{"id":"https://openalex.org/W3096163555","doi":"https://doi.org/10.1021/acs.jcim.0c00681","title":"Semi-supervised Hierarchical Drug Embedding in Hyperbolic Space","display_name":"Semi-supervised Hierarchical Drug Embedding in Hyperbolic Space","publication_year":2020,"publication_date":"2020-11-03","ids":{"openalex":"https://openalex.org/W3096163555","doi":"https://doi.org/10.1021/acs.jcim.0c00681","mag":"3096163555","pmid":"https://pubmed.ncbi.nlm.nih.gov/33140969"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.0c00681","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00681","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":null,"license_id":null,"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":"green","oa_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7943198","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5068979281","display_name":"Ke Yu","orcid":"https://orcid.org/0000-0001-9882-5729"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Ke Yu","raw_affiliation_strings":["Intelligent Systems Program, School of Computing and Information, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States"],"affiliations":[{"raw_affiliation_string":"Intelligent Systems Program, School of Computing and Information, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5036362467","display_name":"Shyam Visweswaran","orcid":"https://orcid.org/0000-0002-2079-8684"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Shyam Visweswaran","raw_affiliation_strings":["Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States","Intelligent Systems Program, School of Computing and Information, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Intelligent Systems Program, School of Computing and Information, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States","institution_ids":["https://openalex.org/I170201317"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5031717623","display_name":"Kayhan Batmanghelich","orcid":"https://orcid.org/0000-0001-9893-9136"},"institutions":[{"id":"https://openalex.org/I170201317","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305","country_code":"US","type":"education","lineage":["https://openalex.org/I170201317"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Kayhan Batmanghelich","raw_affiliation_strings":["Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States","Intelligent Systems Program, School of Computing and Information, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States"],"affiliations":[{"raw_affiliation_string":"Department of Biomedical Informatics, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States","institution_ids":["https://openalex.org/I170201317"]},{"raw_affiliation_string":"Intelligent Systems Program, School of Computing and Information, University of Pittsburgh, Pittsburgh, Pennsylvania 15206, United States","institution_ids":["https://openalex.org/I170201317"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5031717623","https://openalex.org/A5036362467","https://openalex.org/A5068979281"],"corresponding_institution_ids":["https://openalex.org/I170201317"],"apc_list":null,"apc_paid":null,"fwci":1.8765,"has_fulltext":false,"cited_by_count":28,"citation_normalized_percentile":{"value":0.89163549,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"60","issue":"12","first_page":"5647","last_page":"5657"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":1.0,"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":1.0,"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":0.9912999868392944,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.9864000082015991,"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/embedding","display_name":"Embedding","score":0.6763364672660828},{"id":"https://openalex.org/keywords/chemical-space","display_name":"Chemical space","score":0.6450214385986328},{"id":"https://openalex.org/keywords/hierarchy","display_name":"Hierarchy","score":0.6227315664291382},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5671629905700684},{"id":"https://openalex.org/keywords/drug","display_name":"Drug","score":0.4990673065185547},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.48889270424842834},{"id":"https://openalex.org/keywords/tree","display_name":"Tree (set theory)","score":0.46878114342689514},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.44750508666038513},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.43978047370910645},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4294581413269043},{"id":"https://openalex.org/keywords/space","display_name":"Space (punctuation)","score":0.42587965726852417},{"id":"https://openalex.org/keywords/similarity","display_name":"Similarity (geometry)","score":0.41658827662467957},{"id":"https://openalex.org/keywords/cheminformatics","display_name":"Cheminformatics","score":0.41183972358703613},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.344846248626709},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.30288100242614746},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.22214791178703308},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.20041048526763916},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16177904605865479},{"id":"https://openalex.org/keywords/pharmacology","display_name":"Pharmacology","score":0.0824550986289978}],"concepts":[{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.6763364672660828},{"id":"https://openalex.org/C99726746","wikidata":"https://www.wikidata.org/wiki/Q906396","display_name":"Chemical space","level":3,"score":0.6450214385986328},{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.6227315664291382},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5671629905700684},{"id":"https://openalex.org/C2780035454","wikidata":"https://www.wikidata.org/wiki/Q8386","display_name":"Drug","level":2,"score":0.4990673065185547},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.48889270424842834},{"id":"https://openalex.org/C113174947","wikidata":"https://www.wikidata.org/wiki/Q2859736","display_name":"Tree (set theory)","level":2,"score":0.46878114342689514},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.44750508666038513},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.43978047370910645},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4294581413269043},{"id":"https://openalex.org/C2778572836","wikidata":"https://www.wikidata.org/wiki/Q380933","display_name":"Space (punctuation)","level":2,"score":0.42587965726852417},{"id":"https://openalex.org/C103278499","wikidata":"https://www.wikidata.org/wiki/Q254465","display_name":"Similarity (geometry)","level":3,"score":0.41658827662467957},{"id":"https://openalex.org/C68762167","wikidata":"https://www.wikidata.org/wiki/Q910164","display_name":"Cheminformatics","level":2,"score":0.41183972358703613},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.344846248626709},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.30288100242614746},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.22214791178703308},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.20041048526763916},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16177904605865479},{"id":"https://openalex.org/C98274493","wikidata":"https://www.wikidata.org/wiki/Q128406","display_name":"Pharmacology","level":1,"score":0.0824550986289978},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C115961682","wikidata":"https://www.wikidata.org/wiki/Q860623","display_name":"Image (mathematics)","level":2,"score":0.0},{"id":"https://openalex.org/C34447519","wikidata":"https://www.wikidata.org/wiki/Q179522","display_name":"Market economy","level":1,"score":0.0},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D004364","descriptor_name":"Pharmaceutical Preparations","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058492","descriptor_name":"Drug Repositioning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D064420","descriptor_name":"Drug-Related Side Effects and Adverse Reactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.0c00681","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.0c00681","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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:33140969","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/33140969","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:7943198","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7943198","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"}],"best_oa_location":{"id":"pmh:oai:pubmedcentral.nih.gov:7943198","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7943198","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"J Chem Inf Model","raw_type":"Text"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1218672444","display_name":null,"funder_award_id":"1839332 Tripod+X","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G2642891134","display_name":null,"funder_award_id":"R01HL141813","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G6180952742","display_name":null,"funder_award_id":"R01LM012095","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310174","display_name":"University of Pittsburgh","ror":"https://ror.org/01an3r305"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":48,"referenced_works":["https://openalex.org/W1224843282","https://openalex.org/W1516111018","https://openalex.org/W1950993160","https://openalex.org/W1975147762","https://openalex.org/W1984994707","https://openalex.org/W1988037271","https://openalex.org/W1990451437","https://openalex.org/W2027482274","https://openalex.org/W2087640086","https://openalex.org/W2128999403","https://openalex.org/W2136127280","https://openalex.org/W2145578524","https://openalex.org/W2150854591","https://openalex.org/W2151697120","https://openalex.org/W2157177751","https://openalex.org/W2157331557","https://openalex.org/W2444690946","https://openalex.org/W2526253916","https://openalex.org/W2529996553","https://openalex.org/W2578240541","https://openalex.org/W2594183968","https://openalex.org/W2604977777","https://openalex.org/W2607707626","https://openalex.org/W2612436700","https://openalex.org/W2612690371","https://openalex.org/W2753633147","https://openalex.org/W2765224015","https://openalex.org/W2786016794","https://openalex.org/W2797520557","https://openalex.org/W2801091715","https://openalex.org/W2884430236","https://openalex.org/W2896002881","https://openalex.org/W2937307539","https://openalex.org/W2940242941","https://openalex.org/W2948646817","https://openalex.org/W2950635152","https://openalex.org/W2950704620","https://openalex.org/W2956769762","https://openalex.org/W2956961449","https://openalex.org/W2963448675","https://openalex.org/W2966357564","https://openalex.org/W2999905431","https://openalex.org/W3003906593","https://openalex.org/W3005417975","https://openalex.org/W3021857949","https://openalex.org/W3045522182","https://openalex.org/W3098269892","https://openalex.org/W4289436753"],"related_works":["https://openalex.org/W4382246684","https://openalex.org/W4387845407","https://openalex.org/W2902857455","https://openalex.org/W4207004502","https://openalex.org/W4212982662","https://openalex.org/W2160244398","https://openalex.org/W2907885506","https://openalex.org/W2022444336","https://openalex.org/W2601867172","https://openalex.org/W4207063555"],"abstract_inverted_index":{"Learning":[0],"accurate":[1],"drug":[2,11,16,20,64,74,82,89,179,217],"representations":[3,65,75],"is":[4,22,102,164],"essential":[5],"for":[6,166],"tasks":[7],"such":[8],"as":[9],"computational":[10],"repositioning":[12],"and":[13,71,109,113,142,172,187,223],"prediction":[14],"of":[15,29,95,107,124,140,156,202,228],"side":[17,226],"effects.":[18],"A":[19],"hierarchy":[21,123,151],"a":[23,34,81,87],"valuable":[24],"source":[25],"that":[26,39,91,101,117,176,215,233],"encodes":[27],"knowledge":[28],"relations":[30,116,191],"among":[31,192],"drugs":[32,38,108,126,157,208],"in":[33,62,80,120,158,239],"tree-like":[35],"structure":[36,186],"where":[37],"act":[40],"on":[41],"the":[42,46,52,130,137,144,150,154,177,184,189,199,210],"same":[43,47,53],"organs,":[44],"treat":[45],"disease,":[48],"or":[49],"bind":[50],"to":[51,135,152],"biological":[54],"target":[55],"are":[56,118],"grouped":[57],"together.":[58],"However,":[59],"its":[60],"utility":[61],"learning":[63],"has":[66],"not":[67],"yet":[68],"been":[69],"explored,":[70],"currently":[72],"described":[73],"cannot":[76],"place":[77],"novel":[78,203],"molecules":[79,111,141,204],"hierarchy.":[83],"Here,":[84],"we":[85],"develop":[86],"semi-supervised":[88],"embedding":[90,180,211,218],"incorporates":[92],"two":[93],"sources":[94],"information:":[96],"(1)":[97],"underlying":[98],"chemical":[99,105,138,185],"grammar":[100],"inferred":[103],"from":[104,149,209],"structures":[106,139],"drug-like":[110],"(unsupervised)":[112],"(2)":[114],"hierarchical":[115,168,190],"encoded":[119],"an":[121],"expert-crafted":[122],"approved":[125],"(supervised).":[127],"We":[128,213,231],"use":[129,143],"Variational":[131],"Auto-Encoder":[132],"(VAE)":[133],"framework":[134],"encode":[136],"drug-drug":[145],"similarity":[146],"information":[147],"obtained":[148],"induce":[153],"clustering":[155],"hyperbolic":[159,162],"space.":[160,212],"The":[161],"space":[163],"amenable":[165],"encoding":[167],"relations.":[169],"Both":[170],"quantitative":[171],"qualitative":[173],"results":[174],"support":[175],"learned":[178],"can":[181,197,219],"accurately":[182],"reproduce":[183],"recapitulate":[188],"drugs.":[193,230],"Furthermore,":[194],"our":[195,216],"approach":[196],"infer":[198],"pharmacological":[200],"properties":[201],"by":[205],"retrieving":[206],"similar":[207],"demonstrate":[214],"predict":[220],"new":[221,225],"uses":[222],"discover":[224],"effects":[227],"existing":[229],"show":[232],"it":[234],"significantly":[235],"outperforms":[236],"comparison":[237],"methods":[238],"both":[240],"tasks.":[241]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":4},{"year":2024,"cited_by_count":9},{"year":2023,"cited_by_count":8},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1}],"updated_date":"2026-03-12T08:34:05.389933","created_date":"2025-10-10T00:00:00"}
