{"id":"https://openalex.org/W2901115733","doi":"https://doi.org/10.1186/s12859-018-2385-x","title":"Evaluating the impact of topological protein features on the negative examples selection","display_name":"Evaluating the impact of topological protein features on the negative examples selection","publication_year":2018,"publication_date":"2018-11-01","ids":{"openalex":"https://openalex.org/W2901115733","doi":"https://doi.org/10.1186/s12859-018-2385-x","mag":"2901115733","pmid":"https://pubmed.ncbi.nlm.nih.gov/30453879"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-018-2385-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2385-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2385-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2385-x","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5038842358","display_name":"Paolo Boldi","orcid":"https://orcid.org/0000-0002-8297-6255"},"institutions":[{"id":"https://openalex.org/I189158943","display_name":"University of Milan","ror":"https://ror.org/00wjc7c48","country_code":"IT","type":"education","lineage":["https://openalex.org/I189158943"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Paolo Boldi","raw_affiliation_strings":["Department of Computer Science, Universit\u00e0 degli Studi di Milano, Via Comelico 39, Milano, 20135, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Universit\u00e0 degli Studi di Milano, Via Comelico 39, Milano, 20135, Italy","institution_ids":["https://openalex.org/I189158943"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5075385368","display_name":"Marco Frasca","orcid":"https://orcid.org/0000-0002-4170-0922"},"institutions":[{"id":"https://openalex.org/I189158943","display_name":"University of Milan","ror":"https://ror.org/00wjc7c48","country_code":"IT","type":"education","lineage":["https://openalex.org/I189158943"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Marco Frasca","raw_affiliation_strings":["Department of Computer Science, Universit\u00e0 degli Studi di Milano, Via Comelico 39, Milano, 20135, Italy. frasca@di.unimi.it","Department of Computer Science, Universit\u00e0 degli Studi di Milano, Via Comelico 39, Milano, 20135, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Universit\u00e0 degli Studi di Milano, Via Comelico 39, Milano, 20135, Italy. frasca@di.unimi.it","institution_ids":[]},{"raw_affiliation_string":"Department of Computer Science, Universit\u00e0 degli Studi di Milano, Via Comelico 39, Milano, 20135, Italy","institution_ids":["https://openalex.org/I189158943"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5005837237","display_name":"Dario Malchiodi","orcid":"https://orcid.org/0000-0002-7574-697X"},"institutions":[{"id":"https://openalex.org/I189158943","display_name":"University of Milan","ror":"https://ror.org/00wjc7c48","country_code":"IT","type":"education","lineage":["https://openalex.org/I189158943"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Dario Malchiodi","raw_affiliation_strings":["Department of Computer Science, Universit\u00e0 degli Studi di Milano, Via Comelico 39, Milano, 20135, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Computer Science, Universit\u00e0 degli Studi di Milano, Via Comelico 39, Milano, 20135, Italy","institution_ids":["https://openalex.org/I189158943"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5038842358"],"corresponding_institution_ids":["https://openalex.org/I189158943"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.1856,"has_fulltext":true,"cited_by_count":2,"citation_normalized_percentile":{"value":0.54622365,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"19","issue":"S14","first_page":"417","last_page":"417"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.949999988079071,"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":0.949999988079071,"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":0.021700000390410423,"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":0.00570000009611249,"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/protein-function-prediction","display_name":"Protein function prediction","score":0.8574285507202148},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6610618233680725},{"id":"https://openalex.org/keywords/centrality","display_name":"Centrality","score":0.6426985859870911},{"id":"https://openalex.org/keywords/heuristics","display_name":"Heuristics","score":0.6225478649139404},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.5495365262031555},{"id":"https://openalex.org/keywords/feature-selection","display_name":"Feature selection","score":0.5401879549026489},{"id":"https://openalex.org/keywords/pairwise-comparison","display_name":"Pairwise comparison","score":0.5384500026702881},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.5122939348220825},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5101037621498108},{"id":"https://openalex.org/keywords/selection","display_name":"Selection (genetic algorithm)","score":0.47725602984428406},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4301527440547943},{"id":"https://openalex.org/keywords/negative-selection","display_name":"Negative selection","score":0.4294845163822174},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.4237411618232727},{"id":"https://openalex.org/keywords/graph","display_name":"Graph","score":0.42311209440231323},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.416454553604126},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.3723224401473999},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.31888771057128906},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.2991659939289093},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.2894952893257141},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.23047125339508057},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22853609919548035},{"id":"https://openalex.org/keywords/protein-function","display_name":"Protein function","score":0.22367450594902039},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16503003239631653},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1023796796798706}],"concepts":[{"id":"https://openalex.org/C207060522","wikidata":"https://www.wikidata.org/wiki/Q7251473","display_name":"Protein function prediction","level":4,"score":0.8574285507202148},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6610618233680725},{"id":"https://openalex.org/C53811970","wikidata":"https://www.wikidata.org/wiki/Q5062194","display_name":"Centrality","level":2,"score":0.6426985859870911},{"id":"https://openalex.org/C127705205","wikidata":"https://www.wikidata.org/wiki/Q5748245","display_name":"Heuristics","level":2,"score":0.6225478649139404},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.5495365262031555},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.5401879549026489},{"id":"https://openalex.org/C184898388","wikidata":"https://www.wikidata.org/wiki/Q1435712","display_name":"Pairwise comparison","level":2,"score":0.5384500026702881},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.5122939348220825},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5101037621498108},{"id":"https://openalex.org/C81917197","wikidata":"https://www.wikidata.org/wiki/Q628760","display_name":"Selection (genetic algorithm)","level":2,"score":0.47725602984428406},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4301527440547943},{"id":"https://openalex.org/C7386963","wikidata":"https://www.wikidata.org/wiki/Q3954859","display_name":"Negative selection","level":4,"score":0.4294845163822174},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.4237411618232727},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.42311209440231323},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.416454553604126},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3723224401473999},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.31888771057128906},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.2991659939289093},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.2894952893257141},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.23047125339508057},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22853609919548035},{"id":"https://openalex.org/C2986374874","wikidata":"https://www.wikidata.org/wiki/Q8054","display_name":"Protein function","level":3,"score":0.22367450594902039},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16503003239631653},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1023796796798706},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","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":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","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":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D063990","descriptor_name":"Gene Ontology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-018-2385-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2385-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2385-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:30453879","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30453879","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:air.unimi.it:2434/602835","is_oa":true,"landing_page_url":"http://hdl.handle.net/2434/602835","pdf_url":null,"source":{"id":"https://openalex.org/S4306400516","display_name":"Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I189158943","host_organization_name":"University of Milan","host_organization_lineage":["https://openalex.org/I189158943"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:12d38c6be1854db4a6be966bfab023b5","is_oa":true,"landing_page_url":"https://doaj.org/article/12d38c6be1854db4a6be966bfab023b5","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 19, Iss S14, Pp 115-126 (2018)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:5218675","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6245585","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-018-2385-x","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-018-2385-x","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-018-2385-x","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/10","display_name":"Reduced inequalities","score":0.6800000071525574}],"awards":[],"funders":[{"id":"https://openalex.org/F4320313475","display_name":"Universit\u00e0 degli Studi di Milano","ror":"https://ror.org/00wjc7c48"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2901115733.pdf","grobid_xml":"https://content.openalex.org/works/W2901115733.grobid-xml"},"referenced_works_count":45,"referenced_works":["https://openalex.org/W1099525816","https://openalex.org/W1486817521","https://openalex.org/W1533936090","https://openalex.org/W1546155242","https://openalex.org/W1547701650","https://openalex.org/W1590721879","https://openalex.org/W1594031697","https://openalex.org/W1971937094","https://openalex.org/W1982667316","https://openalex.org/W2011986160","https://openalex.org/W2012336263","https://openalex.org/W2014915963","https://openalex.org/W2025844353","https://openalex.org/W2036249298","https://openalex.org/W2044917239","https://openalex.org/W2050871273","https://openalex.org/W2056944867","https://openalex.org/W2096173332","https://openalex.org/W2097391022","https://openalex.org/W2103017472","https://openalex.org/W2109886974","https://openalex.org/W2112090702","https://openalex.org/W2112615110","https://openalex.org/W2117486996","https://openalex.org/W2119821739","https://openalex.org/W2120688086","https://openalex.org/W2122886155","https://openalex.org/W2124204060","https://openalex.org/W2125282516","https://openalex.org/W2127637605","https://openalex.org/W2134784378","https://openalex.org/W2137917513","https://openalex.org/W2149055390","https://openalex.org/W2158261276","https://openalex.org/W2177922486","https://openalex.org/W2227395312","https://openalex.org/W2487155602","https://openalex.org/W2601850923","https://openalex.org/W2612641875","https://openalex.org/W2770983033","https://openalex.org/W2911964244","https://openalex.org/W2913754224","https://openalex.org/W3085162807","https://openalex.org/W3123262389","https://openalex.org/W6843735874"],"related_works":["https://openalex.org/W1630454103","https://openalex.org/W2021723654","https://openalex.org/W3132344302","https://openalex.org/W2082380079","https://openalex.org/W2061838210","https://openalex.org/W2033366093","https://openalex.org/W2039416962","https://openalex.org/W3104092632","https://openalex.org/W2060079687","https://openalex.org/W2411047100"],"abstract_inverted_index":{"BACKGROUND:":[0],"Supervised":[1],"machine":[2],"learning":[3],"methods":[4],"when":[5,354],"applied":[6],"to":[7,27,37,93,101,118,245,261,270,341],"the":[8,16,54,59,67,91,102,139,145,151,162,174,190,210,218,223,254,264,288,309,321,326,334,347],"problem":[9,82,301],"of":[10,18,104,141,147,181,225,357],"automated":[11],"protein-function":[12],"prediction":[13,260],"(AFP)":[14],"require":[15],"availability":[17],"both":[19],"positive":[20,317],"examples":[21,35],"(i.e.,":[22,207,215],"proteins":[23,38,149,165,285],"which":[24,112,123,247,307],"are":[25,115,250,267,359],"known":[26],"possess":[28],"a":[29,64,78,171,229],"given":[30],"protein":[31,113,124,192,202,248,258],"function)":[32],"and":[33,48,80,131,186,196,201,213,239],"negative":[34,68,74,148,255,275,281,338,344],"(corresponding":[36],"not":[39,61],"associated":[40],"with":[41,304,351],"that":[42,121,164,333],"function).":[43],"Unfortunately,":[44],"publicly":[45],"available":[46],"proteome":[47],"genome":[49],"data":[50],"sources":[51,180],"such":[52,183],"as":[53,184],"Gene":[55,152],"Ontology":[56,153],"rarely":[57],"store":[58],"functions":[60],"possessed":[62],"by":[63,277],"protein.":[65],"Thus":[66],"selection,":[69],"consisting":[70],"in":[71,83,128,170,232,346],"identifying":[72],"informative":[73,299],"examples,":[75],"is":[76,158,308,320],"currently":[77],"central":[79],"challenging":[81],"AFP.":[84],"Several":[85],"heuristics":[86],"have":[87],"been":[88],"proposed":[89,191,289,335],"through":[90,287],"years":[92],"solve":[94],"this":[95,119],"problem;":[96],"nevertheless,":[97],"despite":[98],"their":[99],"effectiveness,":[100],"best":[103],"our":[105],"knowledge":[106],"no":[107],"previous":[108],"existing":[109],"work":[110,137],"studied":[111],"features":[114,125,143,249,265,293,336,358],"more":[116,127,251,298],"relevant":[117,311],"task,":[120],"is,":[122],"help":[126],"discriminating":[129],"reliable":[130],"unreliable":[132],"negatives.":[133],"RESULTS:":[134],"The":[135,156,315],"present":[136],"analyses":[138],"impact":[140],"several":[142,179],"on":[144,209,236,284],"selection":[146,244,276,282,339],"for":[150,253,300,325],"(GO)":[154],"terms.":[155],"analysis":[157],"network-based:":[159],"it":[160],"exploits":[161],"fact":[163],"can":[166,204],"be":[167,205],"naturally":[168],"structured":[169],"network,":[172],"considering":[173],"pairwise":[175],"relationships":[176],"coming":[177],"from":[178],"data,":[182],"protein-protein":[185],"genetic":[187],"interactions.":[188],"Overall,":[189],"features,":[193],"including":[194],"local":[195],"global":[197],"graph":[198],"centrality":[199],"measures":[200],"multifunctionality,":[203],"term-aware":[206],"depending":[208],"GO":[211,219,272],"term)":[212],"term-unaware":[214,313],"invariant":[216],"across":[217],"terms).":[220],"We":[221],"validated":[222],"informativeness":[224],"each":[226],"feature":[227,243,324],"utilizing":[228],"temporal":[230,348],"holdout":[231,349],"three":[233],"different":[234,280],"experiments":[235],"yeast,":[237],"mouse":[238],"human":[240],"proteomes:":[241],"(i)":[242],"detect":[246],"helpful":[252],"selection;":[256],"(ii)":[257],"function":[259],"verify":[262],"whether":[263],"considered":[266],"also":[268,360],"useful":[269],"predict":[271],"terms;":[273],"(iii)":[274,331],"applying":[278],"two":[279],"algorithms":[283,340],"represented":[286],"features.":[290,314],"CONCLUSIONS:":[291],"Term-aware":[292],"(with":[294],"some":[295],"exceptions)":[296],"resulted":[297],"(i),":[302],"together":[303],"node":[305,316],"betweenness,":[306],"most":[310,322],"among":[312],"neighborhood":[318],"instead":[319],"predictive":[323],"AFP":[327],"problem,":[328],"while":[329],"experiment":[330],"showed":[332],"allow":[337],"select":[342],"effectively":[343],"instances":[345],"setting,":[350],"better":[352],"results":[353],"nonlinear":[355],"combinations":[356],"exploited.":[361]},"counts_by_year":[{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
