{"id":"https://openalex.org/W4411101184","doi":"https://doi.org/10.1021/acs.jcim.5c00855","title":"MFDSMC: Accurate Identification of Cancer-Driver Synonymous Mutations Using Multiperspective Feature Representation Learning","display_name":"MFDSMC: Accurate Identification of Cancer-Driver Synonymous Mutations Using Multiperspective Feature Representation Learning","publication_year":2025,"publication_date":"2025-06-06","ids":{"openalex":"https://openalex.org/W4411101184","doi":"https://doi.org/10.1021/acs.jcim.5c00855","pmid":"https://pubmed.ncbi.nlm.nih.gov/40474519"},"language":"en","primary_location":{"id":"doi:10.1021/acs.jcim.5c00855","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00855","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102757613","display_name":"Lihua Wang","orcid":"https://orcid.org/0000-0002-7867-8298"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]},{"id":"https://openalex.org/I3132008074","display_name":"Huangshan University","ror":"https://ror.org/05akhmy90","country_code":"CN","type":"education","lineage":["https://openalex.org/I3132008074"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lihua Wang","raw_affiliation_strings":["Anhui University","Huangshan University","Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology","School of Information Engineering","Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Anhui University","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"Huangshan University","institution_ids":["https://openalex.org/I3132008074"]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology","institution_ids":[]},{"raw_affiliation_string":"School of Information Engineering","institution_ids":[]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University, Hefei, Anhui 230601, China","institution_ids":["https://openalex.org/I143868143"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040913574","display_name":"Chen Ye","orcid":"https://orcid.org/0000-0003-2952-6586"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chen Ye","raw_affiliation_strings":["Anhui University","Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Anhui University","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5076713518","display_name":"Na Cheng","orcid":"https://orcid.org/0009-0000-6123-3842"},"institutions":[{"id":"https://openalex.org/I197869895","display_name":"Anhui Medical University","ror":"https://ror.org/03xb04968","country_code":"CN","type":"education","lineage":["https://openalex.org/I197869895"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Na Cheng","raw_affiliation_strings":["Anhui Medical University","School of Biomedical Engineering"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Anhui Medical University","institution_ids":["https://openalex.org/I197869895"]},{"raw_affiliation_string":"School of Biomedical Engineering","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065943710","display_name":"Junfeng Xia","orcid":"https://orcid.org/0000-0003-3024-1705"},"institutions":[{"id":"https://openalex.org/I143868143","display_name":"Anhui University","ror":"https://ror.org/05th6yx34","country_code":"CN","type":"education","lineage":["https://openalex.org/I143868143"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Junfeng Xia","raw_affiliation_strings":["Anhui University","Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology"],"raw_orcid":"https://orcid.org/0000-0003-3024-1705","affiliations":[{"raw_affiliation_string":"Anhui University","institution_ids":["https://openalex.org/I143868143"]},{"raw_affiliation_string":"Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5065943710","https://openalex.org/A5076713518"],"corresponding_institution_ids":["https://openalex.org/I143868143","https://openalex.org/I197869895"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.10127833,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"65","issue":"12","first_page":"6382","last_page":"6396"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9836999773979187,"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"}},"topics":[{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9836999773979187,"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.9818999767303467,"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/T10181","display_name":"Natural Language Processing Techniques","score":0.9779999852180481,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.701974093914032},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5980068445205688},{"id":"https://openalex.org/keywords/feature","display_name":"Feature (linguistics)","score":0.5956705808639526},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.5691378712654114},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4880908727645874},{"id":"https://openalex.org/keywords/mutation","display_name":"Mutation","score":0.4648982584476471},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4376603662967682},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.40656810998916626},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.37165939807891846},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.354327917098999},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3461345434188843}],"concepts":[{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.701974093914032},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5980068445205688},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.5956705808639526},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.5691378712654114},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4880908727645874},{"id":"https://openalex.org/C501734568","wikidata":"https://www.wikidata.org/wiki/Q42918","display_name":"Mutation","level":3,"score":0.4648982584476471},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4376603662967682},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.40656810998916626},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.37165939807891846},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.354327917098999},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3461345434188843},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","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/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"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/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}],"mesh":[{"descriptor_ui":"D000069456","descriptor_name":"Silent Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000069456","descriptor_name":"Silent Mutation","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":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009154","descriptor_name":"Mutation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D009369","descriptor_name":"Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1021/acs.jcim.5c00855","is_oa":false,"landing_page_url":"https://doi.org/10.1021/acs.jcim.5c00855","pdf_url":null,"source":{"id":"https://openalex.org/S167262187","display_name":"Journal of Chemical Information and Modeling","issn_l":"1549-9596","issn":["1549-9596","1549-960X"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320006","host_organization_name":"American Chemical Society","host_organization_lineage":["https://openalex.org/P4310320006"],"host_organization_lineage_names":["American Chemical Society"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Chemical Information and Modeling","raw_type":"journal-article"},{"id":"pmid:40474519","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40474519","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2245046682","display_name":null,"funder_award_id":"U22A2038","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3925882961","display_name":"\u81f4\u75c5\u540c\u4e49\u7a81\u53d8\u7684\u751f\u7269\u4fe1\u606f\u5b66\u7814\u7a76","funder_award_id":"62072003","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5537947129","display_name":null,"funder_award_id":"62402006","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":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":68,"referenced_works":["https://openalex.org/W2011582941","https://openalex.org/W2023568503","https://openalex.org/W2032311106","https://openalex.org/W2038473742","https://openalex.org/W2059300459","https://openalex.org/W2075661710","https://openalex.org/W2088338354","https://openalex.org/W2088544963","https://openalex.org/W2103145565","https://openalex.org/W2106306904","https://openalex.org/W2107804881","https://openalex.org/W2145191876","https://openalex.org/W2148105023","https://openalex.org/W2155845523","https://openalex.org/W2160995259","https://openalex.org/W2167852161","https://openalex.org/W2257370818","https://openalex.org/W2295598076","https://openalex.org/W2510298658","https://openalex.org/W2564367484","https://openalex.org/W2709675480","https://openalex.org/W2742600815","https://openalex.org/W2749837661","https://openalex.org/W2751686252","https://openalex.org/W2754300472","https://openalex.org/W2767826728","https://openalex.org/W2768013244","https://openalex.org/W2898789672","https://openalex.org/W2909194804","https://openalex.org/W2918497364","https://openalex.org/W2921650138","https://openalex.org/W2948505931","https://openalex.org/W2956135855","https://openalex.org/W2966324071","https://openalex.org/W3015320198","https://openalex.org/W3038114454","https://openalex.org/W3089563003","https://openalex.org/W3120153567","https://openalex.org/W3134631034","https://openalex.org/W3183518827","https://openalex.org/W3208710415","https://openalex.org/W4213440895","https://openalex.org/W4214922368","https://openalex.org/W4225093834","https://openalex.org/W4234704838","https://openalex.org/W4308616119","https://openalex.org/W4361011218","https://openalex.org/W4364353419","https://openalex.org/W4366144498","https://openalex.org/W4367173653","https://openalex.org/W4378640002","https://openalex.org/W4389606662","https://openalex.org/W4389747824","https://openalex.org/W4390616142","https://openalex.org/W4391142535","https://openalex.org/W4391144770","https://openalex.org/W4392785459","https://openalex.org/W4393935425","https://openalex.org/W4393943491","https://openalex.org/W4403534323","https://openalex.org/W4403685034","https://openalex.org/W4403733769","https://openalex.org/W4404821554","https://openalex.org/W4405995672","https://openalex.org/W4406089206","https://openalex.org/W4407491631","https://openalex.org/W4410079379","https://openalex.org/W4410102228"],"related_works":["https://openalex.org/W2062195135","https://openalex.org/W2898732673","https://openalex.org/W2410053581","https://openalex.org/W2383658677","https://openalex.org/W3123203398","https://openalex.org/W3147584709","https://openalex.org/W2795079307","https://openalex.org/W2961085424","https://openalex.org/W2977677679","https://openalex.org/W1972473893"],"abstract_inverted_index":{"Synonymous":[0],"mutations":[1,27,35,78,216],"do":[2],"not":[3],"change":[4],"amino":[5],"acid":[6],"sequences,":[7],"but":[8],"they":[9],"can":[10],"drive":[11],"cancer":[12,59,81],"by":[13,31],"influencing":[14],"splicing,":[15],"mRNA":[16],"structure,":[17],"translation":[18],"efficiency,":[19],"and":[20,107,121,186,220],"other":[21],"molecular":[22],"mechanisms.":[23],"Although":[24],"driver":[25,55,194],"synonymous":[26,56,72,77,195,215],"are":[28],"significantly":[29],"outnumbered":[30],"functionally":[32],"neutral":[33],"passenger":[34],"in":[36,58,217],"cancer,":[37],"their":[38],"accurate":[39],"discrimination":[40],"is":[41,224],"critical":[42],"to":[43,65,84,135,202],"understanding":[44],"tumorigenesis.":[45],"In":[46],"this":[47],"study,":[48],"we":[49,75,92],"developed":[50],"multiperspective":[51,144],"feature-based":[52],"predictor":[53],"for":[54,210],"mutation":[57,82],"(MFDSMC),":[60],"a":[61,117,187,207],"computational":[62],"framework":[63],"designed":[64],"improve":[66],"the":[67,137,143,176],"prediction":[68,138,172,212],"of":[69,191,213],"human":[70],"cancer-driver":[71,214],"mutations.":[73],"First,":[74],"curated":[76,188],"from":[79,165],"public":[80],"databases":[83],"construct":[85],"our":[86],"data":[87,189],"sets.":[88],"For":[89],"each":[90],"mutation,":[91],"systematically":[93],"characterized":[94],"features":[95,152,163],"across":[96],"four":[97],"biologically":[98],"informed":[99],"perspectives:":[100],"sequence":[101],"context,":[102],"evolutionary":[103],"conservation,":[104],"epigenetic":[105,162],"modifications,":[106],"regulatory/functional":[108,171],"predictions.":[109],"The":[110],"optimal":[111],"feature":[112,118,157],"subset":[113],"was":[114,133],"identified":[115],"through":[116],"importance":[119],"ranking":[120],"sequential":[122],"forward":[123],"selection.":[124],"After":[125],"multiple":[126],"machine":[127],"learning":[128],"classifiers":[129],"were":[130],"evaluated,":[131],"XGBoost":[132],"selected":[134],"build":[136],"model.":[139],"Results":[140],"revealed":[141],"that":[142],"fusion":[145],"model":[146],"outperformed":[147],"models":[148],"relying":[149],"on":[150,181],"single-perspective":[151],"or":[153],"lacking":[154],"any":[155],"individual":[156],"category.":[158],"Notably,":[159],"newly":[160],"introduced":[161],"derived":[164],"experimental":[166],"sequencing":[167],"data,":[168],"combined":[169],"with":[170],"features,":[173],"collectively":[174],"enhanced":[175],"model's":[177],"performance.":[178],"When":[179],"tested":[180],"two":[182],"independent":[183],"test":[184],"sets":[185],"set":[190],"experimentally":[192],"confirmed":[193],"mutations,":[196],"MFDSMC":[197,223],"exhibited":[198],"superior":[199],"performance":[200],"compared":[201],"existing":[203],"state-of-the-art":[204],"methods,":[205],"providing":[206],"novel":[208],"solution":[209],"precise":[211],"genomic":[218],"research":[219],"clinical":[221],"applications.":[222],"available":[225],"at":[226],"https://github.com/xialab-ahu/MFDSMC.":[227]},"counts_by_year":[],"updated_date":"2026-06-15T08:34:33.830935","created_date":"2025-10-10T00:00:00"}