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This approach has been highly successful owing to the theory, methodology and software that support analysis and learning on graphs. Graphs, however, suffer from information loss when modeling physical systems due to their inability to accurately represent multiobject relationships. Hypergraphs, a generalization of graphs, provide a framework to mitigate information loss and unify disparate graph-based methodologies.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We present a hypergraph-based approach for modeling biological systems and formulate vertex classification, edge classification and link prediction problems on (hyper)graphs as instances of vertex classification on (extended, dual) hypergraphs. We then introduce a novel kernel method on vertex- and edge-labeled (colored) hypergraphs for analysis and learning. The method is based on exact and inexact (via hypergraph edit distances) enumeration of hypergraphlets; i.e. small hypergraphs rooted at a vertex of interest. We empirically evaluate this method on fifteen biological networks and show its potential use in a positive-unlabeled setting to estimate the interactome sizes in various species.<\/jats:p><\/jats:sec><jats:sec><jats:title>Availability and implementation<\/jats:title><jats:p>https:\/\/github.com\/jlugomar\/hypergraphlet-kernels<\/jats:p><\/jats:sec><jats:sec><jats:title>Supplementary information<\/jats:title><jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p><\/jats:sec>","DOI":"10.1093\/bioinformatics\/btaa768","type":"journal-article","created":{"date-parts":[[2020,8,26]],"date-time":"2020-08-26T19:14:10Z","timestamp":1598469250000},"page":"1000-1007","source":"Crossref","is-referenced-by-count":22,"title":["Classification in biological networks with hypergraphlet kernels"],"prefix":"10.1093","volume":"37","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6312-1577","authenticated-orcid":false,"given":"Jose","family":"Lugo-Martinez","sequence":"first","affiliation":[{"name":"Computational Biology Department, Carnegie Mellon University , Pittsburgh, PA 15213, USA"}]},{"given":"Daniel","family":"Zeiberg","sequence":"additional","affiliation":[{"name":"Khoury College of Computer Sciences, Northeastern University , Boston, MA 02115, USA"}]},{"given":"Thomas","family":"Gaudelet","sequence":"additional","affiliation":[{"name":"Department of Computer Science, University College London , London WC1E 6BT, UK"}]},{"given":"No\u00ebl","family":"Malod-Dognin","sequence":"additional","affiliation":[{"name":"Barcelona Supercomputing Center (BSC) , Barcelona 08034, Spain"}]},{"given":"Natasa","family":"Przulj","sequence":"additional","affiliation":[{"name":"Barcelona Supercomputing Center (BSC) , Barcelona 08034, Spain"},{"name":"ICREA, Pg. Lluis Companys 23 , Barcelona 08010, Spain"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6769-0793","authenticated-orcid":false,"given":"Predrag","family":"Radivojac","sequence":"additional","affiliation":[{"name":"Khoury College of Computer Sciences, Northeastern University , Boston, MA 02115, USA"}]}],"member":"286","published-online":{"date-parts":[[2020,9,4]]},"reference":[{"key":"2023051701214184200_btaa768-B1","first-page":"838","author":"Agarwal","year":"2005"},{"key":"2023051701214184200_btaa768-B2","first-page":"17","author":"Agarwal","year":"2006"},{"key":"2023051701214184200_btaa768-B3","first-page":"3880","author":"Bai","year":"2014"},{"key":"2023051701214184200_btaa768-B4","doi-asserted-by":"crossref","first-page":"590","DOI":"10.1016\/S0378-4371(02)00736-7","article-title":"Evolution of the social network of scientific collaborations","volume":"311","author":"Barab\u00e1si","year":"2002","journal-title":"Physica A"},{"key":"2023051701214184200_btaa768-B5","doi-asserted-by":"crossref","first-page":"i38","DOI":"10.1093\/bioinformatics\/bti1016","article-title":"Kernel methods for predicting protein-protein interactions","volume":"21","author":"Ben-Hur","year":"2005","journal-title":"Bioinformatics"},{"key":"2023051701214184200_btaa768-B6","volume-title":"Graphs and Hypergraphs","author":"Berge","year":"1973"},{"key":"2023051701214184200_btaa768-B7","doi-asserted-by":"crossref","first-page":"i57","DOI":"10.1093\/bioinformatics\/btm204","article-title":"Supervised reconstruction of biological networks with local models","volume":"23","author":"Bleakley","year":"2007","journal-title":"Bioinformatics"},{"key":"2023051701214184200_btaa768-B8","first-page":"227","article-title":"Graph reconstruction\u2014a survey","volume":"1","author":"Bondy","year":"1977","journal-title":"J. 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