├── .gitignore ├── LICENSE.md ├── README.md ├── assets ├── Orthrus_movie.gif └── orthrus.png ├── data_prep ├── data_utils.py ├── generate_transcript_dict.py └── split_transcript_dict.py ├── env.yml ├── nbs └── start_here.ipynb ├── orthrus ├── __init__.py ├── _sequence.pyx ├── config │ ├── data.yaml │ ├── model.yaml │ ├── optimizer.yaml │ ├── projector.yaml │ └── train.yaml ├── config_utils.py ├── data.py ├── data_loader.py ├── dilated_resnet.py ├── eval_utils.py ├── finetune.py ├── finetune_config │ ├── data.yaml │ ├── model.yaml │ ├── optimizer.yaml │ ├── projector.yaml │ └── train.yaml ├── finetune_dataloader.py ├── finetune_model.py ├── genome.py ├── gk_utils.py ├── layers.py ├── linear_probe_eval.py ├── losses.py ├── mamba.py ├── mlm_model.py ├── model.py ├── rna_task_config │ ├── data.yaml │ ├── model.yaml │ ├── optimizer.yaml │ ├── projector.yaml │ └── train.yaml ├── rna_task_dataset.py ├── rna_task_train.py ├── saluki.py ├── sequence.py ├── train.py └── util.py ├── settings.ini ├── setup.py ├── slurm ├── subsampling_experiment.sh └── train_contrast.sh └── tests ├── conftest.py ├── test_interval.py ├── test_refseq_dataset.py └── test_transcript.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowang-lab/Orthrus/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowang-lab/Orthrus/HEAD/LICENSE.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bowang-lab/Orthrus/HEAD/README.md -------------------------------------------------------------------------------- /assets/Orthrus_movie.gif: 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