{"id":"https://openalex.org/W2943939637","doi":"https://doi.org/10.1142/s0219720019400079","title":"Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles","display_name":"Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles","publication_year":2019,"publication_date":"2019-05-10","ids":{"openalex":"https://openalex.org/W2943939637","doi":"https://doi.org/10.1142/s0219720019400079","mag":"2943939637","pmid":"https://pubmed.ncbi.nlm.nih.gov/31288636"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720019400079","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720019400079","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","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/A5019402442","display_name":"Teppei Matsubara","orcid":null},"institutions":[{"id":"https://openalex.org/I129634264","display_name":"Toho University","ror":"https://ror.org/02hcx7n63","country_code":"JP","type":"education","lineage":["https://openalex.org/I129634264"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Teppei Matsubara","raw_affiliation_strings":["Department of Information Science, Faculty of Science, Toho University, Funabashi, Chiba, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Information Science, Faculty of Science, Toho University, Funabashi, Chiba, Japan","institution_ids":["https://openalex.org/I129634264"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037589658","display_name":"Tomoshiro Ochiai","orcid":null},"institutions":[{"id":"https://openalex.org/I15605915","display_name":"Otsuma Women's University","ror":"https://ror.org/012322w18","country_code":"JP","type":"education","lineage":["https://openalex.org/I15605915"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tomoshiro Ochiai","raw_affiliation_strings":["Department of Social Information Studies, Otsuma Women\u2019s University, Tokyo, Japan","Department of Social Information Studies, Otsuma Women's University, Tokyo, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Social Information Studies, Otsuma Women\u2019s University, Tokyo, Japan","institution_ids":["https://openalex.org/I15605915"]},{"raw_affiliation_string":"Department of Social Information Studies, Otsuma Women's University, Tokyo, Japan","institution_ids":["https://openalex.org/I15605915"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039138118","display_name":"Morihiro Hayashida","orcid":"https://orcid.org/0000-0001-7961-0175"},"institutions":[{"id":"https://openalex.org/I4210131413","display_name":"National Institute of Technology, Matsue College","ror":"https://ror.org/03qhht705","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210120810","https://openalex.org/I4210131413"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Morihiro Hayashida","raw_affiliation_strings":["Department of Electrical Engineering and Computer Science, National Institute of Technology, Matsue College, Shimane, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Electrical Engineering and Computer Science, National Institute of Technology, Matsue College, Shimane, Japan","institution_ids":["https://openalex.org/I4210131413"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5016330265","display_name":"Tatsuya Akutsu","orcid":"https://orcid.org/0000-0001-9763-797X"},"institutions":[{"id":"https://openalex.org/I4399598384","display_name":"Kyoto University Institute for Chemical Research","ror":"https://ror.org/0349bbg69","country_code":null,"type":"facility","lineage":["https://openalex.org/I22299242","https://openalex.org/I4399598384"]},{"id":"https://openalex.org/I22299242","display_name":"Kyoto University","ror":"https://ror.org/02kpeqv85","country_code":"JP","type":"education","lineage":["https://openalex.org/I22299242"]},{"id":"https://openalex.org/I4210088032","display_name":"Kyoto Bunkyo University","ror":"https://ror.org/0037an472","country_code":"JP","type":"education","lineage":["https://openalex.org/I4210088032"]}],"countries":["JP"],"is_corresponding":false,"raw_author_name":"Tatsuya Akutsu","raw_affiliation_strings":["Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Japan"],"affiliations":[{"raw_affiliation_string":"Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Japan","institution_ids":["https://openalex.org/I4210088032","https://openalex.org/I22299242","https://openalex.org/I4399598384"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5029985835","display_name":"Jose C. Nacher","orcid":"https://orcid.org/0000-0002-7187-6152"},"institutions":[{"id":"https://openalex.org/I129634264","display_name":"Toho University","ror":"https://ror.org/02hcx7n63","country_code":"JP","type":"education","lineage":["https://openalex.org/I129634264"]}],"countries":["JP"],"is_corresponding":true,"raw_author_name":"Jose C. Nacher","raw_affiliation_strings":["Department of Information Science, Faculty of Science, Toho University, Funabashi, Chiba, Japan"],"affiliations":[{"raw_affiliation_string":"Department of Information Science, Faculty of Science, Toho University, Funabashi, Chiba, Japan","institution_ids":["https://openalex.org/I129634264"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5029985835"],"corresponding_institution_ids":["https://openalex.org/I129634264"],"apc_list":null,"apc_paid":null,"fwci":1.6265,"has_fulltext":false,"cited_by_count":33,"citation_normalized_percentile":{"value":0.83842477,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":95,"max":99},"biblio":{"volume":"17","issue":"03","first_page":"1940007","last_page":"1940007"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9976999759674072,"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":0.9976999759674072,"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":0.9965000152587891,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9944999814033508,"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/convolutional-neural-network","display_name":"Convolutional neural network","score":0.7445321083068848},{"id":"https://openalex.org/keywords/lung-cancer","display_name":"Lung cancer","score":0.6593040227890015},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.563657820224762},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.5429049134254456},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.5306533575057983},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5083238482475281},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.49805307388305664},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.42708516120910645},{"id":"https://openalex.org/keywords/artificial-neural-network","display_name":"Artificial neural network","score":0.4109014868736267},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3437069058418274},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.3262638747692108},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.27232909202575684},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.16750943660736084},{"id":"https://openalex.org/keywords/oncology","display_name":"Oncology","score":0.15063470602035522}],"concepts":[{"id":"https://openalex.org/C81363708","wikidata":"https://www.wikidata.org/wiki/Q17084460","display_name":"Convolutional neural network","level":2,"score":0.7445321083068848},{"id":"https://openalex.org/C2776256026","wikidata":"https://www.wikidata.org/wiki/Q47912","display_name":"Lung cancer","level":2,"score":0.6593040227890015},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.563657820224762},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5429049134254456},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.5306533575057983},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5083238482475281},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.49805307388305664},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.42708516120910645},{"id":"https://openalex.org/C50644808","wikidata":"https://www.wikidata.org/wiki/Q192776","display_name":"Artificial neural network","level":2,"score":0.4109014868736267},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3437069058418274},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.3262638747692108},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27232909202575684},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.16750943660736084},{"id":"https://openalex.org/C143998085","wikidata":"https://www.wikidata.org/wiki/Q162555","display_name":"Oncology","level":1,"score":0.15063470602035522},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000069550","descriptor_name":"Machine Learning","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":"D000465","descriptor_name":"Algorithms","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":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D008175","descriptor_name":"Lung Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011897","descriptor_name":"Random Allocation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011897","descriptor_name":"Random Allocation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011897","descriptor_name":"Random Allocation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016000","descriptor_name":"Cluster Analysis","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":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060066","descriptor_name":"Protein Interaction Maps","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D060388","descriptor_name":"Support Vector Machine","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720019400079","is_oa":false,"landing_page_url":"https://doi.org/10.1142/s0219720019400079","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:31288636","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/31288636","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":19,"referenced_works":["https://openalex.org/W1019830208","https://openalex.org/W1481933820","https://openalex.org/W2029033394","https://openalex.org/W2059136964","https://openalex.org/W2069992656","https://openalex.org/W2140883620","https://openalex.org/W2144015117","https://openalex.org/W2160784118","https://openalex.org/W2243910093","https://openalex.org/W2507804718","https://openalex.org/W2581499940","https://openalex.org/W2773462233","https://openalex.org/W2786016794","https://openalex.org/W2798656189","https://openalex.org/W2889498145","https://openalex.org/W2949867299","https://openalex.org/W2963457143","https://openalex.org/W2964304355","https://openalex.org/W3103280005"],"related_works":["https://openalex.org/W4293226380","https://openalex.org/W4321487865","https://openalex.org/W4313906399","https://openalex.org/W2811106690","https://openalex.org/W2064573700","https://openalex.org/W4239306820","https://openalex.org/W2947043951","https://openalex.org/W2318112981","https://openalex.org/W4312417841","https://openalex.org/W2392243736"],"abstract_inverted_index":{"Deep":[0],"learning":[1,110],"technologies":[2],"are":[3],"permeating":[4],"every":[5],"field":[6],"from":[7,142],"image":[8],"and":[9,14,78,136],"speech":[10],"recognition":[11],"to":[12,25,59,82,131],"computational":[13,88,120],"systems":[15],"biology.":[16],"However,":[17],"the":[18,33,96,119,125,133,143],"application":[19],"of":[20,35,94,99,107],"convolutional":[21],"neural":[22,66],"networks":[23,37],"(CCNs)":[24],"\"omics\"":[26],"data":[27,77],"poses":[28],"some":[29],"difficulties,":[30],"such":[31,112],"as":[32,39,41,113],"processing":[34,58],"complex":[36],"structures":[38],"well":[40],"its":[42],"integration":[43],"with":[44],"transcriptome":[45],"data.":[46],"Here,":[47],"we":[48],"propose":[49],"a":[50],"CNN":[51,137],"approach":[52],"that":[53,91,124],"combines":[54],"spectral":[55],"clustering":[56],"information":[57],"classify":[60,83],"lung":[61,84],"cancer.":[62,85],"The":[63,86],"developed":[64],"<i>spectral-convolutional</i>":[65],"network":[67,76,128],"based":[68],"method":[69,102],"achieves":[70],"success":[71],"in":[72,92],"integrating":[73],"protein":[74,127],"interaction":[75],"gene":[79],"expression":[80],"profiles":[81],"performed":[87],"experiments":[89],"suggest":[90],"terms":[93],"accuracy":[95],"predictive":[97],"performance":[98],"our":[100],"proposed":[101],"was":[103],"better":[104],"than":[105],"those":[106],"other":[108],"machine":[109],"methods":[111],"SVM":[114],"or":[115],"Random":[116],"Forest.":[117],"Moreover,":[118],"results":[121],"also":[122],"indicate":[123],"underlying":[126],"structure":[129],"assists":[130],"enhance":[132],"predictions.":[134],"<i>Data":[135],"code":[138],"can":[139],"be":[140],"downloaded":[141],"link:</i>":[144],"https://sites.google.com/site/nacherlab/analysis.":[145]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":6},{"year":2022,"cited_by_count":3},{"year":2021,"cited_by_count":8},{"year":2020,"cited_by_count":4},{"year":2019,"cited_by_count":4}],"updated_date":"2026-03-17T09:09:15.849793","created_date":"2025-10-10T00:00:00"}