SmartDataAnalytics/BioKEEN

BioKEEN (Biological KnowlEdge EmbeddiNgs) is a package for training and evaluating biological knowledge graph embeddings built on PyKEEN. Because we use PyKEEN as the underlying software package, implementations of 10 knowledge graph embedding models are currently available for BioKEEN. Furthermore, BioKEEN can be run in training mode in which users provide their own set of hyper-parameter values, or in hyper-parameter optimization mode to find suitable hyper-parameter values from set of user defined values. Through the integration of the Bio2BEL [2] software numerous biomedical databases are directly accessible within BioKEEN. BioKEEN can also be run without having experience in programing by using its interactive command line interface that can be started with the command "biokeen" from a terminal.