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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.


A brief tutorial on how to get started with BioKEEN is available here.


If you find BioKEEN useful in your work, please consider citing:

[1]Ali, M., et al. (2018). BioKEEN: A library for learning and evaluating biological knowledge graph embeddings. bioRxiv 475202.

Installation Current version on PyPI Stable Supported Python Versions MIT License

biokeen can be installed on any system running Python 3.6+ with the following commands:

$ pip install git+

Alternatively, it can be installed from the source for development with:

$ git clone biokeen
$ cd biokeen
$ pip install -e .


Code examples can be found in the notebooks directory.

CLI Usage

To show BioKEEN’s available commands, please run following command:


Starting the Training/HPO Pipeline - Set Up Your Experiment within 60 seconds

To configure an experiment via the CLI, please run following command:

biokeen start

To start BioKEEN with an existing configuration file, please run the following command:

biokeen start -f /path/to/config.json

Starting 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/directory

Summarize 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.csv

Getting 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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