├── .gitattributes ├── .github └── workflows │ ├── ci.yml │ ├── docs.yml │ ├── pypi.yml │ └── testpypi.yml ├── .gitignore ├── LICENSE.md ├── MANIFEST.in ├── Makefile ├── README.rst ├── cellarium └── ml │ ├── __init__.py │ ├── callbacks │ ├── __init__.py │ ├── compute_norm.py │ ├── get_coord_data.py │ ├── loss_scale_monitor.py │ ├── prediction_writer.py │ └── variance_monitor.py │ ├── cli.py │ ├── core │ ├── __init__.py │ ├── datamodule.py │ ├── module.py │ └── pipeline.py │ ├── data │ ├── __init__.py │ ├── dadc_dataset.py │ ├── distributed_anndata.py │ ├── fileio.py │ ├── pytree_dataset.py │ └── schema.py │ ├── distributions │ ├── __init__.py │ └── negative_binomial.py │ ├── layers │ ├── __init__.py │ ├── attention.py │ ├── embedding.py │ ├── ffn.py │ ├── head.py │ ├── mu_linear.py │ ├── normadd.py │ └── transformer.py │ ├── lr_schedulers │ ├── __init__.py │ └── linear_lr.py │ ├── models │ ├── __init__.py │ ├── cellarium_gpt.py │ ├── geneformer.py │ ├── incremental_pca.py │ ├── logistic_regression.py │ ├── model.py │ ├── onepass_mean_var_std.py │ ├── probabilistic_pca.py │ └── tdigest.py │ ├── preprocessing │ ├── __init__.py │ └── highly_variable_genes.py │ ├── py.typed │ ├── transforms │ ├── __init__.py │ ├── cellarium_gpt_tokenizer.py │ ├── divide_by_scale.py │ ├── filter.py │ ├── log1p.py │ ├── normalize_total.py │ └── z_score.py │ └── utilities │ ├── __init__.py │ ├── core.py │ ├── data.py │ ├── distributed.py │ ├── layers.py │ ├── mup.py │ └── testing.py ├── docs ├── Makefile ├── make.bat └── source │ ├── _static │ └── custom.css │ ├── callbacks.rst │ ├── cli.rst │ ├── conf.py │ ├── core.rst │ ├── data.rst │ ├── distributions.rst │ ├── index.rst │ ├── layers.rst │ ├── lr_schedulers.rst │ ├── models.rst │ ├── preprocessing.rst │ ├── requirements.txt │ ├── transforms.rst │ └── utilities.rst ├── examples └── cli_workflow │ ├── cli_workflow.rst │ ├── ipca_train_config.yaml │ ├── lr_resume_train_config.yaml │ ├── lr_train_config.yaml │ └── onepass_train_config.yaml ├── notebooks ├── geneformer_demo.ipynb ├── mup_mlp.ipynb └── part_i.ipynb ├── pyproject.toml ├── scripts └── update_headers.py └── tests ├── __init__.py ├── common.py ├── dataloader ├── __init__.py ├── test_datamodule.py ├── test_dataset.py ├── test_distributed_anndata.py ├── test_pytree_dataset.py ├── test_read_h5ad.py └── test_schema.py ├── distributed └── test_gather.py ├── distributions └── test_negative_binomial.py ├── test_attention.py ├── test_callbacks.py ├── test_cellarium_gpt.py ├── test_cli.py ├── test_geneformer.py ├── test_highly_variable_genes.py ├── test_ipca.py ├── test_logistic_regression.py ├── test_mup.py ├── test_onepass_mean_var_std.py ├── test_ppca.py ├── test_tdigest.py └── test_transforms.py /.gitattributes: -------------------------------------------------------------------------------- 1 | scvid/_version.py export-subst 2 | -------------------------------------------------------------------------------- /.github/workflows/ci.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/.github/workflows/ci.yml -------------------------------------------------------------------------------- /.github/workflows/docs.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/.github/workflows/docs.yml -------------------------------------------------------------------------------- /.github/workflows/pypi.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/.github/workflows/pypi.yml -------------------------------------------------------------------------------- /.github/workflows/testpypi.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/.github/workflows/testpypi.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/LICENSE.md -------------------------------------------------------------------------------- /MANIFEST.in: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/Makefile -------------------------------------------------------------------------------- /README.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/README.rst -------------------------------------------------------------------------------- /cellarium/ml/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/__init__.py -------------------------------------------------------------------------------- /cellarium/ml/callbacks/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/callbacks/__init__.py -------------------------------------------------------------------------------- /cellarium/ml/callbacks/compute_norm.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/callbacks/compute_norm.py -------------------------------------------------------------------------------- /cellarium/ml/callbacks/get_coord_data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/callbacks/get_coord_data.py -------------------------------------------------------------------------------- /cellarium/ml/callbacks/loss_scale_monitor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/callbacks/loss_scale_monitor.py -------------------------------------------------------------------------------- /cellarium/ml/callbacks/prediction_writer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/callbacks/prediction_writer.py -------------------------------------------------------------------------------- /cellarium/ml/callbacks/variance_monitor.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/callbacks/variance_monitor.py -------------------------------------------------------------------------------- /cellarium/ml/cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/cli.py -------------------------------------------------------------------------------- /cellarium/ml/core/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/core/__init__.py -------------------------------------------------------------------------------- /cellarium/ml/core/datamodule.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/core/datamodule.py -------------------------------------------------------------------------------- /cellarium/ml/core/module.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/core/module.py -------------------------------------------------------------------------------- /cellarium/ml/core/pipeline.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/core/pipeline.py -------------------------------------------------------------------------------- /cellarium/ml/data/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/data/__init__.py -------------------------------------------------------------------------------- /cellarium/ml/data/dadc_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/data/dadc_dataset.py -------------------------------------------------------------------------------- /cellarium/ml/data/distributed_anndata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/data/distributed_anndata.py -------------------------------------------------------------------------------- /cellarium/ml/data/fileio.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/data/fileio.py -------------------------------------------------------------------------------- /cellarium/ml/data/pytree_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/data/pytree_dataset.py -------------------------------------------------------------------------------- /cellarium/ml/data/schema.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/data/schema.py -------------------------------------------------------------------------------- /cellarium/ml/distributions/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/distributions/__init__.py -------------------------------------------------------------------------------- /cellarium/ml/distributions/negative_binomial.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/distributions/negative_binomial.py -------------------------------------------------------------------------------- /cellarium/ml/layers/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/layers/__init__.py -------------------------------------------------------------------------------- /cellarium/ml/layers/attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/layers/attention.py -------------------------------------------------------------------------------- /cellarium/ml/layers/embedding.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/layers/embedding.py -------------------------------------------------------------------------------- /cellarium/ml/layers/ffn.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/layers/ffn.py -------------------------------------------------------------------------------- /cellarium/ml/layers/head.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/layers/head.py -------------------------------------------------------------------------------- /cellarium/ml/layers/mu_linear.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/layers/mu_linear.py -------------------------------------------------------------------------------- /cellarium/ml/layers/normadd.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/layers/normadd.py -------------------------------------------------------------------------------- /cellarium/ml/layers/transformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/layers/transformer.py -------------------------------------------------------------------------------- /cellarium/ml/lr_schedulers/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/lr_schedulers/__init__.py -------------------------------------------------------------------------------- /cellarium/ml/lr_schedulers/linear_lr.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/lr_schedulers/linear_lr.py -------------------------------------------------------------------------------- /cellarium/ml/models/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/models/__init__.py -------------------------------------------------------------------------------- /cellarium/ml/models/cellarium_gpt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/models/cellarium_gpt.py -------------------------------------------------------------------------------- /cellarium/ml/models/geneformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/models/geneformer.py -------------------------------------------------------------------------------- /cellarium/ml/models/incremental_pca.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/models/incremental_pca.py -------------------------------------------------------------------------------- /cellarium/ml/models/logistic_regression.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/models/logistic_regression.py -------------------------------------------------------------------------------- /cellarium/ml/models/model.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/models/model.py -------------------------------------------------------------------------------- /cellarium/ml/models/onepass_mean_var_std.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/models/onepass_mean_var_std.py -------------------------------------------------------------------------------- /cellarium/ml/models/probabilistic_pca.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/models/probabilistic_pca.py -------------------------------------------------------------------------------- /cellarium/ml/models/tdigest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/models/tdigest.py -------------------------------------------------------------------------------- /cellarium/ml/preprocessing/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/preprocessing/__init__.py -------------------------------------------------------------------------------- /cellarium/ml/preprocessing/highly_variable_genes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/preprocessing/highly_variable_genes.py -------------------------------------------------------------------------------- /cellarium/ml/py.typed: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /cellarium/ml/transforms/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/transforms/__init__.py -------------------------------------------------------------------------------- /cellarium/ml/transforms/cellarium_gpt_tokenizer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/transforms/cellarium_gpt_tokenizer.py -------------------------------------------------------------------------------- /cellarium/ml/transforms/divide_by_scale.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/transforms/divide_by_scale.py -------------------------------------------------------------------------------- /cellarium/ml/transforms/filter.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/transforms/filter.py -------------------------------------------------------------------------------- /cellarium/ml/transforms/log1p.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/transforms/log1p.py -------------------------------------------------------------------------------- /cellarium/ml/transforms/normalize_total.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/transforms/normalize_total.py -------------------------------------------------------------------------------- /cellarium/ml/transforms/z_score.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/transforms/z_score.py -------------------------------------------------------------------------------- /cellarium/ml/utilities/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /cellarium/ml/utilities/core.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/utilities/core.py -------------------------------------------------------------------------------- /cellarium/ml/utilities/data.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/utilities/data.py -------------------------------------------------------------------------------- /cellarium/ml/utilities/distributed.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/utilities/distributed.py -------------------------------------------------------------------------------- /cellarium/ml/utilities/layers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/utilities/layers.py -------------------------------------------------------------------------------- /cellarium/ml/utilities/mup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/utilities/mup.py -------------------------------------------------------------------------------- /cellarium/ml/utilities/testing.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/cellarium/ml/utilities/testing.py -------------------------------------------------------------------------------- /docs/Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/Makefile -------------------------------------------------------------------------------- /docs/make.bat: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/make.bat -------------------------------------------------------------------------------- /docs/source/_static/custom.css: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/source/_static/custom.css -------------------------------------------------------------------------------- /docs/source/callbacks.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/source/callbacks.rst -------------------------------------------------------------------------------- /docs/source/cli.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/source/cli.rst -------------------------------------------------------------------------------- /docs/source/conf.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/source/conf.py -------------------------------------------------------------------------------- /docs/source/core.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/source/core.rst -------------------------------------------------------------------------------- /docs/source/data.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/source/data.rst -------------------------------------------------------------------------------- /docs/source/distributions.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/source/distributions.rst -------------------------------------------------------------------------------- /docs/source/index.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/source/index.rst -------------------------------------------------------------------------------- /docs/source/layers.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/source/layers.rst -------------------------------------------------------------------------------- /docs/source/lr_schedulers.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/source/lr_schedulers.rst -------------------------------------------------------------------------------- /docs/source/models.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/source/models.rst -------------------------------------------------------------------------------- /docs/source/preprocessing.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/source/preprocessing.rst -------------------------------------------------------------------------------- /docs/source/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/source/requirements.txt -------------------------------------------------------------------------------- /docs/source/transforms.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/source/transforms.rst -------------------------------------------------------------------------------- /docs/source/utilities.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/docs/source/utilities.rst -------------------------------------------------------------------------------- /examples/cli_workflow/cli_workflow.rst: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/examples/cli_workflow/cli_workflow.rst -------------------------------------------------------------------------------- /examples/cli_workflow/ipca_train_config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/examples/cli_workflow/ipca_train_config.yaml -------------------------------------------------------------------------------- /examples/cli_workflow/lr_resume_train_config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/examples/cli_workflow/lr_resume_train_config.yaml -------------------------------------------------------------------------------- /examples/cli_workflow/lr_train_config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/examples/cli_workflow/lr_train_config.yaml -------------------------------------------------------------------------------- /examples/cli_workflow/onepass_train_config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/examples/cli_workflow/onepass_train_config.yaml -------------------------------------------------------------------------------- /notebooks/geneformer_demo.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/notebooks/geneformer_demo.ipynb -------------------------------------------------------------------------------- /notebooks/mup_mlp.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/notebooks/mup_mlp.ipynb -------------------------------------------------------------------------------- /notebooks/part_i.ipynb: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/notebooks/part_i.ipynb -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/pyproject.toml -------------------------------------------------------------------------------- /scripts/update_headers.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/scripts/update_headers.py -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/common.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/common.py -------------------------------------------------------------------------------- /tests/dataloader/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/dataloader/test_datamodule.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/dataloader/test_datamodule.py -------------------------------------------------------------------------------- /tests/dataloader/test_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/dataloader/test_dataset.py -------------------------------------------------------------------------------- /tests/dataloader/test_distributed_anndata.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/dataloader/test_distributed_anndata.py -------------------------------------------------------------------------------- /tests/dataloader/test_pytree_dataset.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/dataloader/test_pytree_dataset.py -------------------------------------------------------------------------------- /tests/dataloader/test_read_h5ad.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/dataloader/test_read_h5ad.py -------------------------------------------------------------------------------- /tests/dataloader/test_schema.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/dataloader/test_schema.py -------------------------------------------------------------------------------- /tests/distributed/test_gather.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/distributed/test_gather.py -------------------------------------------------------------------------------- /tests/distributions/test_negative_binomial.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/distributions/test_negative_binomial.py -------------------------------------------------------------------------------- /tests/test_attention.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/test_attention.py -------------------------------------------------------------------------------- /tests/test_callbacks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/test_callbacks.py -------------------------------------------------------------------------------- /tests/test_cellarium_gpt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/test_cellarium_gpt.py -------------------------------------------------------------------------------- /tests/test_cli.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/test_cli.py -------------------------------------------------------------------------------- /tests/test_geneformer.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/test_geneformer.py -------------------------------------------------------------------------------- /tests/test_highly_variable_genes.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/test_highly_variable_genes.py -------------------------------------------------------------------------------- /tests/test_ipca.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/test_ipca.py -------------------------------------------------------------------------------- /tests/test_logistic_regression.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/test_logistic_regression.py -------------------------------------------------------------------------------- /tests/test_mup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/test_mup.py -------------------------------------------------------------------------------- /tests/test_onepass_mean_var_std.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/test_onepass_mean_var_std.py -------------------------------------------------------------------------------- /tests/test_ppca.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/test_ppca.py -------------------------------------------------------------------------------- /tests/test_tdigest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/test_tdigest.py -------------------------------------------------------------------------------- /tests/test_transforms.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/cellarium-ai/cellarium-ml/HEAD/tests/test_transforms.py --------------------------------------------------------------------------------