{"id":"https://openalex.org/W4393185967","doi":"https://doi.org/10.1093/bioinformatics/btae164","title":"MoleMCL: a multi-level contrastive learning framework for molecular pre-training","display_name":"MoleMCL: a multi-level contrastive learning framework for molecular pre-training","publication_year":2024,"publication_date":"2024-03-26","ids":{"openalex":"https://openalex.org/W4393185967","doi":"https://doi.org/10.1093/bioinformatics/btae164","pmid":"https://pubmed.ncbi.nlm.nih.gov/38530779"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae164","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae164","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"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/bioinformatics/btae164","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100381570","display_name":"Xinyi Zhang","orcid":"https://orcid.org/0009-0000-9618-5799"},"institutions":[{"id":"https://openalex.org/I75867142","display_name":"Xiamen University of Technology","ror":"https://ror.org/01285e189","country_code":"CN","type":"education","lineage":["https://openalex.org/I75867142"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Xinyi Zhang","raw_affiliation_strings":["Department of Computer Science and Technology, Xiamen University , Xiamen 361005, China","Department of Computer Science and Technology, Xiamen University, Xiamen, 361005, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Xiamen University , Xiamen 361005, China","institution_ids":["https://openalex.org/I75867142"]},{"raw_affiliation_string":"Department of Computer Science and Technology, Xiamen University, Xiamen, 361005, China","institution_ids":["https://openalex.org/I75867142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104669059","display_name":"Yanni Xu","orcid":"https://orcid.org/0009-0004-0326-6960"},"institutions":[{"id":"https://openalex.org/I75867142","display_name":"Xiamen University of Technology","ror":"https://ror.org/01285e189","country_code":"CN","type":"education","lineage":["https://openalex.org/I75867142"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanni Xu","raw_affiliation_strings":["Department of Computer Science and Technology, Xiamen University , Xiamen 361005, China","Department of Computer Science and Technology, Xiamen University, Xiamen, 361005, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Xiamen University , Xiamen 361005, China","institution_ids":["https://openalex.org/I75867142"]},{"raw_affiliation_string":"Department of Computer Science and Technology, Xiamen University, Xiamen, 361005, China","institution_ids":["https://openalex.org/I75867142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102860037","display_name":"Changzhi Jiang","orcid":"https://orcid.org/0000-0003-0765-6320"},"institutions":[{"id":"https://openalex.org/I75867142","display_name":"Xiamen University of Technology","ror":"https://ror.org/01285e189","country_code":"CN","type":"education","lineage":["https://openalex.org/I75867142"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Changzhi Jiang","raw_affiliation_strings":["Department of Computer Science and Technology, Xiamen University , Xiamen 361005, China","Department of Computer Science and Technology, Xiamen University, Xiamen, 361005, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Xiamen University , Xiamen 361005, China","institution_ids":["https://openalex.org/I75867142"]},{"raw_affiliation_string":"Department of Computer Science and Technology, Xiamen University, Xiamen, 361005, China","institution_ids":["https://openalex.org/I75867142"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091431846","display_name":"Lian Shen","orcid":"https://orcid.org/0000-0003-3762-3829"},"institutions":[{"id":"https://openalex.org/I75867142","display_name":"Xiamen University of Technology","ror":"https://ror.org/01285e189","country_code":"CN","type":"education","lineage":["https://openalex.org/I75867142"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lian Shen","raw_affiliation_strings":["Department of Computer Science and Technology, Xiamen University , Xiamen 361005, China","Department of Computer Science and Technology, Xiamen University, Xiamen, 361005, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Xiamen University , Xiamen 361005, China","institution_ids":["https://openalex.org/I75867142"]},{"raw_affiliation_string":"Department of Computer Science and Technology, Xiamen University, Xiamen, 361005, China","institution_ids":["https://openalex.org/I75867142"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026771763","display_name":"Xiangrong Liu","orcid":"https://orcid.org/0000-0001-9885-1978"},"institutions":[{"id":"https://openalex.org/I191208505","display_name":"Xiamen University","ror":"https://ror.org/00mcjh785","country_code":"CN","type":"education","lineage":["https://openalex.org/I191208505"]},{"id":"https://openalex.org/I75867142","display_name":"Xiamen University of Technology","ror":"https://ror.org/01285e189","country_code":"CN","type":"education","lineage":["https://openalex.org/I75867142"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiangrong Liu","raw_affiliation_strings":["Department of Computer Science and Technology, Xiamen University , Xiamen 361005, China","National Institute for Data Science in Health and Medicine, Xiamen University , Xiamen 361005, China","National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361005, China","Department of Computer Science and Technology, Xiamen University, Xiamen, 361005, China"],"affiliations":[{"raw_affiliation_string":"Department of Computer Science and Technology, Xiamen University , Xiamen 361005, China","institution_ids":["https://openalex.org/I75867142"]},{"raw_affiliation_string":"National Institute for Data Science in Health and Medicine, Xiamen University , Xiamen 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"National Institute for Data Science in Health and Medicine, Xiamen University, Xiamen, 361005, China","institution_ids":["https://openalex.org/I191208505"]},{"raw_affiliation_string":"Department of Computer Science and Technology, Xiamen University, Xiamen, 361005, China","institution_ids":["https://openalex.org/I75867142"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5100381570"],"corresponding_institution_ids":["https://openalex.org/I75867142"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":3.5472,"has_fulltext":true,"cited_by_count":10,"citation_normalized_percentile":{"value":0.93267259,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"40","issue":"4","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":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":0.9994999766349792,"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":0.9879000186920166,"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/computer-science","display_name":"Computer science","score":0.7880513668060303},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5297694206237793},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.5208066701889038},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5109016299247742},{"id":"https://openalex.org/keywords/semantics","display_name":"Semantics (computer science)","score":0.4747213125228882},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.4353170096874237},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.4347003102302551},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.4253760576248169},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.421691358089447},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3770385682582855},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3403019309043884},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.23638829588890076}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7880513668060303},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5297694206237793},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.5208066701889038},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5109016299247742},{"id":"https://openalex.org/C184337299","wikidata":"https://www.wikidata.org/wiki/Q1437428","display_name":"Semantics (computer science)","level":2,"score":0.4747213125228882},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.4353170096874237},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.4347003102302551},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.4253760576248169},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.421691358089447},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3770385682582855},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3403019309043884},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.23638829588890076},{"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/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"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/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"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/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012660","descriptor_name":"Semantics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015195","descriptor_name":"Drug Design","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae164","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae164","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38530779","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38530779","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11001485","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11001485","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11001485/pdf/btae164.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae164","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae164","pdf_url":null,"source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5091875258","display_name":null,"funder_award_id":"61872309","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6312213820","display_name":null,"funder_award_id":"62072385","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8390325463","display_name":null,"funder_award_id":"61772441","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8971624103","display_name":null,"funder_award_id":"62072384","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":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":17,"referenced_works":["https://openalex.org/W1757990252","https://openalex.org/W2096541451","https://openalex.org/W2514794892","https://openalex.org/W2594183968","https://openalex.org/W2896457183","https://openalex.org/W2970175280","https://openalex.org/W3011574394","https://openalex.org/W3088409176","https://openalex.org/W3093687066","https://openalex.org/W3102659967","https://openalex.org/W3152893301","https://openalex.org/W3195415198","https://openalex.org/W3203741962","https://openalex.org/W4291288469","https://openalex.org/W4381432349","https://openalex.org/W4382239590","https://openalex.org/W6755207826"],"related_works":["https://openalex.org/W4390516098","https://openalex.org/W2181948922","https://openalex.org/W2905271011","https://openalex.org/W2793270624","https://openalex.org/W3164948662","https://openalex.org/W4289536128","https://openalex.org/W3153597579","https://openalex.org/W4298151006","https://openalex.org/W4390871823","https://openalex.org/W4285218279"],"abstract_inverted_index":{"The":[0],"code":[1],"and":[2],"data":[3],"underlying":[4],"this":[5],"work":[6],"are":[7],"available":[8],"in":[9],"GitHub":[10],"at":[11],"https://github.com/BioSequenceAnalysis/MoleMCL.":[12]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":6},{"year":2024,"cited_by_count":2}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
