├── README.md ├── genomeFactory ├── Data │ ├── Download │ │ ├── Datasets_species_taxonid_dict.json │ │ ├── GenomeDataset.py │ │ └── NcbiDatasetCli.py │ └── Process │ │ └── process_all.py ├── Examples │ ├── download_by_link.yaml │ ├── download_by_species.yaml │ ├── inference_adapter.yaml │ ├── inference_extract.yaml │ ├── inference_extract_evo.yaml │ ├── inference_full.yaml │ ├── inference_generation_evo.yaml │ ├── inference_generation_genomeocean.yaml │ ├── inference_lora.yaml │ ├── process_emp.yaml │ ├── process_enhancer.yaml │ ├── process_normal.yaml │ ├── process_promoter.yaml │ ├── protein_generation.yaml │ ├── sae_regression.yaml │ ├── sae_train.yaml │ ├── train_adapter.yaml │ ├── train_evo_lora.yaml │ ├── train_full.yaml │ └── train_lora.yaml ├── Inference │ ├── classification │ │ ├── Inference_adapter_classification.py │ │ └── Inference_classification.py │ ├── extract_embedding │ │ ├── evo_extract.py │ │ └── extract.py │ ├── generation │ │ ├── evo_generation.py │ │ └── genome_ocean_generation.py │ ├── protein_generation │ │ ├── autocomplete_structure_Evo.py │ │ └── autocomplete_structure_GO.py │ └── regression │ │ ├── Inference_adapter_regression.py │ │ └── Inference_regression.py ├── Interpretation │ └── SAE │ │ ├── dna_data_module.py │ │ ├── dna_sae_module.py │ │ ├── dna_sequence_analysis.py │ │ ├── dna_sequence_analysis_firsttoken.py │ │ ├── dna_training.py │ │ ├── model_wrapper.py │ │ └── sae_model.py ├── Train │ ├── finetune.py │ ├── metric │ │ ├── __pycache__ │ │ │ └── metric_classification.cpython-310.pyc │ │ ├── metric_classification.py │ │ └── metric_regression.py │ ├── train_scripts │ │ ├── adapter │ │ │ ├── train_adapter_classification.py │ │ │ ├── train_adapter_regression.py │ │ │ ├── train_evo_adapter_classification.py │ │ │ └── train_evo_adapter_regression.py │ │ └── full_and_lora │ │ │ ├── train_classification.py │ │ │ └── train_regression.py │ └── workflow │ │ ├── adapter │ │ ├── adapter_model │ │ │ └── Adapter.py │ │ ├── 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