transforna/src/readme.md

This is the transforna package which contains the following modules:

• train is the entry point where data preparation, training and results logging is executed.

• processing contains all classes used for data augmentation, tokenization and splitting.

• model contains the skorch model skorchWrapper that wraps the torch model described in model components

• callbacks contains the learning rate scheduler, loss function and the metrics used to evaluate the model.

• score compute the balanced accuracy of the classification task -major or sub-class- for each of the splits with known labels(train/valid/test).

• novelty_prediction contains two novelty metrics; entropy based(obsolete) and Normalized Levenstein Distance, NLD based (current).

• inference contains all inference functionalities. check transforna/scripts/test_inference_api.py for how-to-use.

A schematic of the TransfoRNA Architecture:

Model evauation image source