tape-neurips2019

(★ 121)

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology. (DEPRECATED)

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- simple_model.py
- simple_model_with_hparams.py
- - __init__.py
  - bepler_contact_map_protein_serializer.py
  - bepler_contact_map_utils.py
  - binary_scop_protein_serializer.py
  - convert_deepsf_to_remote_homology.py
  - fluorescence_protein_serializer.py
  - paired_protein_serializer.py
  - pfam_protein_serializer.py
  - proteinnet_serializer.py
  - remote_homology_deepsf_features.py
  - remote_homology_serializer.py
  - secondary_structure_protein_serializer.py
  - serialize_fasta.py
  - stability_serializer.py
  - tf_data_utils.py
  - vocabs.py
- - __init__.py
  - AbstractTapeModel.py
  - BeplerModel.py
  - BidirectionalLSTM.py
  - ModelBuilder.py
  - OneHotEvolutionaryModel.py
  - OneHotModel.py
  - Resnet.py
  - Transformer.py
  - UniRepModel.py
- - __init__.py
  - AminoAcidClassPredictor.py
  - BeplerContactPredictor.py
  - BidirectionalOutputShift.py
  - ComputeClassVector.py
  - DeepSFModel.py
  - FreezeWeights.py
  - GlobalVectorPredictor.py
  - layers.py
  - NetsurfModel.py
  - OrdinalRegression.py
  - RandomSequenceMask.py
  - ResidueResidueContactPredictor.py
  - SoftSymmetricAlignment.py
- - __init__.py
  - AbstractLanguageModelingTask.py
  - BeplerContactMapTask.py
  - BeplerLanguageModelingTask.py
  - BeplerPairedScopeTask.py
  - ContactMapTask.py
  - FluorescenceTask.py
  - LanguageModelingTask.py
  - MaskedLanguageModelingTask.py
  - NetsurfTask.py
  - RemoteHomologyTask.py
  - SecondaryStructureTask.py
  - StabilityTask.py
  - Task.py
  - TaskBuilder.py
  - UnidirectionalLanguageModelingTask.py
- __init__.py
- __main__.py
- analysis.py
- experiments.py
- losses.py
- run_embed.py
- run_eval.py
- run_supervised_experiments.py
.gitignore
data_refs.bib
download_data.sh
download_pretrained_models.sh
LICENSE
README.md
requirements.txt
setup.py

# Installation Guide

1. Get the code

git clone https://github.com/songlab-cal/tape-neurips2019

Downloads the entire project code from GitHub to your computer.

cd tape-neurips2019

Moves into the project folder you just downloaded.

2. Python

Easy Recommended

Prerequisites

Git Needed to download the project code from GitHub.
Python 3 On Windows, be sure to check 'Add Python to PATH' during installation.

$ pip install -e .

Installs the Python libraries listed in requirements.txt (or similar).

✅ If it runs without errors and prints output in the terminal, it worked.

Pulled directly from this repo's README.