├── CITATION.cff ├── README.md ├── ec ├── README.md ├── annotation_eval.py ├── annotation_eval_emb_EC4050L12.py ├── call_all.sh ├── combining_ig_output_files.py ├── download_swissprot.sh ├── flip.py ├── ig.py ├── ig_cluster.py ├── ig_embedding.py ├── ig_embedding_EC40L1.py ├── ig_embedding_EC40L2.py ├── ig_embedding_EC50L2.py ├── image.def ├── integrated_gradient_helper.py ├── metrics.py ├── processing.py ├── prot_ec.py ├── prot_ec_esm.py ├── prot_ec_mod.py ├── prot_ec_pretrained_shuffled.py ├── sites_helper.py ├── stat_eval.py ├── submit_code.sh ├── submit_prot_ec.sh ├── submit_prot_ec_esm.sh ├── submit_prot_ec_flip.sh ├── submit_prot_ec_pretrained_shuffled.sh └── transformer_pooling.py └── go ├── README.md ├── annotation_eval.py ├── annotation_eval_transmembrane.py ├── call_all.sh ├── combining_ig_output_files.py ├── download_go.sh ├── download_swissprot.sh ├── envs ├── README.md ├── go_environment.yml ├── go_requirements.txt ├── go_spec_file.txt ├── image_environment.yml ├── image_requirements.txt ├── image_spec_file.txt ├── stats_environment.yml ├── stats_requirements.txt └── stats_spec_file.txt ├── evaluate_go.py ├── ig.py ├── ig_embedding.py ├── image.def ├── integrated_gradient_helper.py ├── jaccard.py ├── obtain_go_terms.py ├── parameters.json ├── processing.py ├── prosite_parser.py ├── prot_go.py ├── prot_go_esm.py ├── prot_go_mod.py ├── prot_go_pretrained_shuffled.py ├── schedulers.py ├── sites_helper.py ├── stat_eval.py ├── submit_code.sh ├── submit_prot_go.sh ├── submit_prot_go_esm.sh ├── submit_prot_go_pretrained.sh ├── submit_prot_go_pretrained_shuffled.sh └── transformer_pooling.py /CITATION.cff: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/MarkusWenzel/xai-proteins/HEAD/CITATION.cff -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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