{"id":"https://openalex.org/W4381047109","doi":"https://doi.org/10.1093/bib/bbad229","title":"A feature extraction free approach for protein interactome inference from co-elution data","display_name":"A feature extraction free approach for protein interactome inference from co-elution data","publication_year":2023,"publication_date":"2023-06-16","ids":{"openalex":"https://openalex.org/W4381047109","doi":"https://doi.org/10.1093/bib/bbad229","pmid":"https://pubmed.ncbi.nlm.nih.gov/37328692"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbad229","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad229","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":false,"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":null,"license_id":null,"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":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5101724056","display_name":"Yu\u2010Hsin Chen","orcid":"https://orcid.org/0000-0002-7829-4008"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]},{"id":"https://openalex.org/I4210098366","display_name":"Institute of Information Science, Academia Sinica","ror":"https://ror.org/00z83z196","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210098366","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yu-Hsin Chen","raw_affiliation_strings":["Academia Sinica Institute of Information Science, , Taipei, 11529 , Taiwan","National Taiwan University Bioinformatics Program, Taiwan International Graduate Program, , Taipei 106 , Taiwan","Taiwan International Graduate Program, Academic Sinica Bioinformatics Program, , Taipei 11529 , Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Academia Sinica Institute of Information Science, , Taipei, 11529 , Taiwan","institution_ids":["https://openalex.org/I4210098366"]},{"raw_affiliation_string":"National Taiwan University Bioinformatics Program, Taiwan International Graduate Program, , Taipei 106 , Taiwan","institution_ids":["https://openalex.org/I16733864"]},{"raw_affiliation_string":"Taiwan International Graduate Program, Academic Sinica Bioinformatics Program, , Taipei 11529 , Taiwan","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5055017965","display_name":"Kuan-Hao Chao","orcid":"https://orcid.org/0000-0003-0099-0692"},"institutions":[{"id":"https://openalex.org/I4210098366","display_name":"Institute of Information Science, Academia Sinica","ror":"https://ror.org/00z83z196","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210098366","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Kuan-Hao Chao","raw_affiliation_strings":["Academia Sinica Institute of Information Science, , Taipei, 11529 , Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Academia Sinica Institute of Information Science, , Taipei, 11529 , Taiwan","institution_ids":["https://openalex.org/I4210098366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5031200576","display_name":"Jin Yung Wong","orcid":"https://orcid.org/0000-0002-8705-0283"},"institutions":[{"id":"https://openalex.org/I4210098366","display_name":"Institute of Information Science, Academia Sinica","ror":"https://ror.org/00z83z196","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210098366","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Jin Yung Wong","raw_affiliation_strings":["Academia Sinica Institute of Information Science, , Taipei, 11529 , Taiwan"],"raw_orcid":"https://orcid.org/0000-0002-8705-0283","affiliations":[{"raw_affiliation_string":"Academia Sinica Institute of Information Science, , Taipei, 11529 , Taiwan","institution_ids":["https://openalex.org/I4210098366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002830400","display_name":"Chien-Fu Jeff Liu","orcid":null},"institutions":[{"id":"https://openalex.org/I4210136969","display_name":"Institute of Molecular Biology, Academia Sinica","ror":"https://ror.org/047sbcx71","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210136969","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chien-Fu Liu","raw_affiliation_strings":["Academia Sinica Institute of Molecular Biology, , Taipei, 11529 , Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Academia Sinica Institute of Molecular Biology, , Taipei, 11529 , Taiwan","institution_ids":["https://openalex.org/I4210136969"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082231014","display_name":"Jun\u2010Yi Leu","orcid":"https://orcid.org/0000-0001-5445-2799"},"institutions":[{"id":"https://openalex.org/I4210136969","display_name":"Institute of Molecular Biology, Academia Sinica","ror":"https://ror.org/047sbcx71","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210136969","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Jun-Yi Leu","raw_affiliation_strings":["Academia Sinica Institute of Molecular Biology, , Taipei, 11529 , Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Academia Sinica Institute of Molecular Biology, , Taipei, 11529 , Taiwan","institution_ids":["https://openalex.org/I4210136969"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5000235008","display_name":"Huai\u2010Kuang Tsai","orcid":"https://orcid.org/0000-0002-4200-8137"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]},{"id":"https://openalex.org/I4210098366","display_name":"Institute of Information Science, Academia Sinica","ror":"https://ror.org/00z83z196","country_code":"TW","type":"facility","lineage":["https://openalex.org/I4210098366","https://openalex.org/I84653119"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Huai-Kuang Tsai","raw_affiliation_strings":["Academia Sinica Institute of Information Science, , Taipei, 11529 , Taiwan","National Taiwan University Bioinformatics Program, Taiwan International Graduate Program, , Taipei 106 , Taiwan","Taiwan International Graduate Program, Academic Sinica Bioinformatics Program, , Taipei 11529 , Taiwan"],"raw_orcid":"https://orcid.org/0000-0002-4200-8137","affiliations":[{"raw_affiliation_string":"Academia Sinica Institute of Information Science, , Taipei, 11529 , Taiwan","institution_ids":["https://openalex.org/I4210098366"]},{"raw_affiliation_string":"National Taiwan University Bioinformatics Program, Taiwan International Graduate Program, , Taipei 106 , Taiwan","institution_ids":["https://openalex.org/I16733864"]},{"raw_affiliation_string":"Taiwan International Graduate Program, Academic Sinica Bioinformatics Program, , Taipei 11529 , Taiwan","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5000235008","https://openalex.org/A5082231014"],"corresponding_institution_ids":["https://openalex.org/I16733864","https://openalex.org/I4210098366","https://openalex.org/I4210136969"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.3716,"has_fulltext":false,"cited_by_count":4,"citation_normalized_percentile":{"value":0.53983253,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":97},"biblio":{"volume":"24","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994000196456909,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9994000196456909,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.9973000288009644,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9904999732971191,"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":0.7739266157150269},{"id":"https://openalex.org/keywords/interactome","display_name":"Interactome","score":0.7224365472793579},{"id":"https://openalex.org/keywords/cluster-analysis","display_name":"Cluster analysis","score":0.6010642647743225},{"id":"https://openalex.org/keywords/overfitting","display_name":"Overfitting","score":0.5291367173194885},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5061463713645935},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4998910427093506},{"id":"https://openalex.org/keywords/inference","display_name":"Inference","score":0.47788703441619873},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4670409560203552},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.38078346848487854},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.27903908491134644},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.11926966905593872}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7739266157150269},{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.7224365472793579},{"id":"https://openalex.org/C73555534","wikidata":"https://www.wikidata.org/wiki/Q622825","display_name":"Cluster analysis","level":2,"score":0.6010642647743225},{"id":"https://openalex.org/C22019652","wikidata":"https://www.wikidata.org/wiki/Q331309","display_name":"Overfitting","level":3,"score":0.5291367173194885},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5061463713645935},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4998910427093506},{"id":"https://openalex.org/C2776214188","wikidata":"https://www.wikidata.org/wiki/Q408386","display_name":"Inference","level":2,"score":0.47788703441619873},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4670409560203552},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.38078346848487854},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.27903908491134644},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.11926966905593872},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0}],"mesh":[{"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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","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":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbad229","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbad229","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":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:37328692","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/37328692","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}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3980689656","display_name":null,"funder_award_id":"110-2221-E-001-013-MY3","funder_id":"https://openalex.org/F4320321040","funder_display_name":"National Science Council"}],"funders":[{"id":"https://openalex.org/F4320321040","display_name":"National Science Council","ror":"https://ror.org/02kv4zf79"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":38,"referenced_works":["https://openalex.org/W1611787727","https://openalex.org/W1777916189","https://openalex.org/W1979546531","https://openalex.org/W2055572452","https://openalex.org/W2082565035","https://openalex.org/W2124838818","https://openalex.org/W2143892509","https://openalex.org/W2156355974","https://openalex.org/W2163922914","https://openalex.org/W2616561032","https://openalex.org/W2624282460","https://openalex.org/W2809890174","https://openalex.org/W2888437519","https://openalex.org/W2896601950","https://openalex.org/W2903446149","https://openalex.org/W2911079020","https://openalex.org/W2911520656","https://openalex.org/W2917858269","https://openalex.org/W2946791964","https://openalex.org/W2949606885","https://openalex.org/W2952523648","https://openalex.org/W2957157683","https://openalex.org/W2957180077","https://openalex.org/W2957436444","https://openalex.org/W2959238762","https://openalex.org/W2962804563","https://openalex.org/W2990458240","https://openalex.org/W2992749711","https://openalex.org/W2994716258","https://openalex.org/W3015964336","https://openalex.org/W3037682562","https://openalex.org/W3108344241","https://openalex.org/W3157357317","https://openalex.org/W3176329976","https://openalex.org/W3208691473","https://openalex.org/W4288423437","https://openalex.org/W6737185339","https://openalex.org/W6765615279"],"related_works":["https://openalex.org/W4292634579","https://openalex.org/W1574414179","https://openalex.org/W4362597605","https://openalex.org/W4297676672","https://openalex.org/W4281702477","https://openalex.org/W2922073769","https://openalex.org/W4378510483","https://openalex.org/W2989932438","https://openalex.org/W4387297750","https://openalex.org/W2186333919"],"abstract_inverted_index":{"Protein":[0],"complexes":[1,233],"are":[2],"key":[3],"functional":[4],"units":[5],"in":[6,182],"cellular":[7],"processes.":[8],"High-throughput":[9],"techniques,":[10],"such":[11],"as":[12],"co-fractionation":[13],"coupled":[14],"with":[15,31,156,192],"mass":[16],"spectrometry":[17],"(CF-MS),":[18],"have":[19,63],"advanced":[20],"protein":[21,96,232],"complex":[22,32],"studies":[23],"by":[24,58,173],"enabling":[25],"global":[26],"interactome":[27,171],"inference.":[28],"However,":[29,115],"dealing":[30],"fractionation":[33],"characteristics":[34],"to":[35,48,52,66,93,131,134,162,212,229],"define":[36],"true":[37,201],"interactions":[38],"is":[39,46,245],"not":[40],"a":[41,146],"simple":[42],"task,":[43],"since":[44],"CF-MS":[45,68,86,168,218,237],"prone":[47],"false":[49],"positives":[50],"due":[51,133],"the":[53,104,116,135,179,186,204,221,236],"co-elution":[54],"of":[55,107,154,243],"non-interacting":[56],"proteins":[57],"chance.":[59],"Several":[60],"computational":[61],"methods":[62,78,101,128,181],"been":[64],"designed":[65],"analyze":[67],"data":[69,113,169],"and":[70,88,110,126,170],"construct":[71],"probabilistic":[72],"protein-protein":[73],"interaction":[74],"(PPI)":[75],"networks.":[76],"Current":[77],"usually":[79],"first":[80],"infer":[81,230],"PPIs":[82,184,215],"based":[83,119],"on":[84,120,235],"handcrafted":[85,108,117],"features,":[87],"then":[89],"use":[90],"clustering":[91,222],"algorithms":[92],"form":[94],"potential":[95,105],"complexes.":[97],"While":[98],"powerful,":[99],"these":[100,142],"suffer":[102],"from":[103,166,216],"bias":[106],"features":[109,118],"severely":[111,136],"imbalanced":[112,137,188],"distribution.":[114],"domain":[121],"knowledge":[122],"might":[123],"introduce":[124],"bias,":[125],"current":[127],"also":[129],"tend":[130],"overfit":[132],"PPI":[138],"data.":[139,219],"To":[140],"address":[141],"issues,":[143],"we":[144],"present":[145],"balanced":[147,193],"end-to-end":[148],"learning":[149],"architecture,":[150],"Software":[151],"for":[152,200],"Prediction":[153],"Interactome":[155],"Feature-extraction":[157],"Free":[158],"Elution":[159],"Data":[160],"(SPIFFED),":[161],"integrate":[163,213],"feature":[164],"representation":[165],"raw":[167],"prediction":[172],"convolutional":[174],"neural":[175],"network.":[176],"SPIFFED":[177,195,206,226,244],"outperforms":[178],"state-of-the-art":[180],"predicting":[183],"under":[185],"conventional":[187],"training.":[189],"When":[190],"trained":[191],"data,":[194],"had":[196],"greatly":[197],"improved":[198],"sensitivity":[199],"PPIs.":[202],"Moreover,":[203],"ensemble":[205],"model":[207],"provides":[208],"different":[209],"voting":[210],"schemes":[211],"predicted":[214],"multiple":[217],"Using":[220],"software":[223],"(i.e.":[224],"ClusterONE),":[225],"allows":[227],"users":[228],"high-confidence":[231],"depending":[234],"experimental":[238],"designs.":[239],"The":[240],"source":[241],"code":[242],"freely":[246],"available":[247],"at:":[248],"https://github.com/bio-it-station/SPIFFED.":[249]},"counts_by_year":[{"year":2025,"cited_by_count":3},{"year":2024,"cited_by_count":1}],"updated_date":"2026-07-29T09:40:50.615796","created_date":"2025-10-10T00:00:00"}
