├── .github └── workflows │ ├── docs-pages.yml │ ├── pre-commit.yml │ └── unit.yml ├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── cortex ├── __init__.py ├── acquisition │ ├── __init__.py │ └── _graph_nei.py ├── assets │ ├── __init__.py │ └── protein_seq_tokenizer_32 │ │ ├── __init__.py │ │ ├── special_tokens_map.json │ │ ├── tokenizer_config.json │ │ └── vocab.txt ├── attribution │ ├── __init__.py │ └── _occlusion.py ├── cmdline │ ├── __init__.py │ └── train_cortex_model.py ├── config │ ├── __init__.py │ ├── hydra │ │ ├── __init__.py │ │ ├── branches │ │ │ ├── folding_encoder.yaml │ │ │ ├── generation.yaml │ │ │ ├── protein_property_cnn.yaml │ │ │ └── protein_property_encoder.yaml │ │ ├── general_settings │ │ │ └── default.yaml │ │ ├── logging │ │ │ └── default.yaml │ │ ├── model_globals │ │ │ └── default.yaml │ │ ├── roots │ │ │ ├── protein_seq_cnn.yaml │ │ │ ├── protein_seq_decoder.yaml │ │ │ └── protein_seq_encoder.yaml │ │ ├── tasks │ │ │ ├── folding │ │ │ │ ├── delta_g.yaml │ │ │ │ └── stability.yaml │ │ │ ├── generation │ │ │ │ ├── gfp.yaml │ │ │ │ ├── gfp_autoregressive.yaml │ │ │ │ ├── stable_proteins.yaml │ │ │ │ ├── stable_proteins_autoregressive.yaml │ │ │ │ └── tape_combined.yaml │ │ │ └── protein_property │ │ │ │ └── log_fluorescence.yaml │ │ ├── train_gpt.yaml │ │ ├── train_protein_model.yaml │ │ ├── tree │ │ │ └── protein_model.yaml │ │ └── trunk │ │ │ └── default.yaml │ └── wandb │ │ └── protein_model_sweep.yaml ├── constants │ ├── __init__.py │ └── _protein_constants.py ├── corruption │ ├── __init__.py │ ├── _abstract_corruption.py │ ├── _diffusion_noise_schedule.py │ ├── _gaussian_corruption.py │ ├── _mask_corruption.py │ └── _substitution_corruption.py ├── data │ ├── __init__.py │ ├── data_module │ │ ├── __init__.py │ │ └── _task_data_module.py │ ├── dataset │ │ ├── __init__.py │ │ ├── _data_frame_dataset.py │ │ ├── _numpy_dataset.py │ │ ├── _rfp_dataset.py │ │ ├── _tape_combined.py │ │ ├── _tape_fluorescence.py │ │ ├── _tape_stability.py │ │ └── _transformed_dataset.py │ └── samplers │ │ ├── __init__.py │ │ ├── _minority_upsampler.py │ │ ├── _randomized_minority_sampler.py │ │ └── functional │ │ ├── __init__.py │ │ └── _round_robin_longest.py ├── io │ ├── __init__.py │ ├── _download.py │ ├── _load_hydra_config.py │ ├── _load_model_checkpoint.py │ ├── _md5.py │ ├── _parse_s3_path.py │ ├── _verify_checksum.py │ └── _verify_integrity.py ├── logging │ ├── __init__.py │ └── _wandb_setup.py ├── metrics │ ├── __init__.py │ ├── _blosum.py │ ├── _edit_dist.py │ └── _spearman_rho.py ├── model │ ├── __init__.py │ ├── _infer_with_model.py │ ├── _weight_averaging.py │ ├── block │ │ ├── __init__.py │ │ ├── _conv1d_resid_block.py │ │ └── _transformer_block.py │ ├── branch │ │ ├── __init__.py │ │ ├── _abstract_branch.py │ │ ├── _conv1d_branch.py │ │ └── _transformer_branch.py │ ├── elemental │ │ ├── __init__.py │ │ ├── _apply.py │ │ ├── _bidirectional_self_attention.py │ │ ├── _causal_self_attention.py │ │ ├── _ddp_standardize.py │ │ ├── _expression.py │ │ ├── _functional.py │ │ ├── _layernorm.py │ │ ├── _mean_pooling.py │ │ ├── _mlp.py │ │ ├── _pooling_self_attention.py │ │ └── _sine_pos_encoder.py │ ├── leaf │ │ ├── __init__.py │ │ ├── _abstract_leaf.py │ │ ├── _autoregressive_lm_leaf.py │ │ ├── _classifier_leaf.py │ │ ├── _denoising_lm_leaf.py │ │ ├── _regressor_leaf.py │ │ └── _seq_regressor_leaf.py │ ├── root │ │ ├── __init__.py │ │ ├── _abstract_root.py │ │ ├── _conv1d_root.py │ │ └── _transformer_root.py │ ├── tree │ │ ├── __init__.py │ │ ├── _abstract_tree.py │ │ └── _seq_model_tree.py │ └── trunk │ │ ├── __init__.py │ │ ├── _abstract_trunk.py │ │ └── _sum_trunk.py ├── optim │ ├── __init__.py │ ├── _initialization.py │ └── generative │ │ ├── __init__.py │ │ └── _lambo.py ├── task │ ├── __init__.py │ ├── _abstract_task.py │ ├── _autoregressive_lm_task.py │ ├── _classification.py │ ├── _denoising_lm_task.py │ ├── _regression.py │ └── _sequence_regression.py ├── tokenization │ ├── __init__.py │ ├── _cached_bert_tokenizer.py │ └── _protein_seq_tokenizer.py └── transforms │ ├── __init__.py │ ├── _hf_tokenizer_transform.py │ ├── _pad_transform.py │ ├── _to_tensor.py │ ├── _tokenize_igg_ag_df.py │ ├── _transform.py │ └── functional │ ├── __init__.py │ ├── _to_tensor.py │ └── _tokenize_igg_ag_df.py ├── docs ├── Makefile ├── assets │ ├── cortex_logo_concept_v1.png │ ├── human_brain_white_grey_matter.jpeg │ ├── neural_tree.png │ ├── neural_tree_banner.png │ └── olive-tree-drawing.png ├── make.bat ├── source │ ├── conf.py │ └── index.rst └── task_leaf_config_issue.md ├── pyproject.toml ├── tests └── cortex │ ├── corruption │ ├── test_gaussian_corruption.py │ ├── test_mask_corruption.py │ └── test_substitution_corruption.py │ ├── data │ └── dataset │ │ ├── test_fluorescence_dataset.py │ │ └── test_rfp_dataset.py │ ├── metrics │ └── test_blosum.py │ ├── model │ ├── block │ │ └── test_transformer_block.py │ ├── branch │ │ ├── test_abstract_branch.py │ │ ├── test_conv_1d_branch.py │ │ └── test_transformer_branch.py │ ├── elemental │ │ ├── test_bidirectional_self_attention.py │ │ ├── test_causal_self_attention.py │ │ └── test_mlp.py │ ├── leaf │ │ ├── test_abstract_leaf.py │ │ ├── test_classifier_leaf.py │ │ ├── test_denoising_lm_leaf.py │ │ └── test_regressor_leaf.py │ ├── root │ │ ├── test_abstract_root.py │ │ ├── test_conv_1d_root.py │ │ └── test_transformer_root.py │ ├── tree │ │ ├── test_abstract_tree.py │ │ └── test_seq_model_tree.py │ └── trunk │ │ ├── test_abstract_trunk.py │ │ └── test_sum_trunk.py │ ├── task │ └── test_denoising_lm_task.py │ ├── tokenization │ └── test_protein_seq_tokenizer.py │ └── transforms │ └── test_hf_tokenizer_transform.py ├── tutorials ├── 1_neural_tree_anatomy.ipynb ├── 2_defining_a_task.ipynb ├── 3_training_a_neural_tree.ipynb ├── 4_guided_diffusion.ipynb └── hydra │ ├── 2_defining_a_task.yaml │ ├── 3_training_a_neural_tree.yaml │ ├── 4_guided_diffusion.yaml │ ├── branches │ ├── protein_generation.yaml │ 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