Outputs

The tool creates several files and folders in the specified output directory. Below is the list and description of each output generated by the tool.

  • coembedding_emd.tsv

    This file represents the co-embedding of Protein-Protein Interaction (PPI) and image embeddings. The first column contains identifiers (either gene symbols or sample IDs) while the subsequent columns contain embedding values.

        1   2       3       4
AURKB       -0.06713819     -0.027032608    -0.117943764    -0.14860943
BAZ1B       0.100407355     0.1299548       -0.011916596    0.02393107
BRD7        0.07245989      0.12707146      -0.000744308    0.023155764
CBX3        -0.115645304    -0.1549612      -0.08860879     -0.038656197
CHD1        0.016580202     0.11743456      -0.009839832    -0.008252605
  • muse_latent_x.txt, muse_latent_y.txt, muse_latent.txt

    These files are outputs of the MuSE algorithm and represent the learned latent embeddings for the given data. The x, y, and combined latent representations relate to the embeddings for PPIs (x), images (y), and their co-embedded form.

    0       1       2       3
AURKB       -0.7398974      -0.7328235      -0.47760928     0.799894
BAZ1B       0.73348 0.6329914       0.5768389       -0.866711
BRD7        0.7492436       0.6085141       0.48927978      -0.6845873
CBX3        -0.34629488     -0.85891724     -0.44887647     0.7374519
  • muse_reconstruct_x.txt, muse_reconstruct_y.txt

    The reconstructed embeddings after the MuSE training process.

    0       1       2       3
AURKB       0.009274133     -0.11458938     0.58946913      0.24976397
BAZ1B       0.12864016      -0.1441521      0.066344105     0.16674767
BRD7        0.2039571       -0.13871995     0.067848556     0.16131365
CBX3        0.028114516     -0.11468072     0.65329766      0.2604311
  • muse.pth

    The model related to the MuSE co-embedding process. This file allows for future loading and reuse of the model without needing to retrain it.

  • muse.txt

    A general output from the MuSE co-embedding algorithm.

init_recon_epoch:0  total_loss:1372.44202   reconstruction_loss_x:44.36664  reconstruction_loss_y:52.45499
init_recon_epoch:1  total_loss:1372.45093   reconstruction_loss_x:43.70440  reconstruction_loss_y:53.22675
init_recon_epoch:2  total_loss:1369.79553   reconstruction_loss_x:42.36637  reconstruction_loss_y:52.00960
init_recon_epoch:3  total_loss:1368.55383   reconstruction_loss_x:42.14549  reconstruction_loss_y:51.08870

Logs and Metadata

  • error.log:

    Contains error logs generated during the execution of the script.

  • output.log:

    A log file detailing the standard messages, warnings, or any information generated during the execution.

  • ro-crate-metadata.json:

    Metadata in RO-Crate format, a community effort to establish a lightweight approach to packaging research data with their metadata.

    The main object contains identifier (@id), type (@type), name, descriptions, keywords and isPartOf, that describes the hierarchical relationship (organization and project).

    Graph: The @graph key contains an array of objects that detail other entities related to the main dataset. a. Metadata, Datasets, Software b. Output Files: details of output files generated by the tool.