{"id":"https://openalex.org/W4404020529","doi":"https://doi.org/10.1093/bib/bbae565","title":"Prototype-based contrastive substructure identification for molecular property prediction","display_name":"Prototype-based contrastive substructure identification for molecular property prediction","publication_year":2024,"publication_date":"2024-09-23","ids":{"openalex":"https://openalex.org/W4404020529","doi":"https://doi.org/10.1093/bib/bbae565","pmid":"https://pubmed.ncbi.nlm.nih.gov/39494969"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbae565","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae565","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/bib/bbae565","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5001077607","display_name":"Gaoqi He","orcid":"https://orcid.org/0000-0001-8365-0970"},"institutions":[{"id":"https://openalex.org/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Gaoqi He","raw_affiliation_strings":["School of Computer Science and Technology, East China Normal University , 200062 Shanghai ,"],"raw_orcid":"https://orcid.org/0000-0001-8365-0970","affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, East China Normal University , 200062 Shanghai ,","institution_ids":["https://openalex.org/I66867065"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100358382","display_name":"Liu Shun","orcid":"https://orcid.org/0000-0002-4691-6685"},"institutions":[{"id":"https://openalex.org/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Shun Liu","raw_affiliation_strings":["School of Computer Science and Technology, East China Normal University , 200062 Shanghai ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, East China Normal University , 200062 Shanghai ,","institution_ids":["https://openalex.org/I66867065"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5046771199","display_name":"Zhuoran Liu","orcid":"https://orcid.org/0000-0002-3953-0637"},"institutions":[{"id":"https://openalex.org/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhuoran Liu","raw_affiliation_strings":["School of Computer Science and Technology, East China Normal University , 200062 Shanghai ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, East China Normal University , 200062 Shanghai ,","institution_ids":["https://openalex.org/I66867065"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5063110936","display_name":"Changbo Wang","orcid":"https://orcid.org/0000-0001-8940-6418"},"institutions":[{"id":"https://openalex.org/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Changbo Wang","raw_affiliation_strings":["School of Computer Science and Technology, East China Normal University , 200062 Shanghai ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, East China Normal University , 200062 Shanghai ,","institution_ids":["https://openalex.org/I66867065"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100324058","display_name":"Kai Zhang","orcid":"https://orcid.org/0000-0003-4058-6512"},"institutions":[{"id":"https://openalex.org/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kai Zhang","raw_affiliation_strings":["School of Computer Science and Technology, East China Normal University , 200062 Shanghai ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science and Technology, East China Normal University , 200062 Shanghai ,","institution_ids":["https://openalex.org/I66867065"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100688144","display_name":"Honglin Li","orcid":"https://orcid.org/0000-0003-2270-1900"},"institutions":[{"id":"https://openalex.org/I143593769","display_name":"East China University of Science and Technology","ror":"https://ror.org/01vyrm377","country_code":"CN","type":"education","lineage":["https://openalex.org/I143593769"]},{"id":"https://openalex.org/I66867065","display_name":"East China Normal University","ror":"https://ror.org/02n96ep67","country_code":"CN","type":"education","lineage":["https://openalex.org/I66867065"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Honglin Li","raw_affiliation_strings":["East China University of Science & Technology , School of Pharmacy, , 200237 Shanghai ,","Innovation Center for AI and Drug Discovery, East China Normal University , 200062 Shanghai ,","Shanghai Key Laboratory of New Drug Design , School of Pharmacy, , 200237 Shanghai ,"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"East China University of Science & Technology , School of Pharmacy, , 200237 Shanghai ,","institution_ids":["https://openalex.org/I143593769"]},{"raw_affiliation_string":"Innovation Center for AI and Drug Discovery, East China Normal University , 200062 Shanghai ,","institution_ids":["https://openalex.org/I66867065"]},{"raw_affiliation_string":"Shanghai Key Laboratory of New Drug Design , School of Pharmacy, , 200237 Shanghai ,","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":6,"corresponding_author_ids":["https://openalex.org/A5001077607"],"corresponding_institution_ids":["https://openalex.org/I66867065"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":1.0371,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.8008389,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":98},"biblio":{"volume":"25","issue":"6","first_page":null,"last_page":null},"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":0.9994999766349792,"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":0.9545999765396118,"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/substructure","display_name":"Substructure","score":0.894899845123291},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7744436264038086},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.5658512711524963},{"id":"https://openalex.org/keywords/property","display_name":"Property (philosophy)","score":0.5648243427276611},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4783032536506653},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.4530111253261566},{"id":"https://openalex.org/keywords/consistency","display_name":"Consistency (knowledge bases)","score":0.44057032465934753},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.424783855676651},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4157123863697052},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34338903427124023},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32255682349205017}],"concepts":[{"id":"https://openalex.org/C99679407","wikidata":"https://www.wikidata.org/wiki/Q56761637","display_name":"Substructure","level":2,"score":0.894899845123291},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7744436264038086},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.5658512711524963},{"id":"https://openalex.org/C189950617","wikidata":"https://www.wikidata.org/wiki/Q937228","display_name":"Property (philosophy)","level":2,"score":0.5648243427276611},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4783032536506653},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.4530111253261566},{"id":"https://openalex.org/C2776436953","wikidata":"https://www.wikidata.org/wiki/Q5163215","display_name":"Consistency (knowledge bases)","level":2,"score":0.44057032465934753},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.424783855676651},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4157123863697052},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34338903427124023},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32255682349205017},{"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/C66938386","wikidata":"https://www.wikidata.org/wiki/Q633538","display_name":"Structural engineering","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/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","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/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","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}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D013223","descriptor_name":"Statistics as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015394","descriptor_name":"Molecular Structure","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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019992","descriptor_name":"Databases as Topic","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":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbae565","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae565","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39494969","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39494969","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":"Briefings in bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11533112","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11533112","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11533112/pdf/bbae565.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","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Brief Bioinform","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bib/bbae565","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbae565","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2796437284","display_name":null,"funder_award_id":"CSTB2022NSCQ","funder_id":"https://openalex.org/F4320323172","funder_display_name":"Natural Science Foundation of Chongqing"},{"id":"https://openalex.org/G5125954578","display_name":null,"funder_award_id":"62072183","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5524584715","display_name":null,"funder_award_id":"2022YFC3400501","funder_id":"https://openalex.org/F4320335777","funder_display_name":"National Key Research and Development Program of China"},{"id":"https://openalex.org/G6304150607","display_name":null,"funder_award_id":"62276099","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8781483188","display_name":null,"funder_award_id":"62002121","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"},{"id":"https://openalex.org/F4320323172","display_name":"Natural Science Foundation of Chongqing","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320327639","display_name":"Centre Scientifique et Technique du B\u00e2timent","ror":"https://ror.org/02fsd1928"},{"id":"https://openalex.org/F4320335777","display_name":"National Key Research and Development Program of China","ror":null},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":49,"referenced_works":["https://openalex.org/W1612336946","https://openalex.org/W1975147762","https://openalex.org/W2059770489","https://openalex.org/W2148996722","https://openalex.org/W2187089797","https://openalex.org/W2295598076","https://openalex.org/W2594183968","https://openalex.org/W2914059076","https://openalex.org/W2951659295","https://openalex.org/W2966357564","https://openalex.org/W2968734407","https://openalex.org/W2992586577","https://openalex.org/W3036224891","https://openalex.org/W3040115141","https://openalex.org/W3095617312","https://openalex.org/W3110901318","https://openalex.org/W3137551757","https://openalex.org/W3154492312","https://openalex.org/W3157265962","https://openalex.org/W3163493952","https://openalex.org/W3169827396","https://openalex.org/W3198168376","https://openalex.org/W3210813272","https://openalex.org/W4206367183","https://openalex.org/W4220933632","https://openalex.org/W4280602833","https://openalex.org/W4283814428","https://openalex.org/W4287749054","https://openalex.org/W4290930066","https://openalex.org/W4294974645","https://openalex.org/W4296465376","https://openalex.org/W4297179162","https://openalex.org/W4301409532","https://openalex.org/W4302008537","https://openalex.org/W4311584330","https://openalex.org/W4323644140","https://openalex.org/W4375859821","https://openalex.org/W4386012079","https://openalex.org/W4387848574","https://openalex.org/W4390692245","https://openalex.org/W6636572641","https://openalex.org/W6726873649","https://openalex.org/W6742348326","https://openalex.org/W6753331806","https://openalex.org/W6777265123","https://openalex.org/W6779032261","https://openalex.org/W6779997284","https://openalex.org/W6810059659","https://openalex.org/W6845259520"],"related_works":["https://openalex.org/W3153444835","https://openalex.org/W2153916713","https://openalex.org/W2023846184","https://openalex.org/W2703419385","https://openalex.org/W2329056228","https://openalex.org/W2284584236","https://openalex.org/W2950955148","https://openalex.org/W1979083399","https://openalex.org/W2344320748","https://openalex.org/W2374530195"],"abstract_inverted_index":{"Substructure-based":[0],"representation":[1],"learning":[2],"has":[3],"emerged":[4],"as":[5,75],"a":[6,64,94,115,129],"powerful":[7],"approach":[8],"to":[9,32,40,49,67,76,98,135,139],"featurize":[10],"complex":[11],"attributed":[12],"graphs,":[13],"with":[14,111,173],"promising":[15],"results":[16,153],"in":[17],"molecular":[18,47,79,141],"property":[19],"prediction":[20],"(MPP).":[21],"However,":[22],"existing":[23],"MPP":[24,51],"methods":[25],"mainly":[26],"rely":[27],"on":[28],"manually":[29],"defined":[30],"rules":[31],"extract":[33],"substructures.":[34,175],"It":[35],"remains":[36],"an":[37],"open":[38],"challenge":[39],"adaptively":[41],"identify":[42],"meaningful":[43,104],"substructures":[44,110],"from":[45,154],"numerous":[46],"graphs":[48,73],"accommodate":[50],"tasks.":[52,163],"To":[53],"this":[54,56],"end,":[55],"paper":[57],"proposes":[58],"Prototype-based":[59],"cOntrastive":[60],"Substructure":[61],"IdentificaTion":[62],"(POSIT),":[63],"self-supervised":[65],"framework":[66,148],"autonomously":[68],"discover":[69],"substructural":[70],"prototypes":[71,113],"across":[72],"so":[74],"guide":[77],"end-to-end":[78],"fragmentation.":[80],"During":[81],"pre-training,":[82],"POSIT":[83,147],"emphasizes":[84],"two":[85],"key":[86],"aspects":[87],"of":[88,102,145,170],"substructure":[89],"identification:":[90],"firstly,":[91],"it":[92,107],"imposes":[93],"soft":[95],"connectivity":[96],"constraint":[97],"encourage":[99],"the":[100,126,146,168],"generation":[101],"topologically":[103],"substructures;":[105],"secondly,":[106],"aligns":[108],"resultant":[109],"derived":[112],"through":[114],"prototype-substructure":[116],"contrastive":[117],"clustering":[118],"objective,":[119],"ensuring":[120],"attribute-based":[121],"similarity":[122],"within":[123],"clusters.":[124],"In":[125],"fine-tuning":[127],"stage,":[128],"cross-scale":[130],"attention":[131],"mechanism":[132],"is":[133,149,179],"designed":[134],"integrate":[136],"substructure-level":[137],"information":[138],"enhance":[140],"representations.":[142],"The":[143,176],"effectiveness":[144],"demonstrated":[150],"by":[151],"experimental":[152],"diverse":[155],"real-world":[156],"datasets,":[157],"covering":[158],"both":[159],"classification":[160],"and":[161],"regression":[162],"Moreover,":[164],"visualization":[165],"analysis":[166],"validates":[167],"consistency":[169],"chemical":[171],"priors":[172],"identified":[174],"source":[177],"code":[178],"publicly":[180],"available":[181],"at":[182],"https://github.com/VRPharmer/POSIT.":[183]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":2}],"updated_date":"2025-12-27T23:08:20.325037","created_date":"2025-10-10T00:00:00"}
