BioKEEN (KnowlEdge EmbeddiNgs) is a package for training and evaluating biological knowledge graph embeddings
Project description
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 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.
Tutorial
A brief tutorial on how to get started with BioKEEN is available here.
Citation
If you find BioKEEN useful in your work, please consider citing:
Installation 
biokeen can be installed on any system running Python 3.6+ with the following commands:
$ pip install git+https://github.com/SmartDataAnalytics/BioKEEN.gitAlternatively, it can be installed from the source for development with:
$ git clone https://github.com/SmartDataAnalytics/BioKEEN.git biokeen
$ cd biokeen
$ pip install -e .Usage
Code examples can be found in the notebooks directory.
CLI Usage
To show BioKEEN’s available commands, please run following command:
biokeenStarting the Training/HPO Pipeline - Set Up Your Experiment within 60 seconds
To configure an experiment via the CLI, please run following command:
biokeen startTo start BioKEEN with an existing configuration file, please run the following command:
biokeen start -f /path/to/config.jsonStarting the Prediction Pipeline
To make prediction based on a trained model, please run following command:
biokeen predict -m /path/to/model/directory -d /path/to/data/directorySummarize the Results of All Experiments
To summarize the results of all experiments, please run following command:
biokeen summarize -d /path/to/experiments/directory -o /path/to/output/file.csvGetting Bio2BEL Data
To download and structure the data from a Bio2BEL repository, run:
biokeen data get <name>Where <name> can be any repository name in Bio2BEL such as hippie, mirtarbase.
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