{"id":"https://openalex.org/W3020930839","doi":"https://doi.org/10.1093/bib/bbaa043","title":"Application of deep learning methods in biological networks","display_name":"Application of deep learning methods in biological networks","publication_year":2020,"publication_date":"2020-04-06","ids":{"openalex":"https://openalex.org/W3020930839","doi":"https://doi.org/10.1093/bib/bbaa043","mag":"3020930839","pmid":"https://pubmed.ncbi.nlm.nih.gov/32363401"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbaa043","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa043","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/A5015486123","display_name":"Shuting Jin","orcid":"https://orcid.org/0000-0002-8113-9367"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Shuting Jin","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5027286013","display_name":"Xiangxiang Zeng","orcid":"https://orcid.org/0000-0001-6201-0114"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiangxiang Zeng","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5089615958","display_name":"Feng Xia","orcid":"https://orcid.org/0000-0002-8324-1859"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Feng Xia","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5001389153","display_name":"Wei Huang","orcid":"https://orcid.org/0000-0002-8284-2310"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Wei Huang","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5026771763","display_name":"Xiangrong Liu","orcid":"https://orcid.org/0000-0001-9885-1978"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Xiangrong Liu","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5015486123"],"corresponding_institution_ids":[],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":9.5946,"has_fulltext":false,"cited_by_count":214,"citation_normalized_percentile":{"value":0.98853937,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":97,"max":100},"biblio":{"volume":"22","issue":"2","first_page":"1902","last_page":"1917"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998000264167786,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.9998000264167786,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.998199999332428,"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/T11273","display_name":"Advanced Graph Neural Networks","score":0.9945999979972839,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5921438932418823},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.45846495032310486},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.4475227892398834}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5921438932418823},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.45846495032310486},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.4475227892398834}],"mesh":[{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000077321","descriptor_name":"Deep Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004347","descriptor_name":"Drug Interactions","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005838","descriptor_name":"Genotype","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":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D010641","descriptor_name":"Phenotype","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":"D016503","descriptor_name":"Drug Delivery Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016503","descriptor_name":"Drug Delivery Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016503","descriptor_name":"Drug Delivery Systems","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016571","descriptor_name":"Neural Networks, Computer","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D055808","descriptor_name":"Drug Discovery","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D057225","descriptor_name":"Data Mining","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},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D064307","descriptor_name":"Microbiota","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbaa043","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbaa043","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:32363401","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32363401","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/G1674180717","display_name":null,"funder_award_id":"61922020","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4223954286","display_name":null,"funder_award_id":"2017J01099","funder_id":"https://openalex.org/F4320321878","funder_display_name":"Natural Science Foundation of Fujian Province"},{"id":"https://openalex.org/G5091875258","display_name":null,"funder_award_id":"61872309","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G6565709209","display_name":null,"funder_award_id":"61425002","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8390325463","display_name":null,"funder_award_id":"61772441","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8683327949","display_name":null,"funder_award_id":"61872007","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320321878","display_name":"Natural Science Foundation of Fujian Province","ror":null}],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":120,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1501213224","https://openalex.org/W1892460815","https://openalex.org/W1971106435","https://openalex.org/W1973667149","https://openalex.org/W1996973085","https://openalex.org/W2003390994","https://openalex.org/W2025768430","https://openalex.org/W2043329626","https://openalex.org/W2045870710","https://openalex.org/W2071013590","https://openalex.org/W2074110893","https://openalex.org/W2076063813","https://openalex.org/W2096868555","https://openalex.org/W2107830215","https://openalex.org/W2114533766","https://openalex.org/W2116341502","https://openalex.org/W2118023920","https://openalex.org/W2126671570","https://openalex.org/W2130139983","https://openalex.org/W2133564696","https://openalex.org/W2143612262","https://openalex.org/W2148143831","https://openalex.org/W2153838454","https://openalex.org/W2171543215","https://openalex.org/W2214665483","https://openalex.org/W2290847742","https://openalex.org/W2301363727","https://openalex.org/W2306570595","https://openalex.org/W2346276919","https://openalex.org/W2393319904","https://openalex.org/W2465015709","https://openalex.org/W2508932077","https://openalex.org/W2559655401","https://openalex.org/W2594760713","https://openalex.org/W2607497028","https://openalex.org/W2610153490","https://openalex.org/W2612690371","https://openalex.org/W2615066396","https://openalex.org/W2615071493","https://openalex.org/W2617837836","https://openalex.org/W2620796800","https://openalex.org/W2624407581","https://openalex.org/W2726111596","https://openalex.org/W2731261909","https://openalex.org/W2767178841","https://openalex.org/W2767353193","https://openalex.org/W2768956845","https://openalex.org/W2777863841","https://openalex.org/W2777945434","https://openalex.org/W2782785453","https://openalex.org/W2786016794","https://openalex.org/W2794932993","https://openalex.org/W2796742697","https://openalex.org/W2799351678","https://openalex.org/W2805310212","https://openalex.org/W2806115886","https://openalex.org/W2808867307","https://openalex.org/W2809418595","https://openalex.org/W2809867059","https://openalex.org/W2860192827","https://openalex.org/W2887411239","https://openalex.org/W2902302341","https://openalex.org/W2904900486","https://openalex.org/W2912802963","https://openalex.org/W2943714799","https://openalex.org/W2950947945","https://openalex.org/W2951203227","https://openalex.org/W2951422523","https://openalex.org/W2951424836","https://openalex.org/W2952342008","https://openalex.org/W2955251621","https://openalex.org/W2962756421","https://openalex.org/W2962876161","https://openalex.org/W2963017945","https://openalex.org/W2963312728","https://openalex.org/W2963542991","https://openalex.org/W2963984147","https://openalex.org/W2964015378","https://openalex.org/W2964304355","https://openalex.org/W2964308564","https://openalex.org/W2966795188","https://openalex.org/W2970472075","https://openalex.org/W2993012267","https://openalex.org/W3015490653","https://openalex.org/W3100157108","https://openalex.org/W3105136071","https://openalex.org/W3152893301","https://openalex.org/W4200556375","https://openalex.org/W4210257598","https://openalex.org/W4239253651","https://openalex.org/W4256361765","https://openalex.org/W4293355908","https://openalex.org/W4294558607","https://openalex.org/W4295547865","https://openalex.org/W4309125009","https://openalex.org/W4322614756","https://openalex.org/W6629368666","https://openalex.org/W6631758623","https://openalex.org/W6637568146","https://openalex.org/W6643894919","https://openalex.org/W6661892480","https://openalex.org/W6675582425","https://openalex.org/W6677132398","https://openalex.org/W6688357764","https://openalex.org/W6698577564","https://openalex.org/W6705521318","https://openalex.org/W6719270105","https://openalex.org/W6725434214","https://openalex.org/W6726873649","https://openalex.org/W6730084236","https://openalex.org/W6743410771","https://openalex.org/W6745929367","https://openalex.org/W6747203395","https://openalex.org/W6749904121","https://openalex.org/W6750260501","https://openalex.org/W6758830137","https://openalex.org/W6763812735","https://openalex.org/W6766438228","https://openalex.org/W6766893680"],"related_works":["https://openalex.org/W2731899572","https://openalex.org/W3215138031","https://openalex.org/W4321369474","https://openalex.org/W3009238340","https://openalex.org/W4360585206","https://openalex.org/W4285208911","https://openalex.org/W3082895349","https://openalex.org/W4213079790","https://openalex.org/W2248239756","https://openalex.org/W4323565446"],"abstract_inverted_index":{"The":[0,135],"increase":[1,48],"in":[2,49],"biological":[3,18,21,33,56,186],"data":[4,50,68,75,149,161,172],"and":[5,40,66,80,122,130,146,151],"the":[6,35,41,47,53,74,106,124,157,169,180,191],"formation":[7],"of":[8,26,32,37,55,76,90,102,108,159,182,195],"various":[9],"biomolecule":[10],"interaction":[11],"databases":[12],"enable":[13],"us":[14],"to":[15,71,143,156],"obtain":[16],"diverse":[17],"networks.":[19,187],"These":[20],"networks":[22,57],"provide":[23],"a":[24,88,99,114],"wealth":[25],"raw":[27],"materials":[28],"for":[29,43],"further":[30],"understanding":[31],"systems,":[34],"discovery":[36],"complex":[38,67,145],"diseases":[39],"search":[42],"therapeutic":[44],"drugs.":[45],"However,":[46],"also":[51],"increases":[52],"difficulty":[54],"analysis.":[58],"Therefore,":[59],"algorithms":[60],"that":[61,93],"can":[62,120,140],"handle":[63],"large,":[64],"heterogeneous":[65,147],"are":[69],"needed":[70],"better":[72],"analyze":[73],"these":[77],"network":[78,112,115,160,171],"structures":[79,150],"mine":[81],"their":[82],"useful":[83],"information.":[84,162],"Deep":[85],"learning":[86,92,119,133,138,174,184],"is":[87,152],"branch":[89],"machine":[91],"extracts":[94],"more":[95],"abstract":[96],"features":[97],"from":[98],"larger":[100],"set":[101],"training":[103],"data.":[104],"Through":[105],"establishment":[107],"an":[109],"artificial":[110],"neural":[111],"with":[113],"hierarchy":[116],"structure,":[117],"deep":[118,137,173,183],"extract":[121],"screen":[123],"input":[125],"information":[126],"layer":[127,129],"by":[128],"has":[131],"representation":[132],"ability.":[134],"improved":[136],"algorithm":[139],"be":[141],"used":[142,170],"process":[144],"graph":[148],"increasingly":[153],"being":[154],"applied":[155],"mining":[158],"In":[163],"this":[164,196],"paper,":[165],"we":[166,178,189],"first":[167],"introduce":[168],"models.":[175],"After":[176],"words,":[177],"summarize":[179],"application":[181],"on":[185],"Finally,":[188],"discuss":[190],"future":[192],"development":[193],"prospects":[194],"field.":[197]},"counts_by_year":[{"year":2026,"cited_by_count":3},{"year":2025,"cited_by_count":44},{"year":2024,"cited_by_count":52},{"year":2023,"cited_by_count":24},{"year":2022,"cited_by_count":44},{"year":2021,"cited_by_count":43},{"year":2020,"cited_by_count":4}],"updated_date":"2026-03-28T08:17:26.163206","created_date":"2025-10-10T00:00:00"}
