├── .gitignore ├── LICENSE ├── README.md ├── bioreason ├── __init__.py ├── dataset │ ├── __init__.py │ ├── kegg.py │ ├── utils.py │ └── variant_effect.py ├── dna_modules │ ├── __init__.py │ ├── dna_module.py │ └── nucleotide_module.py ├── models │ ├── __init__.py │ ├── dl │ │ ├── __init__.py │ │ ├── chat_template_dl.py │ │ ├── configuration_dl.py │ │ └── processing_dl.py │ ├── dna_llm.py │ ├── dna_only.py │ └── evo2_tokenizer.py ├── trainer │ ├── __init__.py │ ├── demo_grpo.py │ ├── grpo_config.py │ └── grpo_trainer.py └── utils │ ├── __init__.py │ └── dna_utils.py ├── data ├── BioReasoning_DataCuration_KEGG.ipynb ├── Clinvar_Coding.ipynb ├── Clinvar_SNV_Non_SNV.ipynb ├── Dataset Figures.ipynb ├── KEGG_Data_1.ipynb ├── KEGG_Data_2.ipynb ├── KEGG_Data_3.ipynb ├── README.md └── VEP.ipynb ├── figures ├── Figure1.png ├── Figure2.png └── Figure3.png ├── grpo_trainer_lora_model ├── adapter_config.json └── ds_config_stage2.json ├── pyproject.toml ├── reason.py ├── requirements.txt ├── 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