.gitignore
.pre-commit-config.yaml
CLONE.md
CONTRIBUTING.md
LICENSE.txt
README.md
mammal.png
mammal_preview_2.pdf
pyproject.toml
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.github/ISSUE_TEMPLATE/---feature-request.md
.github/ISSUE_TEMPLATE/---question.md
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.github/workflows/github-actions.yml
.github/workflows/python-publish.yml
biomed_multi_alignment.egg-info/PKG-INFO
biomed_multi_alignment.egg-info/SOURCES.txt
biomed_multi_alignment.egg-info/dependency_links.txt
biomed_multi_alignment.egg-info/entry_points.txt
biomed_multi_alignment.egg-info/requires.txt
biomed_multi_alignment.egg-info/top_level.txt
mammal/__init__.py
mammal/keys.py
mammal/lora.py
mammal/losses.py
mammal/lr_schedulers.py
mammal/main_finetune.py
mammal/metrics.py
mammal/model.py
mammal/task.py
mammal/examples/carcinogenicity/__init__.py
mammal/examples/carcinogenicity/config.yaml
mammal/examples/carcinogenicity/main_infer.py
mammal/examples/carcinogenicity/pl_data_module.py
mammal/examples/carcinogenicity/task.py
mammal/examples/carcinogenicity/data/carcinogens_lagunin.tab
mammal/examples/cell_line_drug_response/__init__.py
mammal/examples/cell_line_drug_response/config.yaml
mammal/examples/cell_line_drug_response/dataset.py
mammal/examples/cell_line_drug_response/main_infer.py
mammal/examples/cell_line_drug_response/pl_data_module.py
mammal/examples/cell_line_drug_response/task.py
mammal/examples/dti_bindingdb_kd/__init__.py
mammal/examples/dti_bindingdb_kd/config.yaml
mammal/examples/dti_bindingdb_kd/main_infer.py
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mammal/examples/dti_bindingdb_kd/task.py
mammal/examples/molnet/__init__.py
mammal/examples/molnet/molnet_infer.py
mammal/examples/protein_solubility/__init__.py
mammal/examples/protein_solubility/config.yaml
mammal/examples/protein_solubility/main_infer.py
mammal/examples/protein_solubility/pl_data_module.py
mammal/examples/protein_solubility/task.py
mammal/examples/scrna_cell_type/README.md
mammal/examples/scrna_cell_type/__init__.py
mammal/examples/scrna_cell_type/anndata_op.py
mammal/examples/scrna_cell_type/cell_type_mapping.csv
mammal/examples/scrna_cell_type/config.yaml
mammal/examples/scrna_cell_type/pl_data_module.py
mammal/examples/scrna_cell_type/scRNA_infer.py
mammal/examples/scrna_cell_type/task.py
mammal/examples/scrna_cell_type/data/Zheng68k_to_anndata.py
mammal/examples/scrna_cell_type/data/process_h5ad_data.py
mammal/examples/tcr_epitope_binding/main_infer.py
mammal/examples/tests/test_drug_carcinogenicity_classification.py
mammal/examples/tests/test_dti_bindingdb_kd.py
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mammal/examples/tests/test_protein_solubility_prediction.py
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mammal/examples/tests/test_tcr_epitope_binding_inference.py
mammal/tests/test_transformers5_config_compat.py
mammal_mcp/.env.example
mammal_mcp/.gitignore
mammal_mcp/README.md
mammal_mcp/dependencies.py
mammal_mcp/pyproject.toml
mammal_mcp/server.py
mammal_mcp/util.py
mammal_mcp/uv.lock
mammal_vllm/README.md
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mammal_vllm/examples/__init__.py
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mammal_vllm/examples/online_mammal_usage.py
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mammal_vllm/vllm_mammal_plugin/__init__.py
mammal_vllm/vllm_mammal_plugin/mammal.py
mammal_vllm/vllm_mammal_plugin/tokenization.py
tutorials/advanced_create_new_task.ipynb
tutorials/begginer_inference.ipynb
tutorials/MAINFRAME_2026/MAMMAL_finetune.ipynb
tutorials/MAINFRAME_2026/MAMMAL_inference.ipynb
tutorials/MAINFRAME_2026/MMELON_finetuning.ipynb
tutorials/MAINFRAME_2026/MMELON_inference.ipynb
tutorials/MAINFRAME_2026/README.md
tutorials/MAINFRAME_2026/data_and_predictions_analysis.ipynb