{"id":"https://openalex.org/W4205184777","doi":"https://doi.org/10.1109/bibm52615.2021.9669479","title":"Predicting Hepatoma-Related Genes Based on Representation Learning of PPI network and Gene Ontology Annotations","display_name":"Predicting Hepatoma-Related Genes Based on Representation Learning of PPI network and Gene Ontology Annotations","publication_year":2021,"publication_date":"2021-12-09","ids":{"openalex":"https://openalex.org/W4205184777","doi":"https://doi.org/10.1109/bibm52615.2021.9669479"},"language":"en","primary_location":{"id":"doi:10.1109/bibm52615.2021.9669479","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm52615.2021.9669479","pdf_url":null,"source":{"id":"https://openalex.org/S4363607735","display_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"},"type":"conference-paper","indexed_in":["crossref"],"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/A5100453553","display_name":"Tao Wang","orcid":"https://orcid.org/0000-0002-5728-6463"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Tao Wang","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi\u2019an, China","School of Computer Science, Northwestern Polytechnical University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi\u2019an, China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066761150","display_name":"Zhiyuan Shao","orcid":"https://orcid.org/0000-0003-2139-6465"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Zhiyuan Shao","raw_affiliation_strings":["Honor College, Northwestern Polytechnical University, Xi\u2019an, China","Honor College, Northwestern Polytechnical University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Honor College, Northwestern Polytechnical University, Xi\u2019an, China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"Honor College, Northwestern Polytechnical University, Xi'an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053517207","display_name":"Yifu Xiao","orcid":null},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yifu Xiao","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi\u2019an, China","School of Computer Science, Northwestern Polytechnical University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi\u2019an, China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5115591852","display_name":"Xuchao Zhang","orcid":null},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuchao Zhang","raw_affiliation_strings":["Honor College, Northwestern Polytechnical University, Xi\u2019an, China","Honor College, Northwestern Polytechnical University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Honor College, Northwestern Polytechnical University, Xi\u2019an, China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"Honor College, Northwestern Polytechnical University, Xi'an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5007778184","display_name":"Yitian Chen","orcid":"https://orcid.org/0000-0001-5259-251X"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yitian Chen","raw_affiliation_strings":["Honor College, Northwestern Polytechnical University, Xi\u2019an, China","Honor College, Northwestern Polytechnical University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Honor College, Northwestern Polytechnical University, Xi\u2019an, China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"Honor College, Northwestern Polytechnical University, Xi'an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5026008687","display_name":"Binze Shi","orcid":null},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Binze Shi","raw_affiliation_strings":["Honor College, Northwestern Polytechnical University, Xi\u2019an, China","Honor College, Northwestern Polytechnical University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Honor College, Northwestern Polytechnical University, Xi\u2019an, China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"Honor College, Northwestern Polytechnical University, Xi'an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100325172","display_name":"Siyu Chen","orcid":"https://orcid.org/0000-0002-3809-1062"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Siyu Chen","raw_affiliation_strings":["Honor College, Northwestern Polytechnical University, Xi\u2019an, China","Honor College, Northwestern Polytechnical University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Honor College, Northwestern Polytechnical University, Xi\u2019an, China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"Honor College, Northwestern Polytechnical University, Xi'an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101477538","display_name":"Yuxian Wang","orcid":"https://orcid.org/0000-0002-3450-2565"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuxian Wang","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi\u2019an, China","School of Computer Science, Northwestern Polytechnical University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi\u2019an, China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5084343474","display_name":"Jiajie Peng","orcid":"https://orcid.org/0000-0002-3857-7927"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jiajie Peng","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi\u2019an, China","School of Computer Science, Northwestern Polytechnical University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi\u2019an, China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an, China","institution_ids":["https://openalex.org/I17145004"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5009944817","display_name":"Xuequn Shang","orcid":"https://orcid.org/0000-0002-7249-8210"},"institutions":[{"id":"https://openalex.org/I17145004","display_name":"Northwestern Polytechnical University","ror":"https://ror.org/01y0j0j86","country_code":"CN","type":"education","lineage":["https://openalex.org/I17145004"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xuequn Shang","raw_affiliation_strings":["School of Computer Science, Northwestern Polytechnical University, Xi\u2019an, China","School of Computer Science, Northwestern Polytechnical University, Xi'an, China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi\u2019an, China","institution_ids":["https://openalex.org/I17145004"]},{"raw_affiliation_string":"School of Computer Science, Northwestern Polytechnical University, Xi'an, China","institution_ids":["https://openalex.org/I17145004"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":[],"corresponding_institution_ids":["https://openalex.org/I17145004"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"1892","last_page":"1898"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9997000098228455,"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":0.9997000098228455,"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":0.9970999956130981,"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/T11297","display_name":"Ferroptosis and cancer prognosis","score":0.9829000234603882,"subfield":{"id":"https://openalex.org/subfields/2740","display_name":"Pulmonary and Respiratory Medicine"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.7603815793991089},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6095665693283081},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.5819282531738281},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5522819757461548},{"id":"https://openalex.org/keywords/representation","display_name":"Representation (politics)","score":0.49779462814331055},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.495025098323822},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.49098971486091614},{"id":"https://openalex.org/keywords/feature-learning","display_name":"Feature learning","score":0.4766686260700226},{"id":"https://openalex.org/keywords/ontology","display_name":"Ontology","score":0.47559651732444763},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.40452077984809875},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.39514467120170593},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26746195554733276},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13958868384361267},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.09556230902671814}],"concepts":[{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.7603815793991089},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6095665693283081},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.5819282531738281},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5522819757461548},{"id":"https://openalex.org/C2776359362","wikidata":"https://www.wikidata.org/wiki/Q2145286","display_name":"Representation (politics)","level":3,"score":0.49779462814331055},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.495025098323822},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.49098971486091614},{"id":"https://openalex.org/C59404180","wikidata":"https://www.wikidata.org/wiki/Q17013334","display_name":"Feature learning","level":2,"score":0.4766686260700226},{"id":"https://openalex.org/C25810664","wikidata":"https://www.wikidata.org/wiki/Q44325","display_name":"Ontology","level":2,"score":0.47559651732444763},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.40452077984809875},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.39514467120170593},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26746195554733276},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13958868384361267},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.09556230902671814},{"id":"https://openalex.org/C111472728","wikidata":"https://www.wikidata.org/wiki/Q9471","display_name":"Epistemology","level":1,"score":0.0},{"id":"https://openalex.org/C199539241","wikidata":"https://www.wikidata.org/wiki/Q7748","display_name":"Law","level":1,"score":0.0},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C94625758","wikidata":"https://www.wikidata.org/wiki/Q7163","display_name":"Politics","level":2,"score":0.0},{"id":"https://openalex.org/C17744445","wikidata":"https://www.wikidata.org/wiki/Q36442","display_name":"Political science","level":0,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/bibm52615.2021.9669479","is_oa":false,"landing_page_url":"https://doi.org/10.1109/bibm52615.2021.9669479","pdf_url":null,"source":{"id":"https://openalex.org/S4363607735","display_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","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":"conference"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.8600000143051147}],"awards":[],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320335787","display_name":"Fundamental Research Funds for the Central Universities","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":42,"referenced_works":["https://openalex.org/W1888005072","https://openalex.org/W2020301095","https://openalex.org/W2031441006","https://openalex.org/W2054782946","https://openalex.org/W2108984616","https://openalex.org/W2110798204","https://openalex.org/W2133299088","https://openalex.org/W2144393227","https://openalex.org/W2149129433","https://openalex.org/W2154851992","https://openalex.org/W2157997136","https://openalex.org/W2492804124","https://openalex.org/W2529646902","https://openalex.org/W2537679995","https://openalex.org/W2548139789","https://openalex.org/W2582585762","https://openalex.org/W2742577494","https://openalex.org/W2750635169","https://openalex.org/W2765775596","https://openalex.org/W2767507021","https://openalex.org/W2798078985","https://openalex.org/W2809583854","https://openalex.org/W2893804842","https://openalex.org/W2911389042","https://openalex.org/W2950834624","https://openalex.org/W2962286297","https://openalex.org/W2962756421","https://openalex.org/W2977235223","https://openalex.org/W2990592286","https://openalex.org/W3004459507","https://openalex.org/W3008117655","https://openalex.org/W3014623641","https://openalex.org/W3022603009","https://openalex.org/W3025871655","https://openalex.org/W3104097132","https://openalex.org/W3126516421","https://openalex.org/W3128822439","https://openalex.org/W3196076186","https://openalex.org/W3201206168","https://openalex.org/W4244879745","https://openalex.org/W6676481782","https://openalex.org/W6729502743"],"related_works":["https://openalex.org/W2669956259","https://openalex.org/W4249005693","https://openalex.org/W4392946183","https://openalex.org/W3088732000","https://openalex.org/W2983142544","https://openalex.org/W2891059443","https://openalex.org/W4281663961","https://openalex.org/W3208888551","https://openalex.org/W4313561566","https://openalex.org/W3208386644"],"abstract_inverted_index":{"Hepatoma":[0],"is":[1],"the":[2,16,22,31,48,65,91,104],"most":[3],"common":[4],"type":[5],"of":[6,21,30,50,67,83],"primary":[7],"liver":[8],"cancer":[9],"with":[10,34,116,187,197],"a":[11,126],"high":[12],"mortality":[13],"rate":[14],"in":[15,39,59,79],"world.":[17],"The":[18],"genetic":[19],"causes":[20],"disease":[23,40,61,76,98],"pathology":[24],"remain":[25],"largely":[26],"unknown.":[27],"Effective":[28],"discovery":[29,78,100],"genes":[32,62,115,132,171,186],"associated":[33],"hepatoma":[35,212],"has":[36,149],"become":[37],"important":[38],"prevention,":[41],"early":[42],"diagnosis,":[43],"and":[44,143,157,189,193],"therapeutic":[45],"treatments.":[46],"With":[47],"developments":[49],"molecular":[51],"networks,":[52],"graph-based":[53],"methods":[54,96,199],"have":[55,74,177],"been":[56],"tremendously":[57],"successful":[58],"predicting":[60,169],"based":[63,133,166],"on":[64,134,167,211],"hypothesis":[66],"guilt-by-association.":[68],"Network":[69],"representation":[70,94,135,203],"learning":[71,136,152,174],"(NRL)":[72],"techniques":[73],"accelerated":[75],"gene":[77,99,105,109,144,158,213],"recent":[80],"years":[81],"because":[82],"their":[84],"powerful":[85],"network":[86,93,142,156],"feature":[87],"extraction":[88],"ability.":[89],"However,":[90],"current":[92],"learning-based":[95],"for":[97],"did":[101],"not":[102],"consider":[103],"features":[106,153,165],"derived":[107],"from":[108,137,154],"ontology":[110,145],"annotations,":[111],"which":[112],"apriori":[113],"group":[114],"similar":[117],"functions.":[118],"To":[119],"fill":[120],"this":[121],"gap,":[122],"here":[123],"we":[124],"propose":[125],"novel":[127],"framework":[128,148,181,206],"to":[129],"predict":[130,184],"hepatoma-related":[131,170,185],"both":[138],"protein-protein":[139],"interactions":[140],"(PPI)":[141],"annotations.":[146],"Our":[147],"three":[150],"steps:":[151],"PPI":[155],"ontologies":[159],"using":[160,172,200],"NRL":[161],"techniques,":[162],"integrating":[163],"different":[164],"autoencoder,":[168],"machine":[173],"classifiers.":[175],"Experiments":[176],"demonstrated":[178],"that":[179],"our":[180,205],"could":[182],"accurately":[183],"AUROC":[188],"AUPRC":[190],"reaching":[191],"0.93":[192],"0.94,":[194],"respectively.":[195],"Compared":[196],"other":[198],"only":[201],"single":[202],"features,":[204],"also":[207],"shows":[208],"superior":[209],"performance":[210],"prediction.":[214]},"counts_by_year":[{"year":2025,"cited_by_count":4},{"year":2023,"cited_by_count":2},{"year":2022,"cited_by_count":3}],"updated_date":"2026-07-14T23:27:15.235271","created_date":"2025-10-10T00:00:00"}
