{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,4]],"date-time":"2026-04-04T06:33:46Z","timestamp":1775284426618,"version":"3.50.1"},"publisher-location":"Cham","reference-count":32,"publisher":"Springer International Publishing","isbn-type":[{"value":"9783030934125","type":"print"},{"value":"9783030934132","type":"electronic"}],"license":[{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022]]},"DOI":"10.1007\/978-3-030-93413-2_54","type":"book-chapter","created":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T03:18:22Z","timestamp":1641007102000},"page":"652-663","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Supervised Gene Function Prediction Using Spectral Clustering on\u00a0Gene Co-expression Networks"],"prefix":"10.1007","author":[{"given":"Miguel","family":"Romero","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"\u00d3scar","family":"Ram\u00edrez","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jorge","family":"Finke","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Camilo","family":"Rocha","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,1,1]]},"reference":[{"issue":"10","key":"54_CR1","first-page":"281","volume":"13","author":"J Bergstra","year":"2012","unstructured":"Bergstra, J., Bengio, Y.: Random search for hyper-parameter optimization. J. Mach. Learn. Res. 13(10), 281\u2013305 (2012)","journal-title":"J. Mach. Learn. Res."},{"key":"54_CR2","unstructured":"Carbon, S., Mungall, C.: Gene Ontology Data Archive, July 2018. Type: dataset"},{"key":"54_CR3","doi-asserted-by":"publisher","first-page":"321","DOI":"10.1613\/jair.953","volume":"16","author":"NV Chawla","year":"2002","unstructured":"Chawla, N.V., Bowyer, K.W., Hall, L.O., Kegelmeyer, W.P.: SMOTE: synthetic minority over-sampling technique. J. Artif. Intell. Res. 16, 321\u2013357 (2002)","journal-title":"J. Artif. Intell. Res."},{"key":"54_CR4","doi-asserted-by":"crossref","unstructured":"Chen, T., Guestrin, C.: XGBoost: a scalable tree boosting system. In: Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining, pp. 785\u2013794 (2016)","DOI":"10.1145\/2939672.2939785"},{"key":"54_CR5","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"62","DOI":"10.1007\/978-3-319-16706-0_9","volume-title":"Research in Computational Molecular Biology","author":"H Cho","year":"2015","unstructured":"Cho, H., Berger, B., Peng, J.: Diffusion component analysis: unraveling functional topology in biological networks. In: Przytycka, T.M. (ed.) RECOMB 2015. LNCS, vol. 9029, pp. 62\u201364. Springer, Cham (2015). https:\/\/doi.org\/10.1007\/978-3-319-16706-0_9"},{"issue":"6","key":"54_CR6","doi-asserted-by":"publisher","first-page":"540","DOI":"10.1016\/j.cels.2016.10.017","volume":"3","author":"H Cho","year":"2016","unstructured":"Cho, H., Berger, B., Peng, J.: Compact integration of multi-network topology for functional analysis of genes. Cell Syst. 3(6), 540-548.e5 (2016)","journal-title":"Cell Syst."},{"issue":"12","key":"54_CR7","doi-asserted-by":"publisher","first-page":"e9667","DOI":"10.15252\/msb.20209667","volume":"16","author":"DF Cruz","year":"2020","unstructured":"Cruz, D.F., et al.: Using single-plant-omics in the field to link maize genes to functions and phenotypes. Mol. Syst. Biol. 16(12), e9667 (2020)","journal-title":"Mol. Syst. Biol."},{"issue":"6","key":"54_CR8","doi-asserted-by":"publisher","first-page":"947","DOI":"10.1089\/106652703322756168","volume":"10","author":"M Deng","year":"2003","unstructured":"Deng, M., Zhang, K., Mehta, S., Chen, T., Sun, F.: Prediction of protein function using protein-protein interaction data. J. Comput. Biol. 10(6), 947\u2013960 (2003)","journal-title":"J. Comput. Biol."},{"issue":"D1","key":"54_CR9","doi-asserted-by":"publisher","first-page":"D330","DOI":"10.1093\/nar\/gky1055","volume":"47","author":"Gene Ontology Consortium","year":"2019","unstructured":"Gene Ontology Consortium: The gene ontology resource: 20 years and still GOing strong. Nucl. Acids Res. 47(D1), D330\u2013D338 (2019)","journal-title":"Nucl. Acids Res."},{"issue":"8","key":"54_CR10","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/gb-2001-2-8-interactions1002","volume":"2","author":"RA Jensen","year":"2001","unstructured":"Jensen, R.A.: Orthologs and paralogs - we need to get it right. Genom. Biol. 2(8), 1\u20133 (2001)","journal-title":"Genom. Biol."},{"issue":"7","key":"54_CR11","doi-asserted-by":"publisher","first-page":"1477","DOI":"10.1007\/s00521-013-1439-2","volume":"24","author":"H Jia","year":"2013","unstructured":"Jia, H., Ding, S., Xu, X., Nie, R.: The latest research progress on spectral clustering. Neural Comput. Appl. 24(7), 1477\u20131486 (2013). https:\/\/doi.org\/10.1007\/s00521-013-1439-2","journal-title":"Neural Comput. Appl."},{"issue":"3","key":"54_CR12","doi-asserted-by":"publisher","first-page":"462","DOI":"10.1007\/s11704-016-5485-7","volume":"10","author":"W Ju","year":"2016","unstructured":"Ju, W., Li, J., Yu, W., Zhang, R.: iGraph: an incremental data processing system for dynamic graph. Front. Comput. Sci. 10(3), 462\u2013476 (2016)","journal-title":"Front. Comput. Sci."},{"key":"54_CR13","unstructured":"Lundberg, S., Lee, S.-I.: A Unified Approach to Interpreting Model Predictions. arXiv:1705.07874, November 2017"},{"issue":"1","key":"54_CR14","doi-asserted-by":"publisher","first-page":"2522","DOI":"10.1038\/s42256-019-0138-9","volume":"2","author":"SM Lundberg","year":"2020","unstructured":"Lundberg, S.M., et al.: From local explanations to global understanding with explainable AI for trees. Nat. Mach. Intell. 2(1), 2522\u20135839 (2020)","journal-title":"Nat. Mach. Intell."},{"issue":"1","key":"54_CR15","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1186\/1471-2105-8-299","volume":"8","author":"F Luo","year":"2007","unstructured":"Luo, F., et al.: Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory. BMC Bioinform. 8(1), 299 (2007)","journal-title":"BMC Bioinform."},{"key":"54_CR16","series-title":"Studies in Classification, Data Analysis, and Knowledge Organization","doi-asserted-by":"publisher","first-page":"175","DOI":"10.1007\/978-3-030-60104-1_20","volume-title":"Data Analysis and Rationality in a Complex World","author":"N Murugesan","year":"2021","unstructured":"Murugesan, N., Cho, I., Tortora, C.: Benchmarking in cluster analysis: a\u00a0study on spectral clustering, DBSCAN, and K-Means. In: Chadjipadelis, T., Lausen, B., Markos, A., Lee, T.R., Montanari, A., Nugent, R. (eds.) IFCS 2019. SCDAKO, pp. 175\u2013185. Springer, Cham (2021). https:\/\/doi.org\/10.1007\/978-3-030-60104-1_20"},{"key":"54_CR17","doi-asserted-by":"crossref","unstructured":"Musungu, B., Bhatnagar, D., Brown, R.L., Fakhoury, A.M., Geisler, M.: A predicted protein interactome identifies conserved global networks and disease resistance subnetworks in maize. Front. Genet. 6 (2015)","DOI":"10.3389\/fgene.2015.00201"},{"issue":"1","key":"54_CR18","doi-asserted-by":"publisher","first-page":"e3","DOI":"10.1093\/pcp\/pcx191","volume":"59","author":"T Obayashi","year":"2018","unstructured":"Obayashi, T., Aoki, Y., Tadaka, S., Kagaya, Y., Kinoshita, K.: ATTED-II in 2018: a plant coexpression database based on investigation of the statistical property of the mutual rank index. Plant Cell Physiol. 59(1), e3\u2013e3 (2018)","journal-title":"Plant Cell Physiol."},{"key":"54_CR19","doi-asserted-by":"publisher","first-page":"D1016","DOI":"10.1093\/nar\/gkq1147","volume":"39","author":"T Obayashi","year":"2011","unstructured":"Obayashi, T., Kinoshita, K.: COXPRESdb: a database to compare gene coexpression in seven model animals. Nucl. Acids Res. 39, D1016\u2013D1022 (2011)","journal-title":"Nucl. Acids Res."},{"issue":"1","key":"54_CR20","doi-asserted-by":"publisher","first-page":"208","DOI":"10.1186\/1471-2105-9-208","volume":"9","author":"M Oti","year":"2008","unstructured":"Oti, M., van Reeuwijk, J., Huynen, M.A., Brunner, H.G.: Conserved co-expression for candidate disease gene prioritization. BMC Bioinform. 9(1), 208 (2008)","journal-title":"BMC Bioinform."},{"issue":"4","key":"54_CR21","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1186\/gb-2009-10-4-104","volume":"10","author":"GA Petsko","year":"2009","unstructured":"Petsko, G.A.: Guilt by association. Genom. Biol. 10(4), 104 (2009)","journal-title":"Genom. Biol."},{"key":"54_CR22","doi-asserted-by":"crossref","unstructured":"Rehman, S.U., Asghar, S., Fong, S., Sarasvady, S.: DBSCAN: past, present and future. In: The Fifth International Conference on the Applications of Digital Information and Web Technologies (ICADIWT 2014), pp. 232\u2013238, Bangalore, India, February 2014","DOI":"10.1109\/ICADIWT.2014.6814687"},{"issue":"1","key":"54_CR23","doi-asserted-by":"publisher","first-page":"e0210236","DOI":"10.1371\/journal.pone.0210236","volume":"14","author":"MZ Rodriguez","year":"2019","unstructured":"Rodriguez, M.Z., et al.: Clustering algorithms: a comparative approach. PLoS One 14(1), e0210236 (2019)","journal-title":"PLoS One"},{"key":"54_CR24","series-title":"Studies in Computational Intelligence","doi-asserted-by":"publisher","first-page":"802","DOI":"10.1007\/978-3-030-36683-4_64","volume-title":"Complex Networks and Their Applications VIII","author":"M Romero","year":"2020","unstructured":"Romero, M., Finke, J., Quimbaya, M., Rocha, C.: In-silico gene annotation prediction using the co-expression network structure. In: Cherifi, H., Gaito, S., Mendes, J.F., Moro, E., Rocha, L.M. (eds.) COMPLEX NETWORKS 2019. SCI, vol. 882, pp. 802\u2013812. Springer, Cham (2020). https:\/\/doi.org\/10.1007\/978-3-030-36683-4_64"},{"issue":"11","key":"54_CR25","doi-asserted-by":"publisher","first-page":"S70","DOI":"10.1016\/S1359-6446(02)02289-4","volume":"7","author":"AG Rust","year":"2002","unstructured":"Rust, A.G., Mongin, E., Birney, E.: Genome annotation techniques: new approaches and challenges. Drug Discov. Today 7(11), S70\u2013S76 (2002)","journal-title":"Drug Discov. Today"},{"key":"54_CR26","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"232","DOI":"10.1007\/978-3-642-02326-2_24","volume-title":"Multiple Classifier Systems","author":"G Valentini","year":"2009","unstructured":"Valentini, G.: True path rule hierarchical ensembles. In: Benediktsson, J.A., Kittler, J., Roli, F. (eds.) MCS 2009. LNCS, vol. 5519, pp. 232\u2013241. Springer, Heidelberg (2009). https:\/\/doi.org\/10.1007\/978-3-642-02326-2_24"},{"issue":"4","key":"54_CR27","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1093\/bib\/bbw139","volume":"19","author":"S van Dam","year":"2017","unstructured":"van Dam, S., V\u00f5sa, U., van der Graaf, A., Franke, L., de Magalh\u00e3es, J.P.: Gene co-expression analysis for functional classification and gene-disease predictions. Briefings Bioinform. 19(4), 139 (2017)","journal-title":"Briefings Bioinform."},{"issue":"2","key":"54_CR28","doi-asserted-by":"publisher","first-page":"535","DOI":"10.1104\/pp.109.136028","volume":"150","author":"K Vandepoele","year":"2009","unstructured":"Vandepoele, K., Quimbaya, M., Casneuf, T., De Veylder, L., Van de Peer, Y.: Unraveling transcriptional control in Arabidopsis using CIS-regulatory elements and coexpression networks. Plant Physiology 150(2), 535\u2013546 (2009)","journal-title":"Plant Physiology"},{"issue":"5","key":"54_CR29","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1038\/nrg3174","volume":"13","author":"M Yandell","year":"2012","unstructured":"Yandell, M., Ence, D.: A beginner\u2019s guide to eukaryotic genome annotation. Nat. Rev. Genet. 13(5), 329\u2013342 (2012)","journal-title":"Nat. Rev. Genet."},{"issue":"7","key":"54_CR30","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1038\/nrg2363","volume":"9","author":"S Yon Rhee","year":"2008","unstructured":"Yon Rhee, S., Wood, V., Dolinski, K., Draghici, S.: Use and misuse of the gene ontology annotations. Nat. Rev. Genet. 9(7), 509\u2013515 (2008)","journal-title":"Nat. Rev. Genet."},{"issue":"S16","key":"54_CR31","doi-asserted-by":"publisher","first-page":"420","DOI":"10.1186\/s12859-020-03745-6","volume":"21","author":"G Zhou","year":"2020","unstructured":"Zhou, G., Wang, J., Zhang, X., Guo, M., Yu, G.: Predicting functions of maize proteins using graph convolutional network. BMC Bioinform. 21(S16), 420 (2020)","journal-title":"BMC Bioinform."},{"issue":"7","key":"54_CR32","doi-asserted-by":"publisher","first-page":"1237","DOI":"10.1093\/bioinformatics\/bti111","volume":"21","author":"Y Zhou","year":"2005","unstructured":"Zhou, Y., Young, J.A., Santrosyan, A., Chen, K., Yan, S.F., Winzeler, E.A.: In silico gene function prediction using ontology-based pattern identification. Bioinformatics 21(7), 1237\u20131245 (2005)","journal-title":"Bioinformatics"}],"container-title":["Studies in Computational Intelligence","Complex Networks & Their Applications X"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-93413-2_54","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,4,27]],"date-time":"2023-04-27T20:30:30Z","timestamp":1682627430000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-030-93413-2_54"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022]]},"ISBN":["9783030934125","9783030934132"],"references-count":32,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-93413-2_54","relation":{},"ISSN":["1860-949X","1860-9503"],"issn-type":[{"value":"1860-949X","type":"print"},{"value":"1860-9503","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022]]},"assertion":[{"value":"1 January 2022","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"COMPLEX NETWORKS","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Complex Networks and Their Applications","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Madrid","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Spain","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2021","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"30 November 2021","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2 December 2021","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"10","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"iwcna2021","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"http:\/\/www.complexnetworks.org\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}