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.
Citation
If you use BioKEEN in your work, please cite:
Installation 
BioKEEN can be installed with the following commands:
python3 -m pip install git+https://github.com/SmartDataAnalytics/BioKEEN.git@masteror in editable mode with:
$ git clone https://github.com/SmartDataAnalytics/BioKEEN.git biokeen
$ cd biokeen
$ python3 -m pip install -e .How to Use
To show BioKEEN’s available commands, please run following command:
biokeenor alternatively:
python3 -m biokeenStarting BioKEEN’s training/HPO pipeline
To configure an experiment, please run following command:
biokeen startor alternatively:
python3 -m biokeen startTo start BioKEEN with an existing configuration file, please run the following command:
biokeen start -f /path/to/config.jsonor alternatively:
python3 -m biokeen start -f /path/to/config.jsonStarting BioKEEN’s 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/directoryor alternatively:
python3 -m 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.csvor alternatively:
python3 -m 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 get <name>Where <name> can be any repository name in Bio2BEL such as hippie, mirtarbase.
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