{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,28]],"date-time":"2025-10-28T00:32:05Z","timestamp":1761611525785,"version":"3.37.3"},"reference-count":50,"publisher":"Wiley","license":[{"start":{"date-parts":[[2021,1,4]],"date-time":"2021-01-04T00:00:00Z","timestamp":1609718400000},"content-version":"unspecified","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100007162","name":"Guangdong Science and Technology Department","doi-asserted-by":"publisher","award":["2017A010405039","201707020007","2018B020203003","17ZR1412500"],"award-info":[{"award-number":["2017A010405039","201707020007","2018B020203003","17ZR1412500"]}],"id":[{"id":"10.13039\/501100007162","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Guangzhou Science and Technology Planning Project","award":["2017A010405039","201707020007","2018B020203003","17ZR1412500"],"award-info":[{"award-number":["2017A010405039","201707020007","2018B020203003","17ZR1412500"]}]},{"name":"Key-Area Research and Development Program of Guangdong Province","award":["2017A010405039","201707020007","2018B020203003","17ZR1412500"],"award-info":[{"award-number":["2017A010405039","201707020007","2018B020203003","17ZR1412500"]}]},{"DOI":"10.13039\/100007219","name":"Natural Science Foundation of Shanghai","doi-asserted-by":"publisher","award":["2017A010405039","201707020007","2018B020203003","17ZR1412500"],"award-info":[{"award-number":["2017A010405039","201707020007","2018B020203003","17ZR1412500"]}],"id":[{"id":"10.13039\/100007219","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Computational and Mathematical Methods in Medicine"],"published-print":{"date-parts":[[2021,1,4]]},"abstract":"<jats:p>Metabolic pathway is an important type of biological pathways. It produces essential molecules and energies to maintain the life of living organisms. Each metabolic pathway consists of a chain of chemical reactions, which always need enzymes to participate in. Thus, chemicals and enzymes are two major components for each metabolic pathway. Although several metabolic pathways have been uncovered, the metabolic pathway system is still far from complete. Some hidden chemicals or enzymes are not discovered in a certain metabolic pathway. Besides the traditional experiments to detect hidden chemicals or enzymes, an alternative pipeline is to design efficient computational methods. In this study, we proposed a powerful multilabel classifier, called iMPTCE-Hnetwork, to uniformly assign chemicals and enzymes to metabolic pathway types reported in KEGG. Such classifier adopted the embedding features derived from a heterogeneous network, which defined chemicals and enzymes as nodes and the interactions between chemicals and enzymes as edges, through a powerful network embedding algorithm, Mashup. The popular RAndom k-labELsets (RAKEL) algorithm was employed to construct the classifier, which incorporated the support vector machine (polynomial kernel) as the basic classifier. The ten-fold cross-validation results indicated that such a classifier had good performance with accuracy higher than 0.800 and exact match higher than 0.750. Several comparisons were done to indicate the superiority of the iMPTCE-Hnetwork.<\/jats:p>","DOI":"10.1155\/2021\/6683051","type":"journal-article","created":{"date-parts":[[2021,1,5]],"date-time":"2021-01-05T23:50:31Z","timestamp":1609890631000},"page":"1-12","source":"Crossref","is-referenced-by-count":30,"title":["iMPTCE-Hnetwork: A Multilabel Classifier for Identifying Metabolic Pathway Types of Chemicals and Enzymes with a Heterogeneous Network"],"prefix":"10.1155","volume":"2021","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7584-5292","authenticated-orcid":true,"given":"Yuanyuan","family":"Zhu","sequence":"first","affiliation":[{"name":"College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9927-2414","authenticated-orcid":true,"given":"Bin","family":"Hu","sequence":"additional","affiliation":[{"name":"State Key Laboratory of Livestock and Poultry Breeding, Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangdong Provincial Key Laboratory of Animal Breeding and Nutrition, Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3068-1583","authenticated-orcid":true,"given":"Lei","family":"Chen","sequence":"additional","affiliation":[{"name":"College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2675-6511","authenticated-orcid":true,"given":"Qi","family":"Dai","sequence":"additional","affiliation":[{"name":"College of Life Sciences, Zhejiang Sci-Tech University, Hangzhou 310018, China"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"311","reference":[{"key":"1","doi-asserted-by":"publisher","DOI":"10.2174\/092986609788923374"},{"key":"2","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkw1092"},{"key":"3","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/28.1.27"},{"key":"4","doi-asserted-by":"publisher","DOI":"10.1007\/s11030-008-9085-9"},{"key":"5","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0029491"},{"key":"6","doi-asserted-by":"publisher","DOI":"10.2174\/1386207319666151110122453"},{"key":"7","doi-asserted-by":"publisher","DOI":"10.1007\/BF00994018"},{"key":"8","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz954"},{"key":"9","doi-asserted-by":"publisher","DOI":"10.2174\/1875036202013010083"},{"key":"10","doi-asserted-by":"publisher","DOI":"10.2174\/1386207319666161215142130"},{"key":"11","doi-asserted-by":"publisher","DOI":"10.1109\/ACCESS.2020.3009439"},{"key":"12","doi-asserted-by":"publisher","DOI":"10.2174\/1386207322666181206112641"},{"key":"13","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0045944"},{"key":"14","doi-asserted-by":"publisher","DOI":"10.1016\/j.cels.2016.10.017"},{"volume-title":"Random K-Labelsets: An Ensemble Method for Multilabel Classification","year":"2007","author":"G. Tsoumakas","key":"15"},{"key":"16","doi-asserted-by":"publisher","DOI":"10.4018\/jdwm.2007070101"},{"key":"17","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkt1207"},{"key":"18","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkm795"},{"key":"19","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gku1003"},{"key":"20","doi-asserted-by":"publisher","DOI":"10.1093\/nar\/gkg034"},{"key":"21","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btz757"},{"key":"22","doi-asserted-by":"publisher","DOI":"10.2174\/1574893614666190220114644"},{"key":"23","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-017-00680-8"},{"key":"24","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-018-2309-9"},{"key":"25","doi-asserted-by":"publisher","DOI":"10.3389\/fgene.2018.00205"},{"key":"26","doi-asserted-by":"publisher","DOI":"10.1186\/s13062-018-0214-9"},{"key":"27","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btx043"},{"key":"28","doi-asserted-by":"publisher","DOI":"10.1109\/icdm.2006.70"},{"key":"29","doi-asserted-by":"publisher","DOI":"10.1016\/j.ajhg.2008.02.013"},{"key":"30","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaa166"},{"key":"31","doi-asserted-by":"publisher","DOI":"10.2174\/1386207322666190702103927"},{"key":"32","doi-asserted-by":"publisher","DOI":"10.1109\/BIBM.2018.8621173"},{"key":"33","doi-asserted-by":"publisher","DOI":"10.1186\/s12859-017-1898-z"},{"key":"34","doi-asserted-by":"publisher","DOI":"10.1109\/tencon.2012.6412321"},{"key":"35","doi-asserted-by":"publisher","DOI":"10.5555\/2946645.2946666"},{"key":"36","doi-asserted-by":"publisher","DOI":"10.1109\/ACCESS.2017.2775703"},{"key":"37","doi-asserted-by":"publisher","DOI":"10.3389\/fbioe.2020.00507"},{"key":"38","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2105-14-S14-S9"},{"key":"39","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/bts700"},{"key":"40","doi-asserted-by":"publisher","DOI":"10.2174\/1570164617999201124142950"},{"volume-title":"Sequential Minimal Optimizaton: A Fast Algorithm for Training Support Vector Machines","year":"1998","author":"J. Platt","key":"41"},{"key":"42","article-title":"A study of cross-validation and bootstrap for accuracy estimation and model selection","volume-title":"International joint Conference on artificial intelligence","author":"R. Kohavi","year":"1995"},{"key":"43","doi-asserted-by":"publisher","DOI":"10.1023\/A:1010933404324"},{"key":"44","doi-asserted-by":"publisher","DOI":"10.1155\/2020\/1573543"},{"key":"45","doi-asserted-by":"publisher","DOI":"10.1016\/j.mbs.2018.09.010"},{"key":"46","doi-asserted-by":"publisher","DOI":"10.1109\/TCBB.2016.2617337"},{"key":"47","doi-asserted-by":"publisher","DOI":"10.1016\/j.jtbi.2018.07.032"},{"key":"48","doi-asserted-by":"publisher","DOI":"10.1145\/2623330.2623732"},{"key":"49","doi-asserted-by":"publisher","DOI":"10.1145\/2939672.2939754"},{"key":"50","first-page":"3111","article-title":"Distributed representations of words and phrases and their compositionality","volume":"26","author":"T. Mikolov","year":"2013","journal-title":"Advances in Neural Information Processing Systems"}],"container-title":["Computational and Mathematical Methods in Medicine"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/downloads.hindawi.com\/journals\/cmmm\/2021\/6683051.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/journals\/cmmm\/2021\/6683051.xml","content-type":"application\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/downloads.hindawi.com\/journals\/cmmm\/2021\/6683051.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,1,5]],"date-time":"2021-01-05T23:50:40Z","timestamp":1609890640000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.hindawi.com\/journals\/cmmm\/2021\/6683051\/"}},"subtitle":[],"editor":[{"given":"Hui","family":"Ding","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2021,1,4]]},"references-count":50,"alternative-id":["6683051","6683051"],"URL":"https:\/\/doi.org\/10.1155\/2021\/6683051","relation":{},"ISSN":["1748-6718","1748-670X"],"issn-type":[{"type":"electronic","value":"1748-6718"},{"type":"print","value":"1748-670X"}],"subject":[],"published":{"date-parts":[[2021,1,4]]}}}