{"id":"https://openalex.org/W7119774373","doi":"https://doi.org/10.1093/bib/bbaf703","title":"A systematic review of molecular representation learning foundation models","display_name":"A systematic review of molecular representation learning foundation models","publication_year":2025,"publication_date":"2025-12-19","ids":{"openalex":"https://openalex.org/W7119774373","doi":"https://doi.org/10.1093/bib/bbaf703","pmid":"https://pubmed.ncbi.nlm.nih.gov/41511463"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaf703","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf703","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/bbaf703","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5122596898","display_name":"Bosheng Song","orcid":null},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]},{"id":"https://openalex.org/I48168531","display_name":"South University","ror":"https://ror.org/01rjfjt94","country_code":"US","type":"education","lineage":["https://openalex.org/I48168531"]}],"countries":["CN","US"],"is_corresponding":true,"raw_author_name":"Bosheng Song","raw_affiliation_strings":["College of Computer Science and Electronic Engineering , Hunan University, 116 Lushan South Road, Yuelu District, 410086 Changsha,"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering , Hunan University, 116 Lushan South Road, Yuelu District, 410086 Changsha,","institution_ids":["https://openalex.org/I16609230","https://openalex.org/I48168531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100357305","display_name":"Jiayi Zhang","orcid":"https://orcid.org/0000-0002-7334-4256"},"institutions":[{"id":"https://openalex.org/I48168531","display_name":"South University","ror":"https://ror.org/01rjfjt94","country_code":"US","type":"education","lineage":["https://openalex.org/I48168531"]},{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Jiayi Zhang","raw_affiliation_strings":["College of Computer Science and Electronic Engineering , Hunan University, 116 Lushan South Road, Yuelu District, 410086 Changsha,"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering , Hunan University, 116 Lushan South Road, Yuelu District, 410086 Changsha,","institution_ids":["https://openalex.org/I16609230","https://openalex.org/I48168531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122474735","display_name":"Ying Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I48168531","display_name":"South University","ror":"https://ror.org/01rjfjt94","country_code":"US","type":"education","lineage":["https://openalex.org/I48168531"]},{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Ying Liu","raw_affiliation_strings":["College of Computer Science and Electronic Engineering , Hunan University, 116 Lushan South Road, Yuelu District, 410086 Changsha,"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering , Hunan University, 116 Lushan South Road, Yuelu District, 410086 Changsha,","institution_ids":["https://openalex.org/I16609230","https://openalex.org/I48168531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122681717","display_name":"Yuansheng Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I48168531","display_name":"South University","ror":"https://ror.org/01rjfjt94","country_code":"US","type":"education","lineage":["https://openalex.org/I48168531"]},{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Yuansheng Liu","raw_affiliation_strings":["College of Computer Science and Electronic Engineering , Hunan University, 116 Lushan South Road, Yuelu District, 410086 Changsha,"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering , Hunan University, 116 Lushan South Road, Yuelu District, 410086 Changsha,","institution_ids":["https://openalex.org/I16609230","https://openalex.org/I48168531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122517806","display_name":"Jing Jiang","orcid":null},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]},{"id":"https://openalex.org/I48168531","display_name":"South University","ror":"https://ror.org/01rjfjt94","country_code":"US","type":"education","lineage":["https://openalex.org/I48168531"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Jing Jiang","raw_affiliation_strings":["College of Computer Science and Electronic Engineering , Hunan University, 116 Lushan South Road, Yuelu District, 410086 Changsha,"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering , Hunan University, 116 Lushan South Road, Yuelu District, 410086 Changsha,","institution_ids":["https://openalex.org/I16609230","https://openalex.org/I48168531"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122445266","display_name":"Sisi Yuan","orcid":null},"institutions":[{"id":"https://openalex.org/I141568987","display_name":"Hong Kong Baptist University","ror":"https://ror.org/0145fw131","country_code":"HK","type":"education","lineage":["https://openalex.org/I141568987"]}],"countries":["HK"],"is_corresponding":false,"raw_author_name":"Sisi Yuan","raw_affiliation_strings":["School of Chinese Medicine , Hong Kong Baptist University, 15 Baptist University Road, Kowloon Tong, Kowloon, Hong Kong SAR 999077,"],"affiliations":[{"raw_affiliation_string":"School of Chinese Medicine , Hong Kong Baptist University, 15 Baptist University Road, Kowloon Tong, Kowloon, Hong Kong SAR 999077,","institution_ids":["https://openalex.org/I141568987"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5122582212","display_name":"Xia Zhen","orcid":null},"institutions":[{"id":"https://openalex.org/I170215575","display_name":"National University of Defense Technology","ror":"https://ror.org/05d2yfz11","country_code":"CN","type":"education","lineage":["https://openalex.org/I170215575"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xia Zhen","raw_affiliation_strings":["National Laboratory for Parallel and Distributed Processing , School of Computer, National University of Defense Technology, No. 109 Deya Road, Kaifu District, 410086 Changsha,"],"affiliations":[{"raw_affiliation_string":"National Laboratory for Parallel and Distributed Processing , School of Computer, National University of Defense Technology, No. 109 Deya Road, Kaifu District, 410086 Changsha,","institution_ids":["https://openalex.org/I170215575"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5114549778","display_name":"Yiping Liu","orcid":"https://orcid.org/0000-0002-0924-7339"},"institutions":[{"id":"https://openalex.org/I16609230","display_name":"Hunan University","ror":"https://ror.org/05htk5m33","country_code":"CN","type":"education","lineage":["https://openalex.org/I16609230"]},{"id":"https://openalex.org/I48168531","display_name":"South University","ror":"https://ror.org/01rjfjt94","country_code":"US","type":"education","lineage":["https://openalex.org/I48168531"]}],"countries":["CN","US"],"is_corresponding":false,"raw_author_name":"Yiping Liu","raw_affiliation_strings":["College of Computer Science and Electronic Engineering , Hunan University, 116 Lushan South Road, Yuelu District, 410086 Changsha,"],"affiliations":[{"raw_affiliation_string":"College of Computer Science and Electronic Engineering , Hunan University, 116 Lushan South Road, Yuelu District, 410086 Changsha,","institution_ids":["https://openalex.org/I16609230","https://openalex.org/I48168531"]}]}],"institutions":[],"countries_distinct_count":3,"institutions_distinct_count":8,"corresponding_author_ids":["https://openalex.org/A5122596898"],"corresponding_institution_ids":["https://openalex.org/I16609230","https://openalex.org/I48168531"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":{"value":4011,"currency":"USD","value_usd":4011},"fwci":3.1375,"has_fulltext":false,"cited_by_count":2,"citation_normalized_percentile":{"value":0.93533641,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":99},"biblio":{"volume":"27","issue":"1","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":0.7918999791145325,"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":0.7918999791145325,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.08799999952316284,"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"}},{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.03020000085234642,"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"}}],"keywords":[{"id":"https://openalex.org/keywords/foundation","display_name":"Foundation (evidence)","score":0.7330999970436096},{"id":"https://openalex.org/keywords/generalizability-theory","display_name":"Generalizability theory","score":0.6092000007629395},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5878999829292297},{"id":"https://openalex.org/keywords/generative-grammar","display_name":"Generative grammar","score":0.46720001101493835},{"id":"https://openalex.org/keywords/transformation","display_name":"Transformation (genetics)","score":0.39989998936653137},{"id":"https://openalex.org/keywords/construct","display_name":"Construct (python library)","score":0.382999986410141},{"id":"https://openalex.org/keywords/generalization","display_name":"Generalization","score":0.36469998955726624}],"concepts":[{"id":"https://openalex.org/C2780966255","wikidata":"https://www.wikidata.org/wiki/Q5474306","display_name":"Foundation (evidence)","level":2,"score":0.7330999970436096},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7199000120162964},{"id":"https://openalex.org/C27158222","wikidata":"https://www.wikidata.org/wiki/Q5532422","display_name":"Generalizability theory","level":2,"score":0.6092000007629395},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5878999829292297},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5357000231742859},{"id":"https://openalex.org/C39890363","wikidata":"https://www.wikidata.org/wiki/Q36108","display_name":"Generative grammar","level":2,"score":0.46720001101493835},{"id":"https://openalex.org/C204241405","wikidata":"https://www.wikidata.org/wiki/Q461499","display_name":"Transformation (genetics)","level":3,"score":0.39989998936653137},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3919999897480011},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.382999986410141},{"id":"https://openalex.org/C177148314","wikidata":"https://www.wikidata.org/wiki/Q170084","display_name":"Generalization","level":2,"score":0.36469998955726624},{"id":"https://openalex.org/C66024118","wikidata":"https://www.wikidata.org/wiki/Q1122506","display_name":"Computational model","level":2,"score":0.3422999978065491},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.33329999446868896},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.2985999882221222},{"id":"https://openalex.org/C148043351","wikidata":"https://www.wikidata.org/wiki/Q4456944","display_name":"Current (fluid)","level":2,"score":0.29789999127388},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.29319998621940613},{"id":"https://openalex.org/C125411270","wikidata":"https://www.wikidata.org/wiki/Q18653","display_name":"Encoding (memory)","level":2,"score":0.28200000524520874},{"id":"https://openalex.org/C2780719617","wikidata":"https://www.wikidata.org/wiki/Q1030752","display_name":"Salient","level":2,"score":0.274399995803833},{"id":"https://openalex.org/C161301231","wikidata":"https://www.wikidata.org/wiki/Q3478658","display_name":"Knowledge representation and reasoning","level":2,"score":0.2526000142097473}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":3,"locations":[{"id":"doi:10.1093/bib/bbaf703","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf703","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:41511463","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41511463","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:12784970","is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12784970/","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":"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/bbaf703","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bib/bbaf703","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":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":89,"referenced_works":["https://openalex.org/W1531674615","https://openalex.org/W1688073391","https://openalex.org/W1898843043","https://openalex.org/W1973965874","https://openalex.org/W1975147762","https://openalex.org/W1983478747","https://openalex.org/W1983691152","https://openalex.org/W2027482274","https://openalex.org/W2043757580","https://openalex.org/W2044834685","https://openalex.org/W2127553917","https://openalex.org/W2135037015","https://openalex.org/W2147638953","https://openalex.org/W2165698076","https://openalex.org/W2249672461","https://openalex.org/W2290847742","https://openalex.org/W2507479832","https://openalex.org/W2570516417","https://openalex.org/W2742127985","https://openalex.org/W2794210286","https://openalex.org/W2802200505","https://openalex.org/W2886313886","https://openalex.org/W2895884529","https://openalex.org/W2906755148","https://openalex.org/W2963609389","https://openalex.org/W2966357564","https://openalex.org/W2985331920","https://openalex.org/W2999242200","https://openalex.org/W3024894285","https://openalex.org/W3034806393","https://openalex.org/W3034999214","https://openalex.org/W3035524453","https://openalex.org/W3093687066","https://openalex.org/W3109493217","https://openalex.org/W3113447514","https://openalex.org/W3145734614","https://openalex.org/W3147983081","https://openalex.org/W3152893301","https://openalex.org/W3157265962","https://openalex.org/W3164864805","https://openalex.org/W3174911916","https://openalex.org/W3179111421","https://openalex.org/W3186432075","https://openalex.org/W3196214900","https://openalex.org/W3204651332","https://openalex.org/W3207373390","https://openalex.org/W3210027319","https://openalex.org/W4206367183","https://openalex.org/W4210313485","https://openalex.org/W4212837331","https://openalex.org/W4214868967","https://openalex.org/W4223499953","https://openalex.org/W4225983336","https://openalex.org/W4239510810","https://openalex.org/W4280602833","https://openalex.org/W4285173593","https://openalex.org/W4286901673","https://openalex.org/W4295808856","https://openalex.org/W4297179162","https://openalex.org/W4306179830","https://openalex.org/W4309218736","https://openalex.org/W4311821345","https://openalex.org/W4313485929","https://openalex.org/W4362632778","https://openalex.org/W4365143687","https://openalex.org/W4366835631","https://openalex.org/W4372330430","https://openalex.org/W4377096651","https://openalex.org/W4379879032","https://openalex.org/W4381679608","https://openalex.org/W4382239902","https://openalex.org/W4382469015","https://openalex.org/W4383373262","https://openalex.org/W4383499296","https://openalex.org/W4385381606","https://openalex.org/W4385572894","https://openalex.org/W4385969371","https://openalex.org/W4386697749","https://openalex.org/W4386973901","https://openalex.org/W4387029257","https://openalex.org/W4387297831","https://openalex.org/W4387617009","https://openalex.org/W4388845139","https://openalex.org/W4389888290","https://openalex.org/W4390221451","https://openalex.org/W4391136507","https://openalex.org/W4391319559","https://openalex.org/W4396678548","https://openalex.org/W4404167537"],"related_works":[],"abstract_inverted_index":{"Molecular":[0],"representation":[1,115,188],"learning":[2,31],"(MRL)":[3],"is":[4,196],"afoundation":[5],"in":[6,66,191],"leveraging":[7],"computational":[8],"methods":[9],"for":[10,29,167],"drug":[11,192],"discovery,":[12],"enabling":[13],"the":[14,35,89,114,138,184,200,212],"transformation":[15,90],"of":[16,39,47,91,104,116,140,186,203,215],"molecular":[17,40,92,107,187],"structure":[18],"and":[19,33,37,43,55,64,71,84,109,126,143,153,156,177,194],"properties":[20],"into":[21,94,132,211],"numerical":[22],"vectors.":[23],"These":[24,59],"vectors":[25],"serve":[26],"as":[27,124],"input":[28],"machine":[30],"models":[32,49,60,74,131,150,190],"facilitate":[34],"prediction":[36],"analysis":[38],"attributes,":[41],"functions,":[42],"reactions.":[44],"The":[45,206],"advent":[46],"foundation":[48,73,130,169,189,217],"has":[50],"introduced":[51],"both":[52],"new":[53],"opportunities":[54],"challenges":[56],"to":[57,78],"MRL.":[58],"have":[61],"improved":[62],"generalizability":[63],"migration":[65],"scarce":[67],"data.":[68],"Through":[69],"pretraining":[70,165],"fine-tuning,":[72],"can":[75],"be":[76],"adapted":[77],"various":[79],"domains.":[80],"Their":[81],"robust":[82],"encoding":[83],"generative":[85],"abilities":[86],"also":[87],"allow":[88],"data":[93],"more":[95],"expressive":[96],"forms.":[97],"This":[98],"paper":[99,207],"provides":[100],"a":[101],"detailed":[102],"review":[103],"current":[105,201],"mainstream":[106],"descriptors":[108],"datasets,":[110],"focusing":[111],"primarily":[112],"on":[113,137,179],"small":[117],"molecules":[118,122],"while":[119],"excluding":[120],"larger":[121],"such":[123],"proteins":[125],"peptides.":[127],"It":[128],"classifies":[129],"two":[133],"primary":[134],"categories":[135],"based":[136],"form":[139],"input:":[141],"unimodal-based":[142],"multimodal-based":[144],"models.":[145,218],"For":[146],"each":[147],"category,":[148],"representative":[149],"are":[151],"identified":[152],"their":[154,172],"advantages":[155],"disadvantages":[157],"evaluated.":[158],"Moreover,":[159],"we":[160],"systematically":[161],"summarize":[162],"four":[163],"core":[164],"strategies":[166],"MRL":[168,216],"models,":[170],"analyzing":[171],"task":[173],"designs,":[174],"applicable":[175],"scenarios,":[176],"impacts":[178],"downstream":[180],"performance.":[181],"In":[182],"addition,":[183],"application":[185],"discovery":[193],"development":[195],"discussed,":[197],"together":[198],"with":[199,209],"status":[202],"model":[204],"interpretability.":[205],"concludes":[208],"insights":[210],"future":[213],"directions":[214]},"counts_by_year":[{"year":2026,"cited_by_count":2}],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2026-01-10T00:00:00"}
