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Molecular interaction networks are our basis for understanding functional interdependencies among genes. Network embedding approaches analyze these complicated networks by representing genes as low-dimensional vectors based on the network topology. These low-dimensional vectors have recently become the building blocks for a larger number of systems biology applications. Despite the success of embedding genes in this way, it remains unclear how to effectively represent gene sets, such as proteindoi:10.1101/519033 fatcat:go2lffjrajbzbilt77tpi3vtxq