{"id":"https://openalex.org/W2117407746","doi":"https://doi.org/10.1093/bioinformatics/btu857","title":"More challenges for machine-learning protein interactions","display_name":"More challenges for machine-learning protein interactions","publication_year":2015,"publication_date":"2015-01-12","ids":{"openalex":"https://openalex.org/W2117407746","doi":"https://doi.org/10.1093/bioinformatics/btu857","mag":"2117407746","pmid":"https://pubmed.ncbi.nlm.nih.gov/25586513"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btu857","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu857","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/10/1521/49012547/bioinformatics_31_10_1521.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/31/10/1521/49012547/bioinformatics_31_10_1521.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5004159021","display_name":"Tobias Hamp","orcid":null},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Tobias Hamp","raw_affiliation_strings":["Department of Informatics, Bioinformatics and Computational Biology I12, Technische Universit\u00e4t M\u00fcnchen, 85748 Garching/Munich, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, Bioinformatics and Computational Biology I12, Technische Universit\u00e4t M\u00fcnchen, 85748 Garching/Munich, Germany","institution_ids":["https://openalex.org/I62916508"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064905883","display_name":"Burkhard Rost","orcid":"https://orcid.org/0000-0003-0179-8424"},"institutions":[{"id":"https://openalex.org/I62916508","display_name":"Technical University of Munich","ror":"https://ror.org/02kkvpp62","country_code":"DE","type":"education","lineage":["https://openalex.org/I62916508"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Burkhard Rost","raw_affiliation_strings":["Department of Informatics, Bioinformatics and Computational Biology I12, Technische Universit\u00e4t M\u00fcnchen, 85748 Garching/Munich, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Informatics, Bioinformatics and Computational Biology I12, Technische Universit\u00e4t M\u00fcnchen, 85748 Garching/Munich, Germany","institution_ids":["https://openalex.org/I62916508"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":3.6148,"has_fulltext":false,"cited_by_count":74,"citation_normalized_percentile":{"value":0.93573253,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"31","issue":"10","first_page":"1521","last_page":"1525"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9991999864578247,"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":0.9991999864578247,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9950000047683716,"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/T10044","display_name":"Protein Structure and Dynamics","score":0.982699990272522,"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":0.6447433829307556},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4326745271682739},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.3836604952812195}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6447433829307556},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4326745271682739},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.3836604952812195}],"mesh":[{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001185","descriptor_name":"Artificial Intelligence","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020539","descriptor_name":"Sequence Analysis, Protein","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":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D029701","descriptor_name":"Saccharomyces cerevisiae Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btu857","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu857","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/10/1521/49012547/bioinformatics_31_10_1521.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:25586513","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/25586513","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:open-archive.highwire.org:bioinfo:31/10/1521","is_oa":false,"landing_page_url":"http://bioinformatics.oxfordjournals.org/cgi/content/short/31/10/1521","pdf_url":null,"source":{"id":"https://openalex.org/S4406923041","display_name":"HighWire Press Open Archive","issn_l":null,"issn":null,"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":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"TEXT"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btu857","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btu857","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/31/10/1521/49012547/bioinformatics_31_10_1521.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320308269","display_name":"Alexander von Humboldt-Stiftung","ror":"https://ror.org/012kf4317"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1680392829","https://openalex.org/W1976952616","https://openalex.org/W1985818354","https://openalex.org/W1993591356","https://openalex.org/W2008840001","https://openalex.org/W2011340259","https://openalex.org/W2067305633","https://openalex.org/W2099254366","https://openalex.org/W2101220662","https://openalex.org/W2108102049","https://openalex.org/W2115595474","https://openalex.org/W2130687290","https://openalex.org/W2133990480","https://openalex.org/W2134396951","https://openalex.org/W2150452800","https://openalex.org/W2151006472","https://openalex.org/W2152705149","https://openalex.org/W2168267323","https://openalex.org/W2170525533","https://openalex.org/W6637386731"],"related_works":["https://openalex.org/W2961085424","https://openalex.org/W4306674287","https://openalex.org/W3046775127","https://openalex.org/W3107602296","https://openalex.org/W3170094116","https://openalex.org/W4386462264","https://openalex.org/W4313488044","https://openalex.org/W3209574120","https://openalex.org/W4364306694","https://openalex.org/W4312192474"],"abstract_inverted_index":{"MOTIVATION:":[0],"Machine":[1],"learning":[2],"may":[3],"be":[4,132,152],"the":[5,47,121,137,141,144,155,168,173,184],"most":[6,169],"popular":[7],"computational":[8],"tool":[9],"in":[10,25,172],"molecular":[11],"biology.":[12,26],"Providing":[13],"sustained":[14],"performance":[15,101,166],"estimates":[16],"is":[17,167],"challenging.":[18],"The":[19,162],"standard":[20],"cross-validation":[21],"protocols":[22,34],"usually":[23],"fail":[24,35],"Park":[27],"and":[28,143,154],"Marcotte":[29],"found":[30,153],"that":[31,115,181],"even":[32],"refined":[33],"for":[36,46,102,186],"protein-protein":[37],"interactions":[38,75,150],"(PPIs).":[39],"RESULTS:":[40],"Here,":[41],"we":[42],"sketch":[43],"additional":[44],"problems":[45],"prediction":[48,122,128,176],"of":[49,64,73,87,123,158,165,175],"PPIs":[50,182],"from":[51],"sequence":[52,138],"alone.":[53],"First,":[54],"it":[55],"not":[56,99],"only":[57],"matters":[58],"whether":[59,79],"proteins":[60,72,86,104],"A":[61,80],"or":[62,81],"B":[63,82],"a":[65,111],"target":[66],"interaction":[67,94],"A-B":[68],"are":[69,83],"similar":[70,84],"to":[71,85,107,131,160],"training":[74,91,114,145],"(positives),":[76],"but":[77],"also":[78],"non-interactions":[88],"(negatives).":[89],"Second,":[90],"on":[92,136],"multiple":[93],"partners":[95],"per":[96],"protein":[97],"did":[98],"improve":[100],"new":[103],"(not":[105],"used":[106],"train).":[108],"In":[109],"contrary,":[110],"strictly":[112],"non-redundant":[113],"ignored":[116],"good":[117],"data":[118],"slightly":[119],"improved":[120],"difficult":[124],"cases.":[125],"Third,":[126],"which":[127],"method":[129],"appears":[130],"best":[133],"crucially":[134],"depends":[135],"similarity":[139],"between":[140],"test":[142],"set,":[146],"how":[147],"many":[148],"true":[149],"should":[151],"expected":[156],"ratio":[157],"negatives":[159],"positives.":[161],"correct":[163],"assessment":[164],"complicated":[170],"task":[171],"development":[174],"methods.":[177],"Our":[178],"analyses":[179],"suggest":[180],"square":[183],"challenge":[185],"this":[187],"task.":[188]},"counts_by_year":[{"year":2026,"cited_by_count":4},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":8},{"year":2023,"cited_by_count":9},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":7},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":6},{"year":2018,"cited_by_count":9},{"year":2017,"cited_by_count":6},{"year":2016,"cited_by_count":7},{"year":2015,"cited_by_count":2}],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2025-10-10T00:00:00"}
