org/I4210126580","display_name":"RIKEN Center for Advanced Intelligence Project","ror":"https://ror.org/03ckxwf91","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210126580"]},{"id":"https://openalex.org/I4210150196","display_name":"Kyoto University Hospital","ror":"https://ror.org/04k6gr834","country_code":"JP","type":"healthcare","lineage":["https://openalex.org/I4210150196"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Haruhisa Inoue","raw_affiliation_strings":["Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan","Medical\u2011Risk Avoidance Based On iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Tokyo, Japan","iPSC\u2011Based Drug Discovery and Development Team, RIKEN BioResource Research Center (BRC), Kyoto, Japan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for iPS Cell Research and Application (CiRA), Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan","institution_ids":["https://openalex.org/I4210150196","https://openalex.org/I22299242"]},{"raw_affiliation_string":"Medical\u2011Risk Avoidance Based On iPS Cells Team, RIKEN Center for Advanced Intelligence Project (AIP), Tokyo, Japan","institution_ids":["https://openalex.org/I4210126580"]},{"raw_affiliation_string":"iPSC\u2011Based Drug Discovery and Development Team, RIKEN BioResource Research Center (BRC), Kyoto, Japan","institution_ids":["https://openalex.org/I4210096362"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053913367","display_name":"Shigeyuki Matsumoto","orcid":"https://orcid.org/0000-0001-9329-6362"},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Shigeyuki Matsumoto","raw_affiliation_strings":["Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan. matsumoto.shigeyuki.4z@kyoto-u.ac.jp"],"raw_orcid":"https://orcid.org/0000-0001-9329-6362","affiliations":[{"raw_affiliation_string":"Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan. matsumoto.shigeyuki.4z@kyoto-u.ac.jp","institution_ids":["https://openalex.org/I22299242"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5103349395","display_name":"Yasushi Okuno","orcid":null},"institutions":[{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4210129730","display_name":"RIKEN Center for Computational Science","ror":"https://ror.org/03r519674","country_code":"JP","type":"facility","lineage":["https://openalex.org/I4210110652","https://openalex.org/I4210129730"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Yasushi Okuno","raw_affiliation_strings":["Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan. okuno.yasushi.4c@kyoto-u.ac.jp","RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan. okuno.yasushi.4c@kyoto-u.ac.jp"],"raw_orcid":"https://orcid.org/0000-0003-3596-4208","affiliations":[{"raw_affiliation_string":"Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan. okuno.yasushi.4c@kyoto-u.ac.jp","institution_ids":["https://openalex.org/I22299242"]},{"raw_affiliation_string":"RIKEN Center for Computational Science, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo, 650-0047, Japan. okuno.yasushi.4c@kyoto-u.ac.jp","institution_ids":["https://openalex.org/I4210129730"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":12,"corresponding_author_ids":["https://openalex.org/A5053913367"],"corresponding_institution_ids":["https://openalex.org/I22299242"],"apc_list":{"value":1290,"currency":"GBP","value_usd":1582},"apc_paid":{"value":1290,"currency":"GBP","value_usd":1582},"fwci":51.8564,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.99578031,"is_in_top_1_percent":true,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"18","issue":"1","first_page":"29","last_page":"29"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.5604000091552734,"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":0.5604000091552734,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.2558000087738037,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.0406000018119812,"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/generalization","display_name":"Generalization","score":0.6431000232696533},{"id":"https://openalex.org/keywords/resource","display_name":"Resource (disambiguation)","score":0.46860000491142273},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.44209998846054077},{"id":"https://openalex.org/keywords/virtual-screening","display_name":"Virtual screening","score":0.42340001463890076},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.420199990272522},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.3828999996185303},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.3580000102519989},{"id":"https://openalex.org/keywords/block","display_name":"Block (permutation group theory)","score":0.3529999852180481}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.8126000165939331},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.6431000232696533},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5519999861717224},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4788999855518341},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.46860000491142273},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.44209998846054077},{"id":"https://openalex.org/C103697762","wikidata":"https://www.wikidata.org/wiki/Q4112105","display_name":"Virtual screening","level":3,"score":0.42340001463890076},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.420199990272522},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3912999927997589},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.3828999996185303},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3580000102519989},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3547999858856201},{"id":"https://openalex.org/C2777210771","wikidata":"https://www.wikidata.org/wiki/Q4927124","display_name":"Block (permutation group theory)","level":2,"score":0.3529999852180481},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.2971000075340271},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.289900004863739},{"id":"https://openalex.org/C51632099","wikidata":"https://www.wikidata.org/wiki/Q3985153","display_name":"Training set","level":2,"score":0.2874999940395355},{"id":"https://openalex.org/C172367668","wikidata":"https://www.wikidata.org/wiki/Q6504956","display_name":"Data visualization","level":3,"score":0.2867000102996826},{"id":"https://openalex.org/C67186912","wikidata":"https://www.wikidata.org/wiki/Q367664","display_name":"Data modeling","level":2,"score":0.2703000009059906},{"id":"https://openalex.org/C179603123","wikidata":"https://www.wikidata.org/wiki/Q1941921","display_name":"Modeling language","level":3,"score":0.2653999924659729},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.258899986743927},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.2563000023365021}],"mesh":[],"locations_count":6,"locations":[{"id":"doi:10.1186/s13321-026-01155-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-026-01155-z","pdf_url":null,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},{"id":"pmid:41618385","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41618385","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:b1c32c2e28234c07982e71be5e7d5256","is_oa":true,"landing_page_url":"https://doaj.org/article/b1c32c2e28234c07982e71be5e7d5256","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics, Vol 18, Iss 1 (2026)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:11730969","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12922394","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:irdb.nii.ac.jp:01221:0007261552","is_oa":true,"landing_page_url":"http://hdl.handle.net/2433/299547","pdf_url":null,"source":{"id":"https://openalex.org/S7407056385","display_name":"Institutional Repositories DataBase (IRDB)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I184597095","host_organization_name":"National Institute of Informatics","host_organization_lineage":["https://openalex.org/I184597095"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12922394","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12922394/","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":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Cheminform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s13321-026-01155-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s13321-026-01155-z","pdf_url":null,"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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Cheminformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G4578889415","display_name":null,"funder_award_id":"22K06112","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"},{"id":"https://openalex.org/G5405343081","display_name":null,"funder_award_id":"JP22bm0804034","funder_id":"https://openalex.org/F4320311405","funder_display_name":"Japan Agency for Medical Research and Development"},{"id":"https://openalex.org/G6772893103","display_name":null,"funder_award_id":"JP24KJ1510","funder_id":"https://openalex.org/F4320334764","funder_display_name":"Japan Society for the Promotion of Science"}],"funders":[{"id":"https://openalex.org/F4320311405","display_name":"Japan Agency for Medical Research and Development","ror":"https://ror.org/004rtk039"},{"id":"https://openalex.org/F4320334764","display_name":"Japan Society for the Promotion of Science","ror":"https://ror.org/00hhkn466"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":45,"referenced_works":["https://openalex.org/W1975147762","https://openalex.org/W1988037271","https://openalex.org/W2031441006","https://openalex.org/W2038264047","https://openalex.org/W2061843861","https://openalex.org/W2064264167","https://openalex.org/W2086286404","https://openalex.org/W2087064593","https://openalex.org/W2096541451","https://openalex.org/W2102461176","https://openalex.org/W2114162221","https://openalex.org/W2134967712","https://openalex.org/W2138512826","https://openalex.org/W2139736926","https://openalex.org/W2163190642","https://openalex.org/W2166410137","https://openalex.org/W2176516200","https://openalex.org/W2194775991","https://openalex.org/W2204695023","https://openalex.org/W2290847742","https://openalex.org/W2342218669","https://openalex.org/W2559588208","https://openalex.org/W2619342418","https://openalex.org/W2767891136","https://openalex.org/W2770647690","https://openalex.org/W2785947426","https://openalex.org/W2899070097","https://openalex.org/W2919115771","https://openalex.org/W2973049920","https://openalex.org/W3018980093","https://openalex.org/W3028589594","https://openalex.org/W3096561213","https://openalex.org/W3177828909","https://openalex.org/W3198923619","https://openalex.org/W3206585172","https://openalex.org/W4224981527","https://openalex.org/W4292265045","https://openalex.org/W4312045033","https://openalex.org/W4313485929","https://openalex.org/W4327550249","https://openalex.org/W4396721167","https://openalex.org/W4399746375","https://openalex.org/W4402265019","https://openalex.org/W4407163143","https://openalex.org/W4411463597"],"related_works":[],"abstract_inverted_index":{"Accurate":[0],"prediction":[1,32,179],"of":[2,103,118,166],"compound-protein":[3],"interactions":[4],"(CPIs)":[5],"is":[6],"crucial":[7,51],"for":[8,130,224],"chemical":[9,42,64],"biology":[10],"and":[11,34,56,65,93,106,139,143,170,189,206,216],"drug":[12,171],"discovery.":[13],"Despite":[14],"recent":[15],"advancements,":[16],"existing":[17],"deep":[18],"learning":[19],"(DL)-based":[20],"CPI":[21,58,128,168,178,204],"models":[22,68],"often":[23],"struggle":[24],"to":[25,47,98,107,195],"simultaneously":[26,182],"achieve":[27],"high":[28,184],"generalization":[29,185],"performance,":[30,186],"quantify":[31],"confidence,":[33],"ensure":[35],"explainability.":[36,190],"Here,":[37],"we":[38,120],"propose":[39],"ChemGLaM,":[40,119],"a":[41,74,86,122,149,176,197,202,221],"genomics":[43],"language":[44,67],"model":[45],"designed":[46],"address":[48],"these":[49],"three":[50],"challenges,":[52],"thereby":[53],"enabling":[54],"reliable":[55],"explainable":[57],"predictions.":[59],"ChemGLaM":[60,97,156],"integrates":[61],"independently":[62],"pre-trained":[63],"protein":[66],"through":[69],"an":[70,158],"interaction":[71],"block":[72],"with":[73],"cross-attention":[75],"mechanism,":[76],"achieving":[77],"near":[78],"state-of-the-art":[79],"performance":[80],"in":[81,148,162,220],"predicting":[82],"novel":[83],"CPIs":[84],"at":[85],"low":[87],"computational":[88],"cost.":[89],"Incorporating":[90],"uncertainty":[91],"estimation":[92],"attention":[94],"visualization":[95],"enables":[96],"enhance":[99],"the":[100,115,164],"success":[101],"rate":[102],"virtual":[104],"screening":[105,223],"provide":[108],"molecular":[109],"insights":[110],"into":[111],"CPIs.":[112],"To":[113],"demonstrate":[114],"practical":[116,146,209],"impact":[117],"constructed":[121],"publicly":[123],"available":[124],"database":[125,205],"containing":[126],"large-scale":[127],"predictions":[129],"every":[131],"possible":[132],"pairing":[133],"between":[134],"all":[135,140],"20,434":[136],"human":[137],"proteins":[138],"11,455":[141],"drugs":[142],"validated":[144],"its":[145,208],"applicability":[147],"case":[150],"study":[151,174],"on":[152],"amyotrophic":[153,225],"lateral":[154,226],"sclerosis.":[155,227],"marks":[157],"important":[159],"step":[160],"forward":[161],"addressing":[163],"challenges":[165],"AI-driven":[167],"exploration":[169],"discovery.Scientific":[172],"ContributionThis":[173],"established":[175],"unified":[177],"framework":[180,194],"that":[181],"achieves":[183],"confidence":[187],"quantification,":[188],"We":[191],"leveraged":[192],"this":[193],"create":[196],"community":[198],"resource":[199],"by":[200,211],"constructing":[201],"comprehensive":[203],"demonstrated":[207],"utility":[210],"successfully":[212],"prioritizing":[213],"hit":[214],"compounds":[215],"deconvoluting":[217],"their":[218],"targets":[219],"phenotypic":[222]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2026-02-01T00:00:00"}
