{"id":"https://openalex.org/W4390193806","doi":"https://doi.org/10.1021/acs.jcim.3c01707","title":"Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery?","display_name":"Can Pretrained Models Really Learn Better Molecular Representations for AI-Aided Drug Discovery?","publication_year":2023,"publication_date":"2023-12-25","ids":{"openalex":"https://openalex.org/W4390193806","doi":"https://doi.org/10.1021/acs.jcim.3c01707","pmid":"https://pubmed.ncbi.nlm.nih.gov/38145387"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.3c01707","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01707","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c01707","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.3c01707","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103007849","display_name":"Ziqiao Zhang","orcid":"https://orcid.org/0000-0003-3747-7673"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ziqiao Zhang","raw_affiliation_strings":["Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200438, China"],"raw_orcid":"https://orcid.org/0000-0003-3747-7673","affiliations":[{"raw_affiliation_string":"Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200438, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045777220","display_name":"Yatao Bian","orcid":"https://orcid.org/0000-0002-2368-4084"},"institutions":[{"id":"https://openalex.org/I2250653659","display_name":"Tencent (China)","ror":"https://ror.org/00hhjss72","country_code":"CN","type":"company","lineage":["https://openalex.org/I2250653659"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yatao Bian","raw_affiliation_strings":["Tencent AI Lab, Shenzhen 518063, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Tencent AI Lab, Shenzhen 518063, China","institution_ids":["https://openalex.org/I2250653659"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102751255","display_name":"Ailin Xie","orcid":"https://orcid.org/0009-0000-9001-4681"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ailin Xie","raw_affiliation_strings":["Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200438, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200438, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101589081","display_name":"Pengju Han","orcid":"https://orcid.org/0000-0002-2973-1048"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pengju Han","raw_affiliation_strings":["Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200438, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200438, China","institution_ids":["https://openalex.org/I24943067"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017862559","display_name":"Shuigeng Zhou","orcid":"https://orcid.org/0000-0002-1949-2768"},"institutions":[{"id":"https://openalex.org/I24943067","display_name":"Fudan University","ror":"https://ror.org/013q1eq08","country_code":"CN","type":"education","lineage":["https://openalex.org/I24943067"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Shuigeng Zhou","raw_affiliation_strings":["Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200438, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Shanghai Key Lab of Intelligent Information Processing, and School of Computer Science, Fudan University, Shanghai 200438, China","institution_ids":["https://openalex.org/I24943067"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5017862559"],"corresponding_institution_ids":["https://openalex.org/I24943067"],"apc_list":null,"apc_paid":null,"fwci":2.2454,"has_fulltext":true,"cited_by_count":13,"citation_normalized_percentile":{"value":0.90243045,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"64","issue":"7","first_page":"2921","last_page":"2930"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9995999932289124,"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":0.9570000171661377,"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/representation","display_name":"Representation (politics)","score":0.7582255601882935},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7019405364990234},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6719937920570374},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.602732241153717},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.5721035003662109},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5261161923408508},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.5166745185852051},{"id":"https://openalex.org/keywords/drug-discovery","display_name":"Drug discovery","score":0.48589104413986206},{"id":"https://openalex.org/keywords/quality","display_name":"Quality (philosophy)","score":0.4743672311306},{"id":"https://openalex.org/keywords/popularity","display_name":"Popularity","score":0.4304000735282898},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.34740716218948364},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.07646384835243225}],"concepts":[{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.7582255601882935},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7019405364990234},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6719937920570374},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.602732241153717},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.5721035003662109},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5261161923408508},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.5166745185852051},{"id":"https://openalex.org/C74187038","wikidata":"https://www.wikidata.org/wiki/Q1418791","display_name":"Drug discovery","level":2,"score":0.48589104413986206},{"id":"https://openalex.org/C2779530757","wikidata":"https://www.wikidata.org/wiki/Q1207505","display_name":"Quality (philosophy)","level":2,"score":0.4743672311306},{"id":"https://openalex.org/C2780586970","wikidata":"https://www.wikidata.org/wiki/Q1357284","display_name":"Popularity","level":2,"score":0.4304000735282898},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.34740716218948364},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.07646384835243225},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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},{"id":"https://openalex.org/C15744967","wikidata":"https://www.wikidata.org/wiki/Q9418","display_name":"Psychology","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","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/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.0},{"id":"https://openalex.org/C77805123","wikidata":"https://www.wikidata.org/wiki/Q161272","display_name":"Social psychology","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006867","descriptor_name":"Hydrolases","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D007858","descriptor_name":"Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D019380","descriptor_name":"Anti-HIV Agents","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D021281","descriptor_name":"Quantitative Structure-Activity Relationship","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1021/acs.jcim.3c01707","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01707","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c01707","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:38145387","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38145387","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:11005046","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11005046","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11005046/pdf/ci3c01707.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-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.3c01707","is_oa":true,"landing_page_url":"https://doi.org/10.1021/acs.jcim.3c01707","pdf_url":"https://pubs.acs.org/doi/pdf/10.1021/acs.jcim.3c01707","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":[{"score":0.7699999809265137,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G1487418658","display_name":"\u5355\u7ec6\u80deRNA\u6d4b\u5e8f\u6570\u636e\u805a\u7c7b\u65b9\u6cd5\u7814\u7a76","funder_award_id":"61972100","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4390193806.pdf","grobid_xml":"https://content.openalex.org/works/W4390193806.grobid-xml"},"referenced_works_count":27,"referenced_works":["https://openalex.org/W764098304","https://openalex.org/W1988037271","https://openalex.org/W2123863721","https://openalex.org/W2125003829","https://openalex.org/W2594183968","https://openalex.org/W2735246657","https://openalex.org/W2944974555","https://openalex.org/W2968734407","https://openalex.org/W2986232138","https://openalex.org/W2992586577","https://openalex.org/W3005552578","https://openalex.org/W3007488165","https://openalex.org/W3027099090","https://openalex.org/W3034516664","https://openalex.org/W3093397714","https://openalex.org/W3095883070","https://openalex.org/W3124172763","https://openalex.org/W3136399186","https://openalex.org/W3137551757","https://openalex.org/W3165630607","https://openalex.org/W3168403139","https://openalex.org/W3169622372","https://openalex.org/W3170424177","https://openalex.org/W3188589934","https://openalex.org/W4212774754","https://openalex.org/W4225907994","https://openalex.org/W4230274588"],"related_works":["https://openalex.org/W2368605798","https://openalex.org/W2518037665","https://openalex.org/W2348524959","https://openalex.org/W2477036161","https://openalex.org/W2368049389","https://openalex.org/W2384861574","https://openalex.org/W4294565801","https://openalex.org/W2170801710","https://openalex.org/W2952704802","https://openalex.org/W2741781807"],"abstract_inverted_index":{"High":[0],"Resolution":[1],"Image":[2],"Download":[3],"MS":[4],"PowerPoint":[5],"Slide":[6],"Self-supervised":[7],"pretrained":[8,24,95,166,176,230],"models":[9,25,167,177],"are":[10,112,128,133,168,200],"gaining":[11],"increasingly":[12],"more":[13,21,23],"popularity":[14],"in":[15,65],"AI-aided":[16],"drug":[17],"discovery,":[18],"leading":[19],"to":[20,85,118,135,218,239,244],"and":[22,61,97,104,110,122,140,145,196,250],"with":[26],"the":[27,39,54,87,90,94,99,102,115,119,123,137,147,174,187,190,193,211,220,237,246],"promise":[28],"that":[29,173],"they":[30],"can":[31,151,178,235],"extract":[32],"better":[33,241],"feature":[34],"representations":[35,43,91,103,150,156,205,224],"for":[36],"molecules.":[37],"Yet,":[38],"quality":[40,88,148,221],"of":[41,57,89,108,126,149,157,182,192,222,248],"learned":[42],"has":[44],"not":[45,201],"been":[46],"fully":[47],"explored.":[48],"In":[49,154],"this":[50],"work,":[51],"inspired":[52],"by":[53,93,143,164,226],"two":[55],"phenomena":[56],"Activity":[58],"Cliffs":[59],"(ACs)":[60],"Scaffold":[62],"Hopping":[63],"(SH)":[64],"traditional":[66],"Quantitative":[67],"Structure\u2013Activity":[68],"Relationship":[69],"analysis,":[70],"we":[71],"propose":[72],"a":[73],"method":[74,215],"named":[75],"Re":[76],"presentation-":[77],"P":[78],"roperty":[79],"R":[80],"elationship":[81],"A":[82],"nalysis":[83],"(RePRA)":[84],"evaluate":[86,219],"extracted":[92],"model":[96],"visualize":[98],"relationship":[100],"between":[101,189],"properties.":[105],"The":[106,170],"concepts":[107],"ACs":[109,139,249],"SH":[111,141],"generalized":[113,138],"from":[114,159],"structure\u2013activity":[116],"context":[117],"representation-property":[120],"context,":[121],"underlying":[124],"principles":[125],"RePRA":[127],"analyzed":[129],"theoretically.":[130],"Two":[131],"scores":[132],"designed":[134],"measure":[136],"detected":[142],"RePRA,":[144],"therefore,":[146],"be":[152,207],"evaluated.":[153],"experiments,":[155],"molecules":[158],"10":[160],"target":[161],"tasks":[162],"generated":[163,225],"7":[165],"analyzed.":[169],"results":[171],"indicate":[172],"state-of-the-art":[175],"overcome":[179],"some":[180,204],"shortcomings":[181],"canonical":[183,212],"Extended-Connectivity":[184],"FingerPrints,":[185],"while":[186],"correlation":[188],"basis":[191],"representation":[194],"space":[195],"specific":[197],"molecular":[198,223],"substructures":[199],"explicit.":[202],"Thus,":[203],"could":[206],"even":[208],"worse":[209],"than":[210],"fingerprints.":[213],"Our":[214],"enables":[216],"researchers":[217],"their":[227],"proposed":[228],"self-supervised":[229],"models.":[231],"And":[232],"our":[233],"findings":[234],"guide":[236],"community":[238],"develop":[240],"pretraining":[242],"techniques":[243],"regularize":[245],"occurrence":[247],"SH.":[251]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":4},{"year":2023,"cited_by_count":1}],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}