.gitignore
.pre-commit-config.yaml
LICENSE
README.md
README.rst
pyproject.toml
requirements-dev.in
requirements.in
requirements.txt
setup.cfg
.github/workflows/ci.yml
.github/workflows/docs-pages.yml
cortex/__init__.py
cortex/acquisition/__init__.py
cortex/acquisition/_graph_nei.py
cortex/assets/__init__.py
cortex/assets/protein_seq_tokenizer_32/__init__.py
cortex/assets/protein_seq_tokenizer_32/special_tokens_map.json
cortex/assets/protein_seq_tokenizer_32/tokenizer_config.json
cortex/assets/protein_seq_tokenizer_32/vocab.txt
cortex/attribution/__init__.py
cortex/attribution/_occlusion.py
cortex/cmdline/__init__.py
cortex/cmdline/optimize_sequences.py
cortex/cmdline/train_cortex_model.py
cortex/config/__init__.py
cortex/config/hydra/__init__.py
cortex/config/hydra/optimize_proteins.yaml
cortex/config/hydra/train_protein_model.yaml
cortex/config/hydra/branches/generation.yaml
cortex/config/hydra/branches/protein_property.yaml
cortex/config/hydra/general_settings/default.yaml
cortex/config/hydra/logging/default.yaml
cortex/config/hydra/model_globals/default.yaml
cortex/config/hydra/roots/protein_seq.yaml
cortex/config/hydra/tasks/generation/gfp.yaml
cortex/config/hydra/tasks/protein_property/delta_g.yaml
cortex/config/hydra/tasks/protein_property/log_fluorescence.yaml
cortex/config/hydra/tasks/protein_property/stability.yaml
cortex/config/hydra/tree/protein_model.yaml
cortex/config/hydra/trunk/default.yaml
cortex/constants/__init__.py
cortex/constants/_protein_constants.py
cortex/corruption/__init__.py
cortex/corruption/_abstract_corruption.py
cortex/corruption/_diffusion_noise_schedule.py
cortex/corruption/_gaussian_corruption.py
cortex/corruption/_mask_corruption.py
cortex/data/__init__.py
cortex/data/data_module/__init__.py
cortex/data/data_module/_task_data_module.py
cortex/data/dataset/__init__.py
cortex/data/dataset/_data_frame_dataset.py
cortex/data/dataset/_rfp_dataset.py
cortex/data/dataset/_tape_fluorescence.py
cortex/data/dataset/_tape_stability.py
cortex/data/dataset/_transformed_dataset.py
cortex/data/samplers/__init__.py
cortex/data/samplers/_minority_upsampler.py
cortex/data/samplers/_randomized_minority_sampler.py
cortex/data/samplers/functional/__init__.py
cortex/data/samplers/functional/_round_robin_longest.py
cortex/io/__init__.py
cortex/io/_download.py
cortex/io/_load_hydra_config.py
cortex/io/_load_model_checkpoint.py
cortex/io/_md5.py
cortex/io/_parse_s3_path.py
cortex/io/_verify_checksum.py
cortex/io/_verify_integrity.py
cortex/logging/__init__.py
cortex/logging/_wandb_setup.py
cortex/metrics/__init__.py
cortex/metrics/_edit_dist.py
cortex/metrics/_spearman_rho.py
cortex/model/__init__.py
cortex/model/_infer_with_model.py
cortex/model/_weight_averaging.py
cortex/model/block/__init__.py
cortex/model/block/_conv1d_resid_block.py
cortex/model/branch/__init__.py
cortex/model/branch/_abstract_branch.py
cortex/model/branch/_conv1d_branch.py
cortex/model/elemental/__init__.py
cortex/model/elemental/_apply.py
cortex/model/elemental/_ddp_standardize.py
cortex/model/elemental/_expression.py
cortex/model/elemental/_functional.py
cortex/model/elemental/_layernorm.py
cortex/model/elemental/_mean_pooling.py
cortex/model/elemental/_sine_pos_encoder.py
cortex/model/leaf/__init__.py
cortex/model/leaf/_abstract_leaf.py
cortex/model/leaf/_classifier_leaf.py
cortex/model/leaf/_denoising_lm_leaf.py
cortex/model/leaf/_regressor_leaf.py
cortex/model/leaf/_seq_regressor_leaf.py
cortex/model/root/__init__.py
cortex/model/root/_abstract_root.py
cortex/model/root/_conv1d_root.py
cortex/model/tree/__init__.py
cortex/model/tree/_abstract_tree.py
cortex/model/tree/_seq_model_tree.py
cortex/model/trunk/__init__.py
cortex/model/trunk/_abstract_trunk.py
cortex/model/trunk/_sum_trunk.py
cortex/optim/__init__.py
cortex/optim/_coordinate_selection.py
cortex/optim/_initialization.py
cortex/optim/generative/__init__.py
cortex/optim/generative/_lambo.py
cortex/task/__init__.py
cortex/task/_abstract_task.py
cortex/task/_classification.py
cortex/task/_denoising_lm_task.py
cortex/task/_regression.py
cortex/task/_sequence_regression.py
cortex/tokenization/__init__.py
cortex/tokenization/_cached_bert_tokenizer.py
cortex/tokenization/_protein_seq_tokenizer.py
cortex/transforms/__init__.py
cortex/transforms/_hf_tokenizer_transform.py
cortex/transforms/_tokenize_igg_ag_df.py
cortex/transforms/_transform.py
cortex/transforms/functional/__init__.py
cortex/transforms/functional/_tokenize_igg_ag_df.py
docs/Makefile
docs/make.bat
docs/assets/cortex_logo_concept_v1.png
docs/assets/human_brain_white_grey_matter.jpeg
docs/assets/neural_tree.png
docs/assets/neural_tree_banner.png
docs/assets/olive-tree-drawing.png
docs/source/conf.py
docs/source/index.rst
pytorch_cortex.egg-info/PKG-INFO
pytorch_cortex.egg-info/SOURCES.txt
pytorch_cortex.egg-info/dependency_links.txt
pytorch_cortex.egg-info/entry_points.txt
pytorch_cortex.egg-info/requires.txt
pytorch_cortex.egg-info/top_level.txt
tests/cortex/corruption/test_gaussian_corruption.py
tests/cortex/corruption/test_mask_corruption.py
tests/cortex/data/dataset/test_fluorescence_dataset.py
tests/cortex/data/dataset/test_rfp_dataset.py
tests/cortex/model/branch/test_abstract_branch.py
tests/cortex/model/branch/test_conv_1d_branch.py
tests/cortex/model/leaf/test_abstract_leaf.py
tests/cortex/model/leaf/test_classifier_leaf.py
tests/cortex/model/leaf/test_regressor_leaf.py
tests/cortex/model/root/test_abstract_root.py
tests/cortex/model/root/test_conv_1d_root.py
tests/cortex/model/tree/test_abstract_tree.py
tests/cortex/model/tree/test_seq_model_tree.py
tests/cortex/model/trunk/test_abstract_trunk.py
tests/cortex/model/trunk/test_sum_trunk.py
tests/cortex/tokenization/test_protein_seq_tokenizer.py
tests/cortex/transforms/test_hf_tokenizer_transform.py
tutorials/1_neural_tree_anatomy.ipynb
tutorials/2_defining_a_task.ipynb
tutorials/3_training_a_neural_tree.ipynb
tutorials/4_guided_diffusion.ipynb
tutorials/hydra/2_defining_a_task.yaml
tutorials/hydra/3_training_a_neural_tree.yaml
tutorials/hydra/4_guided_diffusion.yaml
tutorials/hydra/branches/protein_generation.yaml
tutorials/hydra/branches/protein_property.yaml
tutorials/hydra/guidance_objective/log_fluorescence.yaml
tutorials/hydra/optim/lambo.yaml
tutorials/hydra/roots/protein_seq.yaml
tutorials/hydra/tasks/log_fluorescence.yaml
tutorials/hydra/tasks/protein_seq.yaml
tutorials/hydra/tree/sequence_model.yaml
tutorials/hydra/trunk/sum_trunk.yaml