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.
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:
|||Ali, M., et al. (2018). BioKEEN: A library for learning and evaluating biological knowledge graph embeddings. bioRxiv 475202.|
biokeen can be installed on any system running Python 3.6+ with the following commands:
$ pip install git+https://github.com/SmartDataAnalytics/BioKEEN.git
Alternatively, it can be installed from the source for development with:
$ git clone https://github.com/SmartDataAnalytics/BioKEEN.git biokeen $ cd biokeen $ pip install -e .
Code examples can be found in the notebooks directory.
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:
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.
Release history Release notifications
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
|Filename, size & hash SHA256 hash help||File type||Python version||Upload date|
|biokeen-0.0.12-py36-none-any.whl (14.5 kB) Copy SHA256 hash SHA256||Wheel||py36|
|biokeen-0.0.12.tar.gz (277.9 kB) Copy SHA256 hash SHA256||Source||None|