biokeen 0.0.9

BioKEEN (KnowlEdge EmbeddiNgs) is a package for training and evaluating biological knowledge graph embeddings

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:

[1]

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

Installation

1. BioKEEN can be installed with the following commands:

python3 -m pip install git+https://github.com/SmartDataAnalytics/BioKEEN.git@master

2. or 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:

biokeen

or alternatively:

python3 -m biokeen

Starting BioKEEN’s training/HPO pipeline

To configure an experiment, please run following command:

biokeen start

or alternatively:

python3 -m biokeen start

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

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

or alternatively:

python3 -m biokeen start -f /path/to/config.json

Starting 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/directory

or alternatively:

python3 -m 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

or alternatively:

python3 -m 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 get <name>

Where <name> can be any repository name in Bio2BEL such as hippie, mirtarbase.