{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,6,2]],"date-time":"2026-06-02T01:25:54Z","timestamp":1780363554624,"version":"3.54.1"},"reference-count":35,"publisher":"Oxford University Press (OUP)","issue":"Supplement_2","license":[{"start":{"date-parts":[[2022,9,1]],"date-time":"2022-09-01T00:00:00Z","timestamp":1661990400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100002428","name":"Austrian Science Fund","doi-asserted-by":"publisher","award":["ECCB2022"],"award-info":[{"award-number":["ECCB2022"]}],"id":[{"id":"10.13039\/501100002428","id-type":"DOI","asserted-by":"publisher"}]},{"name":"European Union\u2019s Horizon 2020","award":["826078"],"award-info":[{"award-number":["826078"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,9,16]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Motivation<\/jats:title>\n                    <jats:p>The tremendous success of graphical neural networks (GNNs) already had a major impact on systems biology research. For example, GNNs are currently being used for drug target recognition in protein\u2013drug interaction networks, as well as for cancer gene discovery and more. Important aspects whose practical relevance is often underestimated are comprehensibility, interpretability and explainability.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>In this work, we present a novel graph-based deep learning framework for disease subnetwork detection via explainable GNNs. Each patient is represented by the topology of a protein\u2013protein interaction (PPI) network, and the nodes are enriched with multi-omics features from gene expression and DNA methylation. In addition, we propose a modification of the GNNexplainer that provides model-wide explanations for improved disease subnetwork detection.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Availability and implementation<\/jats:title>\n                    <jats:p>The proposed methods and tools are implemented in the GNN-SubNet Python package, which we have made available on our GitHub for the international research community (https:\/\/github.com\/pievos101\/GNN-SubNet).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Supplementary information<\/jats:title>\n                    <jats:p>Supplementary data are available at Bioinformatics online.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/bioinformatics\/btac478","type":"journal-article","created":{"date-parts":[[2022,8,24]],"date-time":"2022-08-24T13:52:30Z","timestamp":1661349150000},"page":"ii120-ii126","source":"Crossref","is-referenced-by-count":62,"title":["GNN-SubNet: disease subnetwork detection with explainable graph neural networks"],"prefix":"10.1093","volume":"38","author":[{"given":"Bastian","family":"Pfeifer","sequence":"first","affiliation":[{"name":"Institute for Medical Informatics Statistics and Documentation, Medical University Graz , Graz, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna","family":"Saranti","sequence":"additional","affiliation":[{"name":"Institute for Medical Informatics Statistics and Documentation, Medical University Graz , Graz, Austria"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andreas","family":"Holzinger","sequence":"additional","affiliation":[{"name":"Institute for Medical Informatics Statistics and Documentation, Medical University Graz , Graz, Austria"},{"name":"Human-Centered AI Lab, Department of Forest- and Soil Sciences, University of Natural Resources and Life Sciences Vienna , Vienna, Austria"},{"name":"Alberta Machine Intelligence Institute, University of Alberta , Edmonton, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,9,18]]},"reference":[{"key":"2023041408002514100_","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.neunet.2020.06.006","article-title":"A gentle introduction to deep learning for graphs","volume":"129","author":"Bacciu","year":"2020","journal-title":"Neural Netw"},{"key":"2023041408002514100_","doi-asserted-by":"crossref","first-page":"P10008","DOI":"10.1088\/1742-5468\/2008\/10\/P10008","article-title":"Fast unfolding of communities in large networks","volume":"2008","author":"Blondel","year":"2008","journal-title":"J. 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