Predict multi-epitope vaccine subunit candidates using NLP.
Immune Epitope Database (IEDB)
Construct datasets with data/preprocess.py (notebook format used by mainstream editors).
To train, python train.py, or use LSTM.ipynb on Colab. Models are saved in ./runs.
Predict a list of sequences using a model saved at path_to_model as follows:
from api import Predictor
seqs = """
PVAGAAIAAPVAGQQGPQRR
IAADFVEDQEVCKNYTGTVVGFASMVA
ADGAYRFLSGTAAVLAAAETAEAKAAAAAE
GDNLKGIVVIKDRNIGVLGENGSHMPDRCN
""".split()
predictor = Predictor(path_to_model)
predictor.predict_proba(seqs)An application on the spike protein of SARS-CoV-2 is in example.py.
- Models: (CNN+) LSTM/GRU, Transformer
- Different tokenizers and pooling
- Visualize models, data, training:
tensorboard --logdir=runs
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