{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,17]],"date-time":"2026-03-17T05:58:47Z","timestamp":1773727127563,"version":"3.50.1"},"reference-count":18,"publisher":"World Scientific Pub Co Pte Lt","issue":"03","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["J. Bioinform. Comput. Biol."],"published-print":{"date-parts":[[2019,6]]},"abstract":"<jats:p> Deep learning technologies are permeating every field from image and speech recognition to computational and systems biology. However, the application of convolutional neural networks (CCNs) to \u201comics\u201d data poses some difficulties, such as the processing of complex networks structures as well as its integration with transcriptome data. Here, we propose a CNN approach that combines spectral clustering information processing to classify lung cancer. The developed spectral-convolutional neural network based method achieves success in integrating protein interaction network data and gene expression profiles to classify lung cancer. The performed computational experiments suggest that in terms of accuracy the predictive performance of our proposed method was better than those of other machine learning methods such as SVM or Random Forest. Moreover, the computational results also indicate that the underlying protein network structure assists to enhance the predictions. Data and CNN code can be downloaded from the link: https:\/\/sites.google.com\/site\/nacherlab\/analysis <\/jats:p>","DOI":"10.1142\/s0219720019400079","type":"journal-article","created":{"date-parts":[[2019,5,10]],"date-time":"2019-05-10T05:44:12Z","timestamp":1557467052000},"page":"1940007","source":"Crossref","is-referenced-by-count":24,"title":["Convolutional neural network approach to lung cancer classification integrating protein interaction network and gene expression profiles"],"prefix":"10.1142","volume":"17","author":[{"given":"Teppei","family":"Matsubara","sequence":"first","affiliation":[{"name":"Department of Information Science, Faculty of Science, Toho University, Funabashi, Chiba, Japan"}]},{"given":"Tomoshiro","family":"Ochiai","sequence":"additional","affiliation":[{"name":"Department of Social Information Studies, Otsuma Women\u2019s University, Tokyo, Japan"}]},{"given":"Morihiro","family":"Hayashida","sequence":"additional","affiliation":[{"name":"Department of Electrical Engineering and Computer Science, National Institute of Technology, Matsue College, Shimane, Japan"}]},{"given":"Tatsuya","family":"Akutsu","sequence":"additional","affiliation":[{"name":"Bioinformatics Center, Institute for Chemical Research, Kyoto University Uji, Japan"}]},{"given":"Jose C.","family":"Nacher","sequence":"additional","affiliation":[{"name":"Department of Information Science, Faculty of Science, Toho University, Funabashi, Chiba, Japan"}]}],"member":"219","published-online":{"date-parts":[[2019,7,9]]},"reference":[{"key":"S0219720019400079BIB001","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts598"},{"key":"S0219720019400079BIB002","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005324"},{"key":"S0219720019400079BIB003","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2014.2343960"},{"key":"S0219720019400079BIB004","doi-asserted-by":"publisher","DOI":"10.1038\/srep18962"},{"key":"S0219720019400079BIB005","doi-asserted-by":"publisher","DOI":"10.1038\/srep17573"},{"key":"S0219720019400079BIB006","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx780"},{"key":"S0219720019400079BIB007","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btu277"},{"key":"S0219720019400079BIB008","doi-asserted-by":"publisher","DOI":"10.1038\/nbt.3300"},{"key":"S0219720019400079BIB009","doi-asserted-by":"publisher","DOI":"10.1186\/s12864-016-2931-8"},{"key":"S0219720019400079BIB010","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty429"},{"key":"S0219720019400079BIB011","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bty294"},{"key":"S0219720019400079BIB012","doi-asserted-by":"publisher","DOI":"10.1186\/1752-0509-6-92"},{"key":"S0219720019400079BIB014","first-page":"871","volume-title":"Graph Theory, Combinatorics, and Applications","volume":"2","author":"Mohar B","year":"1991"},{"key":"S0219720019400079BIB015","doi-asserted-by":"publisher","DOI":"10.1007\/978-94-015-8937-6_6"},{"key":"S0219720019400079BIB016","doi-asserted-by":"publisher","DOI":"10.1007\/s00026-005-0237-z"},{"key":"S0219720019400079BIB018","doi-asserted-by":"publisher","DOI":"10.1093\/comnet\/cny011"},{"key":"S0219720019400079BIB019","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-017-1490-6"},{"key":"S0219720019400079BIB020","doi-asserted-by":"publisher","DOI":"10.1038\/nrg3000"}],"container-title":["Journal of Bioinformatics and Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.worldscientific.com\/doi\/pdf\/10.1142\/S0219720019400079","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,8,6]],"date-time":"2019-08-06T17:16:47Z","timestamp":1565111807000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.worldscientific.com\/doi\/abs\/10.1142\/S0219720019400079"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,6]]},"references-count":18,"journal-issue":{"issue":"03","published-online":{"date-parts":[[2019,7,9]]},"published-print":{"date-parts":[[2019,6]]}},"alternative-id":["10.1142\/S0219720019400079"],"URL":"https:\/\/doi.org\/10.1142\/s0219720019400079","relation":{},"ISSN":["0219-7200","1757-6334"],"issn-type":[{"value":"0219-7200","type":"print"},{"value":"1757-6334","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,6]]}}}