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Although significant efforts have been devoted to the identification of drugs, the identification of drug combination is still a challenge. The current algorithms assume that the independence of feature selection and drug prediction procedures, which may result in an undesirable performance.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>To address this issue, we develop a novel<jats:italic>Se<\/jats:italic>mi-supervised<jats:italic>H<\/jats:italic>eterogeneous<jats:italic>N<\/jats:italic>etwork<jats:italic>E<\/jats:italic>mbedding algorithm (called SeHNE) to predict the combination patterns of drugs by exploiting the graph embedding. Specifically, the ATC similarity of drugs, drug\u2013target, and protein\u2013protein interaction networks are integrated to construct the heterogeneous networks. Then, SeHNE jointly learns drug features by exploiting the topological structure of heterogeneous networks and predicting drug combination. One distinct advantage of SeHNE is that features of drugs are extracted under the guidance of classification, which improves the quality of features, thereby enhancing the performance of prediction of drugs. Experimental results demonstrate that the proposed algorithm is more accurate than state-of-the-art methods on various data, implying that the joint learning is promising for the identification of drug combination.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>The proposed model and algorithm provide an effective strategy for the prediction of combinatorial patterns of drugs, implying that the graph-based drug prediction is promising for the discovery of drugs.<\/jats:p><\/jats:sec>","DOI":"10.1186\/s12859-022-04567-4","type":"journal-article","created":{"date-parts":[[2022,1,11]],"date-time":"2022-01-11T14:03:41Z","timestamp":1641909821000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":5,"title":["Predicting combinations of drugs by exploiting graph embedding of heterogeneous networks"],"prefix":"10.1186","volume":"23","author":[{"given":"Fei","family":"Song","sequence":"first","affiliation":[]},{"given":"Shiyin","family":"Tan","sequence":"additional","affiliation":[]},{"given":"Zengfa","family":"Dou","sequence":"additional","affiliation":[]},{"given":"Xiaogang","family":"Liu","sequence":"additional","affiliation":[]},{"given":"Xiaoke","family":"Ma","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2022,1,11]]},"reference":[{"issue":"3","key":"4567_CR1","doi-asserted-by":"publisher","first-page":"200","DOI":"10.1038\/s41573-020-00114-z","volume":"20","author":"AG Atanasov","year":"2020","unstructured":"Atanasov AG, Supuran CT, Zotchev SB, Dirsch VM. 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