{"id":"https://openalex.org/W4411565709","doi":"https://doi.org/10.1021/acs.jcim.5c00430","title":"Advancing Drug Discovery with Enhanced Chemical Understanding via Asymmetric Contrastive Multimodal Learning","display_name":"Advancing Drug Discovery with Enhanced Chemical Understanding via Asymmetric Contrastive Multimodal Learning","publication_year":2025,"publication_date":"2025-06-23","ids":{"openalex":"https://openalex.org/W4411565709","doi":"https://doi.org/10.1021/acs.jcim.5c00430","pmid":"https://pubmed.ncbi.nlm.nih.gov/40548496"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00430","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00430","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00430?ref=article_openPDF","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"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 Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00430?ref=article_openPDF","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100365594","display_name":"Yifei Wang","orcid":"https://orcid.org/0000-0002-8295-5534"},"institutions":[{"id":"https://openalex.org/I6902469","display_name":"Brandeis University","ror":"https://ror.org/05abbep66","country_code":"US","type":"education","lineage":["https://openalex.org/I6902469"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yifei Wang","raw_affiliation_strings":["Brandeis University","Department of Computer Science"],"raw_orcid":"https://orcid.org/0000-0002-8295-5534","affiliations":[{"raw_affiliation_string":"Brandeis University","institution_ids":["https://openalex.org/I6902469"]},{"raw_affiliation_string":"Department of Computer Science","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5108931953","display_name":"Yingying Li","orcid":"https://orcid.org/0000-0002-2978-908X"},"institutions":[{"id":"https://openalex.org/I6902469","display_name":"Brandeis University","ror":"https://ror.org/05abbep66","country_code":"US","type":"education","lineage":["https://openalex.org/I6902469"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yunrui Li","raw_affiliation_strings":["Brandeis University","Department of Computer Science"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Brandeis University","institution_ids":["https://openalex.org/I6902469"]},{"raw_affiliation_string":"Department of Computer Science","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091763718","display_name":"Lin Liu","orcid":"https://orcid.org/0000-0001-7982-6005"},"institutions":[{"id":"https://openalex.org/I97018004","display_name":"Stanford University","ror":"https://ror.org/00f54p054","country_code":"US","type":"education","lineage":["https://openalex.org/I97018004"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lin Liu","raw_affiliation_strings":["Department of Chemistry","Stanford University"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Chemistry","institution_ids":[]},{"raw_affiliation_string":"Stanford University","institution_ids":["https://openalex.org/I97018004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033168441","display_name":"Pengyu Hong","orcid":"https://orcid.org/0000-0002-3177-2754"},"institutions":[{"id":"https://openalex.org/I6902469","display_name":"Brandeis University","ror":"https://ror.org/05abbep66","country_code":"US","type":"education","lineage":["https://openalex.org/I6902469"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pengyu Hong","raw_affiliation_strings":["Brandeis University","Department of Computer Science"],"raw_orcid":"https://orcid.org/0000-0002-3177-2754","affiliations":[{"raw_affiliation_string":"Brandeis University","institution_ids":["https://openalex.org/I6902469"]},{"raw_affiliation_string":"Department of Computer Science","institution_ids":[]}]},{"author_position":"last","author":{"id":null,"display_name":"Hao Xu","orcid":"https://orcid.org/0000-0002-9795-5633"},"institutions":[{"id":"https://openalex.org/I12912129","display_name":"Northeastern University","ror":"https://ror.org/04t5xt781","country_code":"US","type":"education","lineage":["https://openalex.org/I12912129"]},{"id":"https://openalex.org/I136199984","display_name":"Harvard University","ror":"https://ror.org/03vek6s52","country_code":"US","type":"education","lineage":["https://openalex.org/I136199984"]},{"id":"https://openalex.org/I4210148319","display_name":"Woman's Hospital","ror":"https://ror.org/05f9h3891","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I4210148319"]},{"id":"https://openalex.org/I87182695","display_name":"Universidad del Noreste","ror":"https://ror.org/02ahky613","country_code":"MX","type":"education","lineage":["https://openalex.org/I87182695"]}],"countries":["MX","US"],"is_corresponding":true,"raw_author_name":"Hao Xu","raw_affiliation_strings":["Department of Medicine, Brigham and Woman\u2019s Hospital","Department of Physics","Harvard Medical School","Northeastern University","Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States","Department of Medicine, Brigham and Woman's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States"],"raw_orcid":"https://orcid.org/0000-0002-9795-5633","affiliations":[{"raw_affiliation_string":"Department of Medicine, Brigham and Woman\u2019s Hospital","institution_ids":["https://openalex.org/I4210148319"]},{"raw_affiliation_string":"Department of Physics","institution_ids":[]},{"raw_affiliation_string":"Harvard Medical School","institution_ids":["https://openalex.org/I136199984"]},{"raw_affiliation_string":"Northeastern University","institution_ids":["https://openalex.org/I87182695"]},{"raw_affiliation_string":"Department of Physics, Northeastern University, Boston, Massachusetts 02115, United States","institution_ids":["https://openalex.org/I12912129"]},{"raw_affiliation_string":"Department of Medicine, Brigham and Woman's Hospital, Harvard Medical School, Boston, Massachusetts 02115, United States","institution_ids":["https://openalex.org/I4210148319"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":5,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I12912129","https://openalex.org/I136199984","https://openalex.org/I4210148319","https://openalex.org/I87182695"],"apc_list":null,"apc_paid":null,"fwci":6.2656,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.96640722,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":96,"max":99},"biblio":{"volume":"65","issue":"13","first_page":"6547","last_page":"6557"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.998199999332428,"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":0.998199999332428,"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/T11550","display_name":"Text and Document Classification Technologies","score":0.968999981880188,"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/T10911","display_name":"Chemical Synthesis and Analysis","score":0.9664000272750854,"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/drug-discovery","display_name":"Drug discovery","score":0.7422710061073303},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.476977676153183},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.45442795753479004},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.35439950227737427},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3290434181690216},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.3265429735183716},{"id":"https://openalex.org/keywords/psychology","display_name":"Psychology","score":0.32256871461868286},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.20874321460723877},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.1696247160434723},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.16153979301452637},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1455599069595337}],"concepts":[{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.7422710061073303},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.476977676153183},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.45442795753479004},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.35439950227737427},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3290434181690216},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.3265429735183716},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.32256871461868286},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.20874321460723877},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.1696247160434723},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.16153979301452637},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1455599069595337}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.5c00430","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00430","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00430?ref=article_openPDF","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"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 Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40548496","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40548496","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 chemical information and modeling","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:12264933","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/12264933","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-nc-nd","license_id":"https://openalex.org/licenses/cc-by-nc-nd","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.5c00430","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00430","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.5c00430?ref=article_openPDF","source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"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 Chemical Information and Modeling","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3069889119","display_name":null,"funder_award_id":"1920147","funder_id":"https://openalex.org/F4320337377","funder_display_name":"Office of Advanced Cyberinfrastructure"},{"id":"https://openalex.org/G4746626639","display_name":"MRI: Acquisition of a GPU-Accelerated Research Cluster","funder_award_id":"1920147","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G5736883624","display_name":null,"funder_award_id":"OAC-1920147","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310134","display_name":"Brandeis University","ror":"https://ror.org/05abbep66"},{"id":"https://openalex.org/F4320337377","display_name":"Office of Advanced Cyberinfrastructure","ror":"https://ror.org/04nh1dc89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4411565709.pdf","grobid_xml":"https://content.openalex.org/works/W4411565709.grobid-xml"},"referenced_works_count":52,"referenced_works":["https://openalex.org/W1975147762","https://openalex.org/W1981276685","https://openalex.org/W2075843680","https://openalex.org/W2096733369","https://openalex.org/W2594183968","https://openalex.org/W2773405722","https://openalex.org/W2964007201","https://openalex.org/W2981851019","https://openalex.org/W2990623796","https://openalex.org/W3009928773","https://openalex.org/W3012107310","https://openalex.org/W3087318293","https://openalex.org/W3100078588","https://openalex.org/W3116202926","https://openalex.org/W3138683983","https://openalex.org/W3153673236","https://openalex.org/W3165630607","https://openalex.org/W3174146526","https://openalex.org/W3203895579","https://openalex.org/W3211728852","https://openalex.org/W3211951295","https://openalex.org/W3215187068","https://openalex.org/W4206042814","https://openalex.org/W4210737721","https://openalex.org/W4214868967","https://openalex.org/W4224035735","https://openalex.org/W4285078220","https://openalex.org/W4293821372","https://openalex.org/W4295846611","https://openalex.org/W4296551289","https://openalex.org/W4300563891","https://openalex.org/W4304731455","https://openalex.org/W4307468223","https://openalex.org/W4308885870","https://openalex.org/W4309218736","https://openalex.org/W4312933868","https://openalex.org/W4315646977","https://openalex.org/W4321370919","https://openalex.org/W4362471278","https://openalex.org/W4362579348","https://openalex.org/W4362598872","https://openalex.org/W4366366661","https://openalex.org/W4376270841","https://openalex.org/W4381679608","https://openalex.org/W4383888061","https://openalex.org/W4387579216","https://openalex.org/W4388623498","https://openalex.org/W4389100943","https://openalex.org/W4390456525","https://openalex.org/W4393371966","https://openalex.org/W4394606408","https://openalex.org/W4402352439"],"related_works":["https://openalex.org/W2480711475","https://openalex.org/W4206379684","https://openalex.org/W2061997414","https://openalex.org/W1587522533","https://openalex.org/W2366105490","https://openalex.org/W2153190755","https://openalex.org/W2580680567","https://openalex.org/W2803627340","https://openalex.org/W2121182182","https://openalex.org/W3204019825"],"abstract_inverted_index":{"The":[0],"versatility":[1],"of":[2,25,68,103,122,149,187],"multimodal":[3,47],"deep":[4],"learning":[5,48,72,114],"holds":[6],"tremendous":[7],"promise":[8],"for":[9,194],"advancing":[10],"scientific":[11],"research":[12,199],"and":[13,39,58,91,129,144,165,190,200],"practical":[14],"applications.":[15],"As":[16],"this":[17,123],"field":[18],"continues":[19],"to":[20,29,54,73,81,111,175],"evolve,":[21],"the":[22,66,101,120,146,184,192],"collective":[23],"power":[24,67,148],"cross-modal":[26],"analysis":[27],"promises":[28],"drive":[30],"transformative":[31],"innovations,":[32],"opening":[33],"new":[34],"frontiers":[35],"in":[36,61,141,158,197],"chemical":[37,79,88,105,139,185,198],"understanding":[38,57],"drug":[40,62,201],"discovery.":[41,63,202],"Hence,":[42],"we":[43],"introduce":[44],"asymmetric":[45,70],"contrastive":[46,71],"(ACML),":[49],"a":[50,92],"specifically":[51],"designed":[52],"approach":[53],"enhance":[55],"molecular":[56,82,159,177],"accelerate":[59],"advancements":[60,196],"ACML":[64,99,134,171],"harnesses":[65],"effective":[69],"seamlessly":[74],"transfer":[75],"information":[76],"from":[77,107,163],"various":[78],"modalities":[80,189],"graph":[83,94,142,150],"representations.":[84],"By":[85],"combining":[86],"pretrained":[87],"unimodal":[89],"encoders":[90],"shallow-designed":[93],"encoder":[95],"with":[96,115],"5":[97],"layers,":[98],"facilitates":[100],"assimilation":[102],"coordinated":[104],"semantics":[106,140,186],"different":[108],"modalities,":[109],"leading":[110],"comprehensive":[112],"representation":[113],"efficient":[116],"training.":[117],"We":[118],"demonstrate":[119],"effectiveness":[121],"framework":[124],"through":[125],"large-scale":[126],"cross-modality":[127],"retrieval":[128],"isomer":[130],"discrimination":[131],"tasks.":[132],"Additionally,":[133],"enhances":[135],"interpretability":[136],"by":[137,155],"revealing":[138],"presentations":[143],"bolsters":[145],"expressive":[147],"neural":[151],"networks,":[152],"as":[153],"evidenced":[154],"improved":[156],"performance":[157],"property":[160],"prediction":[161],"tasks":[162],"MoleculeNet":[164],"Therapeutics":[166],"Data":[167],"Commons":[168],"(TDC).":[169],"Ultimately,":[170],"exemplifies":[172],"its":[173],"potential":[174],"revolutionize":[176],"representational":[178],"learning,":[179],"offering":[180],"deeper":[181],"insights":[182],"into":[183],"diverse":[188],"paving":[191],"way":[193],"groundbreaking":[195]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":3}],"updated_date":"2026-06-22T08:00:12.763002","created_date":"2025-10-10T00:00:00"}
