biokeen 0.0.14

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

where the value for the argument -m is the directory containing the model, in more detail following files must be contained in the directory:

• configuration.json

• entities_to_embeddings.json

• relations_to_embeddings.json

• trained_model.pkl

These files are created automatically created after model is trained (and evaluated) and exported in your specified output directory.

The value for the argument -d is the directory containing the data for which inference should be applied, and it needs to contain following files:

• entities.tsv

• relations.tsv

where entities.tsv contains all entities of interest, and relations.tsv all relations. Both files should contain should contain a single column containing all the entities/relations. Based on these files, PyKEEN will create all triple permutations, and computes the predictions for them, and saves them in data directory in predictions.tsv.

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.