The tool provides functionalities for embedding protein-protein interactions (PPIs). By default, it employs the Node2Vec algorithm for generating embeddings but can also produce fake embeddings for testing purposes.

In a project

To use cellmaps_ppi_embedding in a project:

import cellmaps_ppi_embedding

On the command line

For information invoke -h

Usage [outdir] [--inputdir PPIDOWNLOADER_OUT_DIR] [OPTIONS]


  • outdir

    The directory where the output will be written to.


  • --inputdir:

    Directory with the ppi_edgelist.tsv file. Output of the cellmaps_ppidownloader package.


  • --dimensions:

    The size of the embedding to generate. Default value is 1024.

  • --walk_length:

    The length of the walk for Node2Vec. Default is 80.

  • --num_walks:

    The number of walks for Node2Vec. Default is 10.

  • --workers:

    The number of worker threads to use. Default is 8.

  • --p:

    The p value to pass to Node2Vec. Default is 2.

  • --q:

    The q value to pass to Node2Vec. Default is 1.

  • --fake_embedder:

    If set, the script will generate a fake embedding.

  • --skip_logging:

    If set, certain log files will not be created.

  • --logconf:

    Path to the python logging configuration file.

  • -v or --verbose:

    Increases verbosity of the logger to standard error for log messages in the module. -v sets logging to ERROR, -vv to WARNING, -vvv to INFO, -vvvv to DEBUG, and -vvvvv to NOTSET.

  • --version:

    Displays the version of the script.

Example usage

The output directory for the PPI download is required (see Cell Maps PPI Downloader). ./cellmaps_ppi_embedding_outdir --inputdir ./cellmaps_ppidownloader_outdir

Via Docker

Example usage

Coming soon...