{"id":"https://openalex.org/W4411446595","doi":"https://doi.org/10.1109/tcbbio.2025.3581509","title":"BTR-MCL: A Bioinformatics Tool Recommendation Method With Multi-View Contrastive Learning","display_name":"BTR-MCL: A Bioinformatics Tool Recommendation Method With Multi-View Contrastive Learning","publication_year":2025,"publication_date":"2025-06-19","ids":{"openalex":"https://openalex.org/W4411446595","doi":"https://doi.org/10.1109/tcbbio.2025.3581509","pmid":"https://pubmed.ncbi.nlm.nih.gov/40811265"},"language":"en","primary_location":{"id":"doi:10.1109/tcbbio.2025.3581509","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3581509","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","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/A5074459001","display_name":"Deyou Tang","orcid":"https://orcid.org/0000-0002-3796-3965"},"institutions":[{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Deyou Tang","raw_affiliation_strings":["School of Software Engineering, South China University of Technology, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"School of Software Engineering, South China University of Technology, Guangzhou, China","institution_ids":["https://openalex.org/I90610280"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5113418900","display_name":"B. Lv","orcid":null},"institutions":[{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Biyao Lv","raw_affiliation_strings":["School of Software Engineering, South China University of Technology, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"School of Software Engineering, South China University of Technology, Guangzhou, China","institution_ids":["https://openalex.org/I90610280"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100568799","display_name":"Zhao Rong","orcid":"https://orcid.org/0009-0008-8613-4072"},"institutions":[{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Rong Zhao","raw_affiliation_strings":["School of Software Engineering, South China University of Technology, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"School of Software Engineering, South China University of Technology, Guangzhou, China","institution_ids":["https://openalex.org/I90610280"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048283341","display_name":"Pingjian Zhang","orcid":"https://orcid.org/0000-0002-9087-4494"},"institutions":[{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Pingjian Zhang","raw_affiliation_strings":["School of Software Engineering, South China University of Technology, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"School of Software Engineering, South China University of Technology, Guangzhou, China","institution_ids":["https://openalex.org/I90610280"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5060036625","display_name":"Chao Liu","orcid":"https://orcid.org/0000-0003-1665-778X"},"institutions":[{"id":"https://openalex.org/I90610280","display_name":"South China University of Technology","ror":"https://ror.org/0530pts50","country_code":"CN","type":"education","lineage":["https://openalex.org/I90610280"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chao Liu","raw_affiliation_strings":["School of Software Engineering, South China University of Technology, Guangzhou, China"],"affiliations":[{"raw_affiliation_string":"School of Software Engineering, South China University of Technology, Guangzhou, China","institution_ids":["https://openalex.org/I90610280"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5074459001"],"corresponding_institution_ids":["https://openalex.org/I90610280"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.15700982,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"5","first_page":"2068","last_page":"2081"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9567000269889832,"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/T13937","display_name":"Genetics, Bioinformatics, and Biomedical Research","score":0.9567000269889832,"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":0.717615008354187},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4095798432826996},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.394319623708725},{"id":"https://openalex.org/keywords/natural-language-processing","display_name":"Natural language processing","score":0.3897196054458618},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3849726915359497},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.3570997416973114},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.10291007161140442}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.717615008354187},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4095798432826996},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.394319623708725},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.3897196054458618},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3849726915359497},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.3570997416973114},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.10291007161140442}],"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":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","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":"D012984","descriptor_name":"Software","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":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"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},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1109/tcbbio.2025.3581509","is_oa":false,"landing_page_url":"https://doi.org/10.1109/tcbbio.2025.3581509","pdf_url":null,"source":{"id":"https://openalex.org/S5407042751","display_name":"IEEE Transactions on Computational Biology and Bioinformatics","issn_l":"2998-4165","issn":["2998-4165"],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"IEEE Transactions on Computational Biology and Bioinformatics","raw_type":"journal-article"},{"id":"pmid:40811265","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40811265","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":"IEEE transactions on computational biology and bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":54,"referenced_works":["https://openalex.org/W317957491","https://openalex.org/W1969739015","https://openalex.org/W2033278690","https://openalex.org/W2040588310","https://openalex.org/W2048679005","https://openalex.org/W2055043387","https://openalex.org/W2141541659","https://openalex.org/W2145360759","https://openalex.org/W2145374174","https://openalex.org/W2211150216","https://openalex.org/W2283196293","https://openalex.org/W2509893387","https://openalex.org/W2741249238","https://openalex.org/W2792839191","https://openalex.org/W2801992635","https://openalex.org/W2802296168","https://openalex.org/W2884134047","https://openalex.org/W2911489562","https://openalex.org/W2913560138","https://openalex.org/W2917207851","https://openalex.org/W2945623882","https://openalex.org/W2956159526","https://openalex.org/W2963911286","https://openalex.org/W2972993521","https://openalex.org/W3035524453","https://openalex.org/W3045200674","https://openalex.org/W3046375318","https://openalex.org/W3081170586","https://openalex.org/W3091993229","https://openalex.org/W3097300053","https://openalex.org/W3113332183","https://openalex.org/W3113410469","https://openalex.org/W3122109253","https://openalex.org/W3129482887","https://openalex.org/W3160531185","https://openalex.org/W3203589076","https://openalex.org/W3208227120","https://openalex.org/W3209186881","https://openalex.org/W4221142212","https://openalex.org/W4224914537","https://openalex.org/W4225412853","https://openalex.org/W4225463176","https://openalex.org/W4281747803","https://openalex.org/W4312122891","https://openalex.org/W4321480047","https://openalex.org/W4384625597","https://openalex.org/W4389050432","https://openalex.org/W4389950236","https://openalex.org/W4390191048","https://openalex.org/W4391376193","https://openalex.org/W4395467502","https://openalex.org/W4396767577","https://openalex.org/W4400844648","https://openalex.org/W4404458588"],"related_works":["https://openalex.org/W2748952813","https://openalex.org/W3188962172","https://openalex.org/W2772917594","https://openalex.org/W4312825515","https://openalex.org/W4306742369","https://openalex.org/W4303457083","https://openalex.org/W2131146434","https://openalex.org/W2951359407","https://openalex.org/W4376623224","https://openalex.org/W3204019825"],"abstract_inverted_index":{"Digital":[0],"informatization":[1],"in":[2,9,19,158],"bioinformatics":[3,17,32,44,60,89,103,144],"research":[4],"has":[5],"developed":[6],"rapidly,":[7],"resulting":[8],"the":[10,35,41,49,66,74,102,107,123,136,139,143,153,169,173,178,184],"emergence":[11],"of":[12,14,16,59,69,155],"tens":[13],"thousands":[15],"tools":[18,61,145],"recent":[20],"decades.":[21],"However,":[22],"few":[23],"researchers":[24],"systematically":[25],"study":[26],"how":[27],"to":[28,51,62,76,121],"manage":[29],"and":[30,56,92,105,126,142,151,160],"recommend":[31],"tools.":[33,81],"Meanwhile,":[34],"existing":[36],"recommendation":[37,175],"methods":[38],"suffer":[39],"from":[40,94],"incompatibility":[42],"with":[43,112],"tool":[45,156],"recommendations,":[46],"specifically,":[47],"i)":[48],"inability":[50,75],"mine":[52],"rich":[53],"semantic":[54],"information":[55,125],"potential":[57],"correlations":[58],"make":[63],"up":[64],"for":[65,101,131],"sparse":[67],"problem":[68],"operation-tool":[70,140],"history":[71],"interaction;":[72],"ii)":[73],"accommodate":[77],"recommendations":[78],"dominated":[79],"by":[80,181],"To":[82],"address":[83],"these":[84],"problems,":[85],"we":[86],"collected":[87],"quantitative":[88],"operations,":[90],"tools,":[91,104],"context":[93],"https://bio.tools,":[95],"constructed":[96],"a":[97],"knowledge":[98,146],"graph":[99],"dataset":[100],"proposed":[106],"Bioinformatics":[108],"Tool":[109],"Recommendation":[110],"Method":[111],"Multi-view":[113],"Contrastive":[114],"Learning":[115],"(BTR-MCL).":[116],"The":[117],"method":[118],"utilizes":[119],"BERT":[120],"enrich":[122],"descriptive":[124],"constructs":[127],"three":[128],"fine-grained":[129],"views":[130],"multi-view":[132],"contrastive":[133,162],"learning,":[134,163],"namely":[135],"tool-tool":[137],"graph,":[138,141],"graph.":[147],"By":[148],"data":[149],"augmentation":[150],"enhancing":[152],"importance":[154],"embedding":[157],"local":[159],"global":[161],"BTR-MCL":[164],"achieves":[165],"significant":[166],"improvements":[167],"over":[168],"state-of-the-art":[170],"baselines":[171],"on":[172,183],"top-K":[174],"task,":[176],"outperforming":[177],"best":[179],"baseline":[180],"82.71%":[182],"Recall@10":[185],"metric.":[186]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}