├── .gitignore ├── .travis.yml ├── Convolutional variable length peptide network.ipynb ├── LICENSE ├── README.md ├── conv.png ├── conv_large.png ├── conv_small.png ├── experiments ├── eval_architectures_class2_mhc_binding.py ├── eval_conv_architectures_for_class2_binding.py ├── eval_conv_architectures_with_reduced_string_similarity.py ├── eval_conv_saturation.py └── eval_increasing_numbers_of_decoys.py ├── lint.sh ├── pepnet ├── __init__.py ├── discrete_input.py ├── encoder.py ├── keras_layers │ ├── __init__.py │ ├── drop_mask.py │ ├── masked_conv1d.py │ ├── masked_global_average_pooling.py │ ├── masked_global_max_pooling.py │ ├── masked_maxpooling1d.py │ └── masked_slice.py ├── losses.py ├── nn_helpers.py ├── numeric.py ├── numeric_input.py ├── output.py ├── predictor.py ├── sequence_helpers.py ├── sequence_input.py └── synthetic_data │ ├── __init__.py │ ├── random_peptides.py │ └── subsequence.py ├── pylintrc ├── requirements.txt ├── setup.py └── test ├── test_conv.py ├── test_discrete_input.py ├── test_encoder.py ├── test_feedforward.py ├── test_highway_network_helper.py ├── test_predictor.py ├── test_predictor_serialization.py ├── test_rnn.py └── test_sequence_context.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openvax/pepnet/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openvax/pepnet/HEAD/.travis.yml -------------------------------------------------------------------------------- /Convolutional variable length peptide network.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/openvax/pepnet/HEAD/Convolutional variable length peptide network.ipynb 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