{"id":"https://openalex.org/W4391835389","doi":"https://doi.org/10.1109/tcbb.2024.3477313","title":"Improving Molecule Generation and Drug Discovery With a Knowledge-Enhanced Generative Model","display_name":"Improving Molecule Generation and Drug Discovery With a Knowledge-Enhanced Generative Model","publication_year":2024,"publication_date":"2024-10-09","ids":{"openalex":"https://openalex.org/W4391835389","doi":"https://doi.org/10.1109/tcbb.2024.3477313","pmid":"https://pubmed.ncbi.nlm.nih.gov/38410649"},"language":"en","primary_location":{"id":"doi:10.1109/tcbb.2024.3477313","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3477313","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["arxiv","crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/2402.08790","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5104701040","display_name":"Aditya Malusare","orcid":null},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Aditya Malusare","raw_affiliation_strings":["Edwardson School of Industrial Engineering and the Institute of Cancer Research, Purdue University, West Lafayette, IN, USA","Institute of Cancer Research, Purdue University, USA"],"raw_orcid":"https://orcid.org/0009-0000-3670-1261","affiliations":[{"raw_affiliation_string":"Edwardson School of Industrial Engineering and the Institute of Cancer Research, Purdue University, West Lafayette, IN, USA","institution_ids":["https://openalex.org/I219193219"]},{"raw_affiliation_string":"Institute of Cancer Research, Purdue University, USA","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064822688","display_name":"Vaneet Aggarwal","orcid":"https://orcid.org/0000-0001-9131-4723"},"institutions":[{"id":"https://openalex.org/I219193219","display_name":"Purdue University West Lafayette","ror":"https://ror.org/02dqehb95","country_code":"US","type":"education","lineage":["https://openalex.org/I219193219"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Vaneet Aggarwal","raw_affiliation_strings":["Edwardson School of Industrial Engineering and the Institute of Cancer Research, Purdue University, West Lafayette, IN, USA","Institute of Cancer Research, Purdue University, USA"],"raw_orcid":"https://orcid.org/0000-0001-9131-4723","affiliations":[{"raw_affiliation_string":"Edwardson School of Industrial Engineering and the Institute of Cancer Research, Purdue University, West Lafayette, IN, USA","institution_ids":["https://openalex.org/I219193219"]},{"raw_affiliation_string":"Institute of Cancer Research, Purdue University, USA","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5104701040"],"corresponding_institution_ids":["https://openalex.org/I219193219"],"apc_list":null,"apc_paid":null,"fwci":1.0301,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.76467827,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"22","issue":"1","first_page":"375","last_page":"381"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9991999864578247,"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":0.9991999864578247,"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":0.9959999918937683,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.934499979019165,"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":0.7724387645721436},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.6661909818649292},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4561440646648407},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4542444944381714},{"id":"https://openalex.org/keywords/generative-model","display_name":"Generative model","score":0.4146078824996948},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.27504870295524597},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.1928102672100067},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.19048964977264404},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.18833374977111816}],"concepts":[{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.7724387645721436},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.6661909818649292},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4561440646648407},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4542444944381714},{"id":"https://openalex.org/C167966045","wikidata":"https://www.wikidata.org/wiki/Q5532625","display_name":"Generative model","level":3,"score":0.4146078824996948},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.27504870295524597},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.1928102672100067},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.19048964977264404},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.18833374977111816},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1109/tcbb.2024.3477313","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbb.2024.3477313","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"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":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38410649","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38410649","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":"ArXiv","raw_type":null},{"id":"pmid:39383070","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39383070","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null},{"id":"pmh:oai:arXiv.org:2402.08790","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2402.08790","pdf_url":"https://arxiv.org/pdf/2402.08790","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"pmh:oai:pubmedcentral.nih.gov:10896363","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10896363","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10896363/pdf/nihpp-2402.08790v2.pdf","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-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"ArXiv","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:2402.08790","is_oa":true,"landing_page_url":"http://arxiv.org/abs/2402.08790","pdf_url":"https://arxiv.org/pdf/2402.08790","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-nc-sa","license_id":"https://openalex.org/licenses/cc-by-nc-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320306542","display_name":"Walther Cancer Foundation","ror":"https://ror.org/02seeba69"},{"id":"https://openalex.org/F4320309036","display_name":"Purdue University","ror":"https://ror.org/02dqehb95"},{"id":"https://openalex.org/F4320337377","display_name":"Office of Advanced Cyberinfrastructure","ror":"https://ror.org/04nh1dc89"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4391835389.pdf"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W1970577443","https://openalex.org/W1975147762","https://openalex.org/W1999798000","https://openalex.org/W2027482274","https://openalex.org/W2034549041","https://openalex.org/W2080635178","https://openalex.org/W2160592148","https://openalex.org/W2184957013","https://openalex.org/W2529996553","https://openalex.org/W2610148085","https://openalex.org/W2728059831","https://openalex.org/W2786016794","https://openalex.org/W2886544065","https://openalex.org/W2887447356","https://openalex.org/W2891820987","https://openalex.org/W2949311246","https://openalex.org/W2964677890","https://openalex.org/W3009321976","https://openalex.org/W3030536242","https://openalex.org/W3036527662","https://openalex.org/W3043230842","https://openalex.org/W3093030756","https://openalex.org/W3093988619","https://openalex.org/W3098269892","https://openalex.org/W3111168552","https://openalex.org/W3116099552","https://openalex.org/W3165146808","https://openalex.org/W4210706440","https://openalex.org/W4211219865","https://openalex.org/W4220798957","https://openalex.org/W4252707176","https://openalex.org/W4283810898","https://openalex.org/W4309413039","https://openalex.org/W4318983406","https://openalex.org/W4379184641","https://openalex.org/W4385851436","https://openalex.org/W4386704875","https://openalex.org/W4387498148","https://openalex.org/W4401041686","https://openalex.org/W6608344535","https://openalex.org/W6679045638","https://openalex.org/W6734023787","https://openalex.org/W6747927160","https://openalex.org/W6748327735","https://openalex.org/W6771848067","https://openalex.org/W6773935867","https://openalex.org/W6780409856","https://openalex.org/W6781649520","https://openalex.org/W6785440645","https://openalex.org/W6801696791","https://openalex.org/W6809966130","https://openalex.org/W6810414285","https://openalex.org/W6838573743","https://openalex.org/W6838745961","https://openalex.org/W6843464061","https://openalex.org/W6852885910","https://openalex.org/W6853146131","https://openalex.org/W6855566964"],"related_works":["https://openalex.org/W4365211920","https://openalex.org/W3014948380","https://openalex.org/W4380551139","https://openalex.org/W4317695495","https://openalex.org/W4287117424","https://openalex.org/W4387506531","https://openalex.org/W2087346071","https://openalex.org/W4238433571","https://openalex.org/W2967848559","https://openalex.org/W4299831724"],"abstract_inverted_index":{"Recent":[0],"advancements":[1],"in":[2,9],"generative":[3,26,46,70,97,112,134],"models":[4,27,71,135],"have":[5],"established":[6],"state-of-the-art":[7,133],"benchmarks":[8],"the":[10,29,81],"generation":[11,141],"of":[12,31,83,106],"molecules":[13],"and":[14,28,44,90,129,139],"novel":[15,58,120],"drug":[16,121],"candidates.":[17],"Despite":[18],"these":[19],"successes,":[20],"a":[21,57,66,76,96,101,115],"significant":[22],"gap":[23],"persists":[24],"between":[25],"utilization":[30],"extensive":[32],"biomedical":[33],"knowledge,":[34],"often":[35],"systematized":[36],"within":[37],"knowledge":[38,84,107],"graphs,":[39],"whose":[40],"potential":[41],"to":[42,79,99],"inform":[43],"enhance":[45],"processes":[47],"has":[48],"not":[49],"been":[50],"realized.":[51],"In":[52],"this":[53,62,92],"paper,":[54],"we":[55],"present":[56],"approach":[59],"that":[60],"bridges":[61],"divide":[63],"by":[64],"developing":[65],"framework":[67,98],"for":[68,118],"knowledge-enhanced":[69],"called":[72],"KARL.":[73],"We":[74],"develop":[75],"scalable":[77],"methodology":[78],"extend":[80],"functionality":[82],"graphs":[85],"while":[86,126],"preserving":[87],"semantic":[88],"integrity,":[89],"incorporate":[91],"contextual":[93],"information":[94],"into":[95],"guide":[100],"diffusion-based":[102],"model.":[103],"The":[104],"integration":[105],"graph":[108],"embeddings":[109],"with":[110],"our":[111],"model":[113],"furnishes":[114],"robust":[116],"mechanism":[117],"producing":[119],"candidates":[122],"possessing":[123],"specific":[124],"characteristics":[125],"ensuring":[127],"validity":[128],"synthesizability.":[130],"KARL":[131],"outperforms":[132],"on":[136],"both":[137],"unconditional":[138],"targeted":[140],"tasks.":[142]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-05-05T08:41:31.759640","created_date":"2024-02-16T00:00:00"}
