├── README.md ├── config_args.py ├── data ├── 3line_to_json.py ├── __init__.py ├── analyze_yang_ppi_data.py ├── convert_sppi_to_json.py ├── create_interSPPI_data_from_biogrid.py ├── create_interSPPI_data_from_mine.py ├── evaluate_psiblast.py ├── evaluate_psiblast_new.py ├── fasta_to_json.py ├── generate_hhblits.py ├── h5_to_json.py ├── json_to_fasta.py ├── json_to_txt.py ├── lmdb_to_json.py ├── process_barman_ppi_data.py ├── process_covid_tab3_from_biogrid.py ├── process_covid_tab3_from_mine.py ├── process_denovo_ppi_data.py ├── process_escape.py ├── process_human_tab3.py ├── process_interSPPI_results.py ├── process_sarscov2.py ├── process_yang_ppi_data.py ├── process_zhou_ppi_data.py ├── utils │ ├── create_new_fasta.py │ ├── merge_pairs.py │ └── n_gram_analysis.py └── vocab.py ├── dataset.py ├── fb_esm ├── __init__.py ├── constants.py ├── data.py ├── embedding.py ├── model.py ├── modules.py ├── multihead_attention.py ├── pretrained.py └── version.py ├── main.py ├── model ├── __init__.py ├── bert.py ├── embedding.py ├── layers.py ├── model_initializer.py ├── models.py └── utils.py ├── test_lm.py ├── train_lm.py ├── train_multitask.py ├── train_pair.py ├── train_single.py ├── utils ├── __init__.py ├── logger.py ├── metrics.py └── optim_schedule.py └── zmedia ├── deepVH2.png ├── deepVH3.png └── deepVH4.png /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/README.md -------------------------------------------------------------------------------- /config_args.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/config_args.py -------------------------------------------------------------------------------- /data/3line_to_json.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/3line_to_json.py -------------------------------------------------------------------------------- /data/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/__init__.py -------------------------------------------------------------------------------- /data/analyze_yang_ppi_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/analyze_yang_ppi_data.py -------------------------------------------------------------------------------- /data/convert_sppi_to_json.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/convert_sppi_to_json.py -------------------------------------------------------------------------------- /data/create_interSPPI_data_from_biogrid.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/create_interSPPI_data_from_biogrid.py -------------------------------------------------------------------------------- /data/create_interSPPI_data_from_mine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/create_interSPPI_data_from_mine.py -------------------------------------------------------------------------------- /data/evaluate_psiblast.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/evaluate_psiblast.py -------------------------------------------------------------------------------- /data/evaluate_psiblast_new.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/evaluate_psiblast_new.py -------------------------------------------------------------------------------- /data/fasta_to_json.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/fasta_to_json.py -------------------------------------------------------------------------------- /data/generate_hhblits.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/generate_hhblits.py -------------------------------------------------------------------------------- /data/h5_to_json.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/h5_to_json.py -------------------------------------------------------------------------------- /data/json_to_fasta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/json_to_fasta.py -------------------------------------------------------------------------------- /data/json_to_txt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/json_to_txt.py -------------------------------------------------------------------------------- /data/lmdb_to_json.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/lmdb_to_json.py -------------------------------------------------------------------------------- /data/process_barman_ppi_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/process_barman_ppi_data.py -------------------------------------------------------------------------------- /data/process_covid_tab3_from_biogrid.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/process_covid_tab3_from_biogrid.py -------------------------------------------------------------------------------- /data/process_covid_tab3_from_mine.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/process_covid_tab3_from_mine.py -------------------------------------------------------------------------------- /data/process_denovo_ppi_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/process_denovo_ppi_data.py -------------------------------------------------------------------------------- /data/process_escape.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/process_escape.py -------------------------------------------------------------------------------- /data/process_human_tab3.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/process_human_tab3.py -------------------------------------------------------------------------------- /data/process_interSPPI_results.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/process_interSPPI_results.py -------------------------------------------------------------------------------- /data/process_sarscov2.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/process_sarscov2.py -------------------------------------------------------------------------------- /data/process_yang_ppi_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/process_yang_ppi_data.py -------------------------------------------------------------------------------- /data/process_zhou_ppi_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/process_zhou_ppi_data.py -------------------------------------------------------------------------------- /data/utils/create_new_fasta.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/utils/create_new_fasta.py -------------------------------------------------------------------------------- /data/utils/merge_pairs.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/utils/merge_pairs.py -------------------------------------------------------------------------------- /data/utils/n_gram_analysis.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/utils/n_gram_analysis.py -------------------------------------------------------------------------------- /data/vocab.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/data/vocab.py -------------------------------------------------------------------------------- /dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/dataset.py -------------------------------------------------------------------------------- /fb_esm/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/fb_esm/__init__.py -------------------------------------------------------------------------------- /fb_esm/constants.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/fb_esm/constants.py -------------------------------------------------------------------------------- /fb_esm/data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/fb_esm/data.py -------------------------------------------------------------------------------- /fb_esm/embedding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/fb_esm/embedding.py -------------------------------------------------------------------------------- /fb_esm/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/fb_esm/model.py -------------------------------------------------------------------------------- /fb_esm/modules.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/fb_esm/modules.py -------------------------------------------------------------------------------- /fb_esm/multihead_attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/fb_esm/multihead_attention.py -------------------------------------------------------------------------------- /fb_esm/pretrained.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/fb_esm/pretrained.py -------------------------------------------------------------------------------- /fb_esm/version.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/fb_esm/version.py -------------------------------------------------------------------------------- /main.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/main.py -------------------------------------------------------------------------------- /model/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/model/__init__.py -------------------------------------------------------------------------------- /model/bert.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/model/bert.py -------------------------------------------------------------------------------- /model/embedding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/model/embedding.py -------------------------------------------------------------------------------- /model/layers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/model/layers.py -------------------------------------------------------------------------------- /model/model_initializer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/model/model_initializer.py -------------------------------------------------------------------------------- /model/models.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/model/models.py -------------------------------------------------------------------------------- /model/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/model/utils.py -------------------------------------------------------------------------------- /test_lm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/test_lm.py -------------------------------------------------------------------------------- /train_lm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/train_lm.py -------------------------------------------------------------------------------- /train_multitask.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/train_multitask.py -------------------------------------------------------------------------------- /train_pair.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/train_pair.py -------------------------------------------------------------------------------- /train_single.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/train_single.py -------------------------------------------------------------------------------- /utils/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/utils/__init__.py -------------------------------------------------------------------------------- /utils/logger.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/utils/logger.py -------------------------------------------------------------------------------- /utils/metrics.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/utils/metrics.py -------------------------------------------------------------------------------- /utils/optim_schedule.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/utils/optim_schedule.py -------------------------------------------------------------------------------- /zmedia/deepVH2.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/zmedia/deepVH2.png -------------------------------------------------------------------------------- /zmedia/deepVH3.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/zmedia/deepVH3.png -------------------------------------------------------------------------------- /zmedia/deepVH4.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/QData/DeepVHPPI/HEAD/zmedia/deepVH4.png --------------------------------------------------------------------------------