BioKEEN (Biological KnowlEdge EmbeddiNgs) is a package for training and evaluating biological knowledge graph embeddings built on PyKEEN. Within BioKEEN several biomedical databases are directly accessible for training and evaluating biological knowledge graph embeddings (see Biological Databases).
Because we use PyKEEN as the core underlying framework, currently, implementations of 10 knowledge graph emebddings models are avaialble for BioKEEN. Furthermore, it 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. 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.
Installation is as easy as getting the code from PyPI with
python3 -m pip install biokeen.
If you use BioKEEN in your work, please cite :
|||Ali, M., et al. (2018). BioKEEN: A library for learning and evaluating biological knowledge graph embeddings.|
- Train and Evaluate
- Apply a Hyper-Parameter Optimization