├── INSTALL.md ├── LICENSE ├── README.md ├── bin ├── calc_logprobs_seqs_fr ├── calc_logprobs_seqs_nanobody ├── generate_sample_seqs_fr ├── library_selection_birch ├── make_birch_feature_matrix ├── process_output_sequences └── run_autoregressive_fr ├── examples ├── README.md ├── demo_calc_logprobs.sh ├── demo_generate.sh ├── demo_train.sh ├── download_effect_predictions.sh ├── download_example_data.sh ├── download_generated_nanobodies.sh ├── download_sequences.sh └── run_example.sh ├── linux_setup.sh ├── requirements.txt ├── requirements_gpu.txt ├── seqdesign ├── __init__.py ├── aws_utils.py ├── birch.py ├── helper.py ├── hyper_conv_auto.py ├── layers_auto_b.py ├── scripts │ ├── __init__.py │ ├── calc_logprobs_seqs_fr.py │ ├── calc_logprobs_seqs_nanobody.py │ ├── generate_sample_seqs_fr.py │ ├── library_selection_birch.py │ ├── make_birch_feature_matrix.py │ ├── process_output_sequences.py │ ├── run_autoregressive_fr.py │ └── train_nanobody_autoregressive_fr.py ├── text_histogram.py ├── 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