- `test`: computes test metrics (AUROC, AUPRC, F1, MCC, Presicion, Recall, Accuracy) on a given dataset
- `test`: computes test metrics (AUROC, AUPRC, F1, MCC, Presicion, Recall, Accuracy) for a given dataset
- `predict`: predicts interactions for a given dataset
- `predict_string`: predicts interactions for a given dataset using STRING database: the interactions are taken from the STRING database (based on seed proteins). Predictions are compared with the STRING database. Optionally, the graphs can be constructed.
- `create_dataset`: creates a dataset from the STRING database based on the taxonomic ID of the organism.
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@@ -44,8 +44,8 @@ Predict
options:
-h, --help show this help message and exit
-v, --version show program's version number and exit
--min_len MIN_LEN Minimum length of the protein sequence. The sequences with smaller length will not be considered and will be deleted from the fasta file. (Default: 50)
--max_len MAX_LEN Maximum length of the protein sequence. The sequences with larger length will not be considered and will be deleted from the fasta file. (Default: 800)
--min_len MIN_LEN Minimum length of the protein sequence. The sequences with smaller length will not be considered and will be deleted from the fasta file. (Default: 0)
--max_len MAX_LEN Maximum length of the protein sequence. The sequences with larger length will not be considered and will be deleted from the fasta file. (Default: None)
--device {cpu,gpu,mps,auto}
Device to use for computations. Options include: cpu, gpu, mps (for MacOS), and auto.If not selected the device is set by torch automatically. WARNING: mps is temporarily disabled, if it is chosen, cpu will
