{"id":"https://openalex.org/W4416263560","doi":"https://doi.org/10.1021/acs.jcim.5c02053","title":"REINFORCE-ING Chemical Language Models for Drug Discovery","display_name":"REINFORCE-ING Chemical Language Models for Drug Discovery","publication_year":2025,"publication_date":"2025-11-16","ids":{"openalex":"https://openalex.org/W4416263560","doi":"https://doi.org/10.1021/acs.jcim.5c02053","pmid":"https://pubmed.ncbi.nlm.nih.gov/41241844"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c02053","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02053","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","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://doi.org/10.1021/acs.jcim.5c02053","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5064256420","display_name":"Morgan Thomas","orcid":"https://orcid.org/0000-0002-1610-3499"},"institutions":[{"id":"https://openalex.org/I176601375","display_name":"Khalifa University of Science and Technology","ror":"https://ror.org/05hffr360","country_code":"AE","type":"education","lineage":["https://openalex.org/I176601375"]},{"id":"https://openalex.org/I2801864671","display_name":"Barcelona Biomedical Research Park","ror":"https://ror.org/05sajct49","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801864671"]}],"countries":["AE","ES"],"is_corresponding":true,"raw_author_name":"Morgan Thomas","raw_affiliation_strings":["Computational Science Laboratory, Barcelona Biomedical Research Park (PRBB), Universitat Pompeu Fabra, C Dr. Aiguader 88, 08003 Barcelona, Spain","Department of Medical Sciences","Khalifa University of Science and Technology","Department of Medical SciencesKhalifa University of Science and Technology, 127788 Abu Dhabi, UAE"],"raw_orcid":"https://orcid.org/0000-0002-1610-3499","affiliations":[{"raw_affiliation_string":"Computational Science Laboratory, Barcelona Biomedical Research Park (PRBB), Universitat Pompeu Fabra, C Dr. Aiguader 88, 08003 Barcelona, Spain","institution_ids":["https://openalex.org/I2801864671"]},{"raw_affiliation_string":"Department of Medical Sciences","institution_ids":[]},{"raw_affiliation_string":"Khalifa University of Science and Technology","institution_ids":["https://openalex.org/I176601375"]},{"raw_affiliation_string":"Department of Medical SciencesKhalifa University of Science and Technology, 127788 Abu Dhabi, UAE","institution_ids":["https://openalex.org/I176601375"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020298420","display_name":"Albert Bou","orcid":"https://orcid.org/0000-0001-6027-4538"},"institutions":[{"id":"https://openalex.org/I2801864671","display_name":"Barcelona Biomedical Research Park","ror":"https://ror.org/05sajct49","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801864671"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Albert Bou","raw_affiliation_strings":["Computational Science Laboratory, Barcelona Biomedical Research Park (PRBB), Universitat Pompeu Fabra, C Dr. Aiguader 88, 08003 Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0001-6027-4538","affiliations":[{"raw_affiliation_string":"Computational Science Laboratory, Barcelona Biomedical Research Park (PRBB), Universitat Pompeu Fabra, C Dr. Aiguader 88, 08003 Barcelona, Spain","institution_ids":["https://openalex.org/I2801864671"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5072476426","display_name":"Jos\u00e9 Carlos G\u00f3mez-Tamayo","orcid":"https://orcid.org/0000-0003-4709-6030"},"institutions":[{"id":"https://openalex.org/I137982388","display_name":"Janssen (Belgium)","ror":"https://ror.org/04yzcpd71","country_code":"BE","type":"company","lineage":["https://openalex.org/I1330063522","https://openalex.org/I137982388"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Jose Carlos G\u00f3mez-Tamayo","raw_affiliation_strings":["In Silico Discovery, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"In Silico Discovery, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium","institution_ids":["https://openalex.org/I137982388"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5022201149","display_name":"Gary Tresadern","orcid":"https://orcid.org/0000-0002-4801-1644"},"institutions":[{"id":"https://openalex.org/I137982388","display_name":"Janssen (Belgium)","ror":"https://ror.org/04yzcpd71","country_code":"BE","type":"company","lineage":["https://openalex.org/I1330063522","https://openalex.org/I137982388"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Gary Tresadern","raw_affiliation_strings":["In Silico Discovery, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium"],"raw_orcid":"https://orcid.org/0000-0002-4801-1644","affiliations":[{"raw_affiliation_string":"In Silico Discovery, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium","institution_ids":["https://openalex.org/I137982388"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063961921","display_name":"Mazen Ahmad","orcid":"https://orcid.org/0000-0003-4010-7227"},"institutions":[{"id":"https://openalex.org/I137982388","display_name":"Janssen (Belgium)","ror":"https://ror.org/04yzcpd71","country_code":"BE","type":"company","lineage":["https://openalex.org/I1330063522","https://openalex.org/I137982388"]}],"countries":["BE"],"is_corresponding":false,"raw_author_name":"Mazen Ahmad","raw_affiliation_strings":["In Silico Discovery, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium"],"raw_orcid":"https://orcid.org/0000-0003-4010-7227","affiliations":[{"raw_affiliation_string":"In Silico Discovery, Janssen Research & Development, Janssen Pharmaceutica N. V., Turnhoutseweg 30, B-2340 Beerse, Belgium","institution_ids":["https://openalex.org/I137982388"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5027026045","display_name":"Gianni De Fabritiis","orcid":"https://orcid.org/0000-0003-3913-4877"},"institutions":[{"id":"https://openalex.org/I11932220","display_name":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats","ror":"https://ror.org/0371hy230","country_code":"ES","type":"nonprofit","lineage":["https://openalex.org/I11932220"]},{"id":"https://openalex.org/I2801864671","display_name":"Barcelona Biomedical Research Park","ror":"https://ror.org/05sajct49","country_code":"ES","type":"facility","lineage":["https://openalex.org/I2801864671"]},{"id":"https://openalex.org/I4210153560","display_name":"Acellera (Spain)","ror":"https://ror.org/051pfzb30","country_code":"ES","type":"company","lineage":["https://openalex.org/I4210153560"]}],"countries":["ES"],"is_corresponding":true,"raw_author_name":"Gianni De Fabritiis","raw_affiliation_strings":["Acellera Labs, C Dr Trueta 183, 08005 Barcelona, Spain","Computational Science Laboratory, Barcelona Biomedical Research Park (PRBB), Universitat Pompeu Fabra, C Dr. Aiguader 88, 08003 Barcelona, Spain","Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain"],"raw_orcid":"https://orcid.org/0000-0003-3913-4877","affiliations":[{"raw_affiliation_string":"Acellera Labs, C Dr Trueta 183, 08005 Barcelona, Spain","institution_ids":["https://openalex.org/I4210153560"]},{"raw_affiliation_string":"Computational Science Laboratory, Barcelona Biomedical Research Park (PRBB), Universitat Pompeu Fabra, C Dr. Aiguader 88, 08003 Barcelona, Spain","institution_ids":["https://openalex.org/I2801864671"]},{"raw_affiliation_string":"Instituci\u00f3 Catalana de Recerca i Estudis Avan\u00e7ats (ICREA), Passeig Lluis Companys 23, 08010 Barcelona, Spain","institution_ids":["https://openalex.org/I11932220"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5027026045","https://openalex.org/A5064256420"],"corresponding_institution_ids":["https://openalex.org/I11932220","https://openalex.org/I176601375","https://openalex.org/I2801864671","https://openalex.org/I4210153560"],"apc_list":null,"apc_paid":null,"fwci":1.3257,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.86931804,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":95},"biblio":{"volume":"65","issue":"23","first_page":"12752","last_page":"12763"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.49549999833106995,"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":0.49549999833106995,"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":0.3456000089645386,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.019200000911951065,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.772599995136261},{"id":"https://openalex.org/keywords/traverse","display_name":"Traverse","score":0.6797000169754028},{"id":"https://openalex.org/keywords/reinforcement-learning","display_name":"Reinforcement learning","score":0.6241999864578247},{"id":"https://openalex.org/keywords/chemical-space","display_name":"Chemical space","score":0.605400025844574},{"id":"https://openalex.org/keywords/language-model","display_name":"Language model","score":0.5612000226974487}],"concepts":[{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.772599995136261},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.746399998664856},{"id":"https://openalex.org/C176809094","wikidata":"https://www.wikidata.org/wiki/Q15401496","display_name":"Traverse","level":2,"score":0.6797000169754028},{"id":"https://openalex.org/C97541855","wikidata":"https://www.wikidata.org/wiki/Q830687","display_name":"Reinforcement learning","level":2,"score":0.6241999864578247},{"id":"https://openalex.org/C99726746","wikidata":"https://www.wikidata.org/wiki/Q906396","display_name":"Chemical space","level":3,"score":0.605400025844574},{"id":"https://openalex.org/C137293760","wikidata":"https://www.wikidata.org/wiki/Q3621696","display_name":"Language model","level":2,"score":0.5612000226974487},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5501999855041504},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5275999903678894},{"id":"https://openalex.org/C8642999","wikidata":"https://www.wikidata.org/wiki/Q4171168","display_name":"Hyperparameter","level":2,"score":0.38109999895095825},{"id":"https://openalex.org/C2776135515","wikidata":"https://www.wikidata.org/wiki/Q17143721","display_name":"Regularization (linguistics)","level":2,"score":0.36169999837875366},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3294999897480011},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.266400009393692},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.26579999923706055}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008956","descriptor_name":"Models, Chemical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012054","descriptor_name":"Reinforcement, Psychology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012054","descriptor_name":"Reinforcement, Psychology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012054","descriptor_name":"Reinforcement, Psychology","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.5c02053","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02053","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:41241844","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41241844","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:12690592","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12690592/","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 Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1021/acs.jcim.5c02053","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c02053","pdf_url":null,"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","license_id":"https://openalex.org/licenses/cc-by","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/G8530933779","display_name":null,"funder_award_id":"HBC.2021.1123","funder_id":"https://openalex.org/F4320313460","funder_display_name":"Agentschap Innoveren en Ondernemen"}],"funders":[{"id":"https://openalex.org/F4320313460","display_name":"Agentschap Innoveren en Ondernemen","ror":"https://ror.org/032xdry56"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W1975147762","https://openalex.org/W2034549041","https://openalex.org/W2050972073","https://openalex.org/W2090869973","https://openalex.org/W2096541451","https://openalex.org/W2165810843","https://openalex.org/W2303511142","https://openalex.org/W2568182039","https://openalex.org/W2578240541","https://openalex.org/W2610148085","https://openalex.org/W2736601468","https://openalex.org/W2773987374","https://openalex.org/W2895677720","https://openalex.org/W2900694120","https://openalex.org/W2964067469","https://openalex.org/W3009321976","https://openalex.org/W3094686696","https://openalex.org/W3101155908","https://openalex.org/W3103098434","https://openalex.org/W3116865743","https://openalex.org/W3127493072","https://openalex.org/W3133989558","https://openalex.org/W3185391990","https://openalex.org/W4221062742","https://openalex.org/W4239714346","https://openalex.org/W4241811150","https://openalex.org/W4283270512","https://openalex.org/W4300861533","https://openalex.org/W4310819703","https://openalex.org/W4318952054","https://openalex.org/W4376129086","https://openalex.org/W4392121102","https://openalex.org/W4393317648","https://openalex.org/W4394994059","https://openalex.org/W4396641782","https://openalex.org/W4396815997","https://openalex.org/W4399175418","https://openalex.org/W4403570743","https://openalex.org/W4411463597","https://openalex.org/W4411887163"],"related_works":[],"abstract_inverted_index":{"Chemical":[0],"language":[1,147],"models,":[2],"combined":[3],"with":[4],"reinforcement":[5],"learning":[6,108],"(RL),":[7],"have":[8],"shown":[9],"significant":[10],"promise":[11],"to":[12,63,78,101,141,145],"efficiently":[13],"traverse":[14],"large":[15],"chemical":[16,146],"spaces":[17],"for":[18,32,92,149],"drug":[19,34,103,150],"discovery.":[20,151],"However,":[21],"the":[22,42,45,50,129,134],"performance":[23],"of":[24,44,52],"various":[25],"RL":[26,56,87,125,144],"algorithms":[27],"and":[28,66,84,94,132],"their":[29],"best":[30],"practices":[31],"practical":[33,102],"discovery":[35,104],"are":[36],"still":[37],"unclear.":[38],"Here,":[39],"starting":[40],"from":[41,55],"principles":[43],"REINFORCE":[46,79],"algorithm,":[47],"we":[48,97],"investigate":[49],"effect":[51],"different":[53],"components":[54],"theory":[57],"including":[58],"experience":[59],"replay,":[60],"hill-climbing,":[61],"baselines":[62],"reduce":[64],"variance,":[65],"alternative":[67],"reward":[68,120],"shaping.":[69],"We":[70,122],"propose":[71],"a":[72,119,139],"new":[73],"regularization":[74],"method":[75],"more":[76],"aligned":[77],"than":[80],"current":[81],"standard":[82],"practices,":[83],"demonstrate":[85],"how":[86],"hyperparameters":[88],"can":[89],"be":[90],"fine-tuned":[91],"effectiveness":[93],"efficiency.":[95],"Lastly,":[96],"apply":[98],"our":[99,124],"learnings":[100],"by":[105,115],"demonstrating":[106],"enhanced":[107],"efficiency":[109],"on":[110],"frontier":[111],"binding":[112],"affinity":[113],"models":[114,126,148],"using":[116],"Boltz2":[117],"as":[118,138],"model.":[121],"share":[123],"used":[127],"in":[128],"ACEGEN":[130],"repository,":[131],"hope":[133],"experiments":[135],"here":[136],"act":[137],"guide":[140],"researchers":[142],"applying":[143]},"counts_by_year":[{"year":2025,"cited_by_count":1}],"updated_date":"2025-12-10T02:45:41.426853","created_date":"2025-11-16T00:00:00"}
