{"id":"https://openalex.org/W2804848440","doi":"https://doi.org/10.1145/3326172.3326228","title":"Analysis of Novel Annotations in the Gene Ontology for Boosting the Selection of Negative Examples","display_name":"Analysis of Novel Annotations in the Gene Ontology for Boosting the Selection of Negative Examples","publication_year":2019,"publication_date":"2019-03-28","ids":{"openalex":"https://openalex.org/W2804848440","doi":"https://doi.org/10.1145/3326172.3326228","mag":"2804848440"},"language":"en","primary_location":{"id":"doi:10.1145/3326172.3326228","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3326172.3326228","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2019 9th International Conference on Biomedical Engineering and Technology","raw_type":"proceedings-article"},"type":"preprint","indexed_in":["arxiv","crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://arxiv.org/pdf/1805.09135","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102834081","display_name":"Maryam Sepehri","orcid":"https://orcid.org/0000-0001-8751-5143"},"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":"Maryam Sepehri","raw_affiliation_strings":["Dipartimento di Informatica, Universit\u00e0 Degli Studi di Milano, Milan, Italy","Dipartimento Di Informatica, Universita\u2019 degli Studi di Milano, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica, Universit\u00e0 Degli Studi di Milano, Milan, Italy","institution_ids":["https://openalex.org/I189158943"]},{"raw_affiliation_string":"Dipartimento Di Informatica, Universita\u2019 degli Studi di Milano, Milan, Italy","institution_ids":["https://openalex.org/I189158943"]}]},{"author_position":"last","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":["Dipartimento di Informatica, Universit\u00e0 Degli Studi di Milano, Milan, Italy","Dipartimento Di Informatica, Universita\u2019 degli Studi di Milano, Milan, Italy"],"affiliations":[{"raw_affiliation_string":"Dipartimento di Informatica, Universit\u00e0 Degli Studi di Milano, Milan, Italy","institution_ids":["https://openalex.org/I189158943"]},{"raw_affiliation_string":"Dipartimento Di Informatica, Universita\u2019 degli Studi di Milano, Milan, Italy","institution_ids":["https://openalex.org/I189158943"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5102834081"],"corresponding_institution_ids":["https://openalex.org/I189158943"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":{"value":0.00216323,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"294","last_page":"301"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9976000189781189,"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":0.9976000189781189,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9972000122070312,"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":0.988099992275238,"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/gene-ontology","display_name":"Gene ontology","score":0.729274332523346},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6862713098526001},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.6177133321762085},{"id":"https://openalex.org/keywords/negative-selection","display_name":"Negative selection","score":0.5757671594619751},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.5616289973258972},{"id":"https://openalex.org/keywords/boosting","display_name":"Boosting (machine learning)","score":0.557887852191925},{"id":"https://openalex.org/keywords/proteome","display_name":"Proteome","score":0.5359846353530884},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5109704732894897},{"id":"https://openalex.org/keywords/hierarchy","display_name":"Hierarchy","score":0.5053480267524719},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4863213002681732},{"id":"https://openalex.org/keywords/function","display_name":"Function (biology)","score":0.4768715500831604},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.42186206579208374},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.41466203331947327},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.38754546642303467},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.34130674600601196},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.33736515045166016},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.32175007462501526},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.23608869314193726},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.19941073656082153},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.12179762125015259},{"id":"https://openalex.org/keywords/programming-language","display_name":"Programming language","score":0.09472328424453735}],"concepts":[{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.729274332523346},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6862713098526001},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.6177133321762085},{"id":"https://openalex.org/C7386963","wikidata":"https://www.wikidata.org/wiki/Q3954859","display_name":"Negative selection","level":4,"score":0.5757671594619751},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.5616289973258972},{"id":"https://openalex.org/C46686674","wikidata":"https://www.wikidata.org/wiki/Q466303","display_name":"Boosting (machine learning)","level":2,"score":0.557887852191925},{"id":"https://openalex.org/C104397665","wikidata":"https://www.wikidata.org/wiki/Q860947","display_name":"Proteome","level":2,"score":0.5359846353530884},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5109704732894897},{"id":"https://openalex.org/C31170391","wikidata":"https://www.wikidata.org/wiki/Q188619","display_name":"Hierarchy","level":2,"score":0.5053480267524719},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4863213002681732},{"id":"https://openalex.org/C14036430","wikidata":"https://www.wikidata.org/wiki/Q3736076","display_name":"Function (biology)","level":2,"score":0.4768715500831604},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.42186206579208374},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.41466203331947327},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.38754546642303467},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.34130674600601196},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.33736515045166016},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.32175007462501526},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.23608869314193726},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.19941073656082153},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.12179762125015259},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.09472328424453735},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C34447519","wikidata":"https://www.wikidata.org/wiki/Q179522","display_name":"Market economy","level":1,"score":0.0},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C162324750","wikidata":"https://www.wikidata.org/wiki/Q8134","display_name":"Economics","level":0,"score":0.0},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1145/3326172.3326228","is_oa":false,"landing_page_url":"https://doi.org/10.1145/3326172.3326228","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Proceedings of the 2019 9th International Conference on Biomedical Engineering and Technology","raw_type":"proceedings-article"},{"id":"pmh:oai:arXiv.org:1805.09135","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1805.09135","pdf_url":"https://arxiv.org/pdf/1805.09135","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"mag:2804848440","is_oa":true,"landing_page_url":"https://arxiv.org/pdf/1805.09135","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"arXiv (Cornell University)","raw_type":null},{"id":"doi:10.48550/arxiv.1805.09135","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.1805.09135","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"pmh:oai:arXiv.org:1805.09135","is_oa":true,"landing_page_url":"http://arxiv.org/abs/1805.09135","pdf_url":"https://arxiv.org/pdf/1805.09135","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320313475","display_name":"Universit\u00e0 degli Studi di Milano","ror":"https://ror.org/00wjc7c48"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2804848440.pdf","grobid_xml":"https://content.openalex.org/works/W2804848440.grobid-xml"},"referenced_works_count":10,"referenced_works":["https://openalex.org/W1590721879","https://openalex.org/W1857789879","https://openalex.org/W2012336263","https://openalex.org/W2060900933","https://openalex.org/W2103017472","https://openalex.org/W2117486996","https://openalex.org/W2125282516","https://openalex.org/W2601850923","https://openalex.org/W2999549716","https://openalex.org/W4252684946"],"related_works":["https://openalex.org/W2962905145","https://openalex.org/W3126250723","https://openalex.org/W2126072631","https://openalex.org/W2223216628","https://openalex.org/W2036389830","https://openalex.org/W2547983958","https://openalex.org/W2124320575","https://openalex.org/W2786164586","https://openalex.org/W2032104514","https://openalex.org/W1571935984","https://openalex.org/W2293073759","https://openalex.org/W1597559145","https://openalex.org/W2782901658","https://openalex.org/W2186578971","https://openalex.org/W2062350236","https://openalex.org/W2770565711","https://openalex.org/W2158897405","https://openalex.org/W2098432760","https://openalex.org/W2432911131","https://openalex.org/W2117235735"],"abstract_inverted_index":{"Public":[0],"repositories":[1],"for":[2,37],"genome":[3,134],"and":[4],"proteome":[5],"annotations,":[6,16],"such":[7],"as":[8,113],"the":[9,30,39,67,72,79,86,93,99,145],"Gene":[10],"Ontology":[11],"(GO),":[12],"rarely":[13],"stores":[14],"negative":[15,33,53,114,142],"i.e.":[17],"proteins":[18,46,54,108],"not":[19],"possessing":[20],"a":[21,121,133],"given":[22],"function.":[23],"This":[24,64],"leaves":[25],"undefined":[26],"or":[27],"ill":[28],"defined":[29],"set":[31],"of":[32,41,71,75,95,124,147],"examples,which":[34],"is":[35],"crucial":[36],"training":[38],"majority":[40],"machine":[42],"learning":[43],"methods":[44],"inferring":[45],"functions.":[47],"Automated":[48],"techniques":[49],"to":[50,58,91,110,140],"choose":[51,141],"reliable":[52],"are":[55],"thereby":[56],"required":[57],"train":[59],"accurate":[60],"function":[61],"prediction":[62],"models.":[63],"study":[65],"proposes":[66],"first":[68],"extensive":[69],"analysis":[70],"temporal":[73],"evolution":[74],"protein":[76],"annotations":[77,83],"in":[78,98,132,144],"GO":[80,100],"repository.":[81],"Novel":[82],"registered":[84],"through":[85],"years":[87],"have":[88],"been":[89,118],"analyzed":[90],"verify":[92],"presence":[94],"annotation":[96],"patterns":[97],"hierarchy.":[101],"Our":[102],"research":[103],"supplied":[104],"fundamental":[105],"clues":[106],"about":[107],"likely":[109],"be":[111],"unreliable":[112],"examples,":[115],"that":[116],"has":[117],"verified":[119],"into":[120],"novel":[122],"algorithm":[123],"our":[125],"own":[126],"construction,":[127],"validated":[128],"on":[129],"two":[130],"organisms":[131],"wide":[135],"fashion":[136],"against":[137],"approaches":[138],"proposed":[139],"examples":[143],"context":[146],"functional":[148],"prediction.":[149]},"counts_by_year":[],"updated_date":"2026-03-20T23:20:44.827607","created_date":"2025-10-10T00:00:00"}
