├── README.md ├── bin ├── LICENSE ├── PROBE.py ├── __init__.py ├── binding_affinity_estimator.py ├── function_predictor.py ├── probe_config.yaml ├── semantic_similarity_infer.py └── target_family_classifier.py ├── data ├── .gitignore └── representation_vectors │ ├── AAC_UNIPROT_HUMAN.csv │ └── skempi_aac_representation_multi_col.csv ├── evalprotrep_summary_figure.jpg ├── paper_reproduction_scripts ├── .gitignore ├── Visualization │ └── Data-based-performance.ipynb ├── binding_affinity_estimation │ ├── Affinity_Plots.ipynb │ ├── Affinity_Prediction.ipynb │ └── Affinity_Significance.ipynb ├── function_prediction │ ├── GO_Term_Prediction_Figures.ipynb │ ├── GO_Term_Prediction_Significance.ipynb │ ├── dataset_construction.py │ ├── dataset_statistics.py │ ├── feature_formatting.py │ ├── goterm_similarity.R │ ├── model_generation.py │ ├── preprocess_go_prediction.ipynb │ └── produce_go_term_pairs.R ├── preprocess │ ├── GOIdNumberCalculator.ipynb │ ├── GO_stats.R │ ├── Representation_Vector_Convert.ipynb │ ├── Similarity_Matrix_Stats.ipynb │ ├── calculateHighestAnnotatedProteins.ipynb │ ├── calculate_semSim.R │ ├── folds_for_family_classification.py │ ├── getGenesFromGOTerms4Test.R │ ├── go_preprocess_for_cytoscape.ipynb │ └── preprocess_annotation.py ├── semantic_similarity_inference │ ├── Cosine_Euclidian_Test.ipynb │ ├── Gene2Vec_embedding_similarity_calculator.ipynb │ ├── Learned_embedding_similarity_calculator.ipynb │ ├── Mut2Vec_embedding_similarity_calculator.ipynb │ ├── SeqVec_embedding_similarity_calculator.ipynb │ ├── Similarity-Visualizer.ipynb │ ├── SimilarityTCGA_Embedding_Sparse_highest_500.csv │ ├── SimilarityTableBuilder.ipynb │ ├── Similarity_Table.csv │ ├── Sparsify_Protein_Similarities.ipynb │ ├── apaac_embedding_similarity_calculator.ipynb │ ├── auxilary_input │ │ ├── SparsifiedSimilarites_for_highest_500.npy │ │ ├── SparsifiedSimilarityCoordinates_BP_for_highest_500.npy │ │ ├── SparsifiedSimilarityCoordinates_CC_for_highest_500.npy │ │ ├── SparsifiedSimilarityCoordinates_MF_for_highest_500.npy │ │ └── SparsifiedSimilarityCoordinates_for_highest_500.npy │ ├── ksep_embedding_similarity_calculator.ipynb │ ├── protvec_embedding_similarity_calculator.ipynb │ ├── smilesvec_embedding_similarity_calculator.ipynb │ ├── tape_new_bert_embedding_similarity_calculator.ipynb │ ├── tcga_embedding_similarity_calculator.ipynb │ ├── tmp_CC_SimilarityProtVec_highest_200.csv │ └── unirep_embedding_similarity_calculator.ipynb └── target_family_classification │ ├── mcc_general_table.py │ ├── multiclass_merged.ipynb │ ├── plots_class_based.py │ └── plots_general.py └── results ├── .gitignore ├── Affinity_prediction_skempiv1_AAC.csv ├── Affinity_prediction_skempiv1_AAC_detail.csv ├── Drug_target_protein_family_classification_class_based_results_mm15_AAC.csv ├── Drug_target_protein_family_classification_class_based_results_nc_AAC.csv ├── 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