├── .gitignore ├── LICENSE ├── MANIFEST.in ├── README.md ├── docs ├── Makefile ├── _static │ └── custom.css ├── make.bat ├── requirements.txt └── source │ ├── GATA1_example.rst │ ├── _autosummary │ ├── perturbnet.baselines.knn.rst │ ├── perturbnet.baselines.linear.rst │ ├── perturbnet.baselines.rst │ ├── perturbnet.chemicalvae.chemicalVAE.rst │ ├── perturbnet.chemicalvae.rst │ ├── perturbnet.cinn.FeatureAttr.rst │ ├── perturbnet.cinn.flow.rst │ ├── perturbnet.cinn.flow_generate.rst │ ├── perturbnet.cinn.rst │ ├── perturbnet.genotypevae.genotypeVAE.rst │ ├── perturbnet.genotypevae.rst │ ├── perturbnet.pytorch_scvi.distributions.rst │ ├── perturbnet.pytorch_scvi.rst │ ├── perturbnet.pytorch_scvi.scvi_generate_z.rst │ └── perturbnet.util.rst │ ├── _static │ └── custom.css │ ├── api.rst │ ├── chemical_perturbation.rst │ ├── coding_variant.rst │ ├── conf.py │ ├── feature_attribution.rst │ ├── genetic_perturbation.rst │ ├── index.rst │ ├── tutorials │ ├── GATA1_example.nblink │ ├── GATA1_prediction_analysis.ipynb │ ├── Integrated_gradients_example.ipynb │ ├── Tutorial_PerturbNet_Chemicals.ipynb │ ├── Tutorial_PerturbNet_Genetic.ipynb │ ├── Tutorial_PerturbNet_coding_variants.ipynb │ ├── chemical_perturbation.nblink │ ├── coding_variant.nblink │ ├── feature_attribution.nblink │ └── genetic_perturbation.nblink │ └── usage.rst ├── notebooks ├── Benchmark_Jorge_Example.ipynb ├── Benchmark_LINCS_Example.ipynb ├── Benchmark_Norman_Example.ipynb ├── Benchmark_Sciplex_Example.ipynb ├── Benchmark_Ursu_Example.ipynb ├── GATA1_prediction_analysis.ipynb ├── Integrated_gradients_example.ipynb ├── Tutorial_PerturbNet_Chemicals.ipynb ├── Tutorial_PerturbNet_Genetic.ipynb └── Tutorial_PerturbNet_coding_variants.ipynb ├── perturbnet ├── __init__.py ├── baselines │ ├── __init__.py │ ├── knn.py │ └── linear.py ├── chemicalvae │ ├── README.md │ ├── __init__.py │ └── chemicalVAE.py ├── cinn │ ├── FeatureAttr.py │ ├── __init__.py │ ├── flow.py │ └── flow_generate.py ├── data_vae │ ├── __init__.py │ ├── util.py │ └── vae.py ├── genotypevae │ ├── README.md │ ├── __init__.py │ └── genotypeVAE.py ├── net2net │ ├── __init__.py │ ├── ckpt_util.py │ ├── data │ │ ├── __init__.py │ │ ├── base.py │ │ ├── coco.py │ │ ├── faces.py │ │ ├── utils.py │ │ └── zcodes.py │ ├── models │ │ ├── __init__.py │ │ ├── autoencoder.py │ │ └── flows │ │ │ ├── __init__.py │ │ │ ├── flow.py │ │ │ ├── scviflow.py │ │ │ └── util.py │ └── modules │ │ ├── __init__.py │ │ ├── __pycache__ │ │ ├── __init__.cpython-37.pyc │ │ ├── __init__.cpython-39.pyc │ │ ├── util.cpython-37.pyc │ │ └── util.cpython-39.pyc │ │ ├── autoencoder │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-37.pyc │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── basic.cpython-37.pyc │ │ │ └── basic.cpython-39.pyc │ │ ├── basic.py │ │ ├── decoder.py │ │ ├── encoder.py │ │ ├── loss.py │ │ └── lpips.py │ │ ├── captions │ │ ├── __init__.py │ │ ├── model.py │ │ └── models.py │ │ ├── discriminator │ │ ├── __init__.py │ │ └── model.py │ │ ├── distributions │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-37.pyc │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── distributions.cpython-37.pyc │ │ │ └── distributions.cpython-39.pyc │ │ └── distributions.py │ │ ├── facenet │ │ ├── __init__.py │ │ ├── inception_resnet_v1.py │ │ └── model.py │ │ ├── flow │ │ ├── __init__.py │ │ ├── __pycache__ │ │ │ ├── __init__.cpython-37.pyc │ │ │ ├── __init__.cpython-39.pyc │ │ │ ├── base.cpython-37.pyc │ │ │ ├── base.cpython-39.pyc │ │ │ ├── blocks.cpython-37.pyc │ │ │ ├── blocks.cpython-39.pyc │ │ │ ├── flatflow.cpython-37.pyc │ │ │ ├── flatflow.cpython-39.pyc │ │ │ ├── loss.cpython-37.pyc │ │ │ └── loss.cpython-39.pyc │ │ ├── base.py │ │ ├── blocks.py │ │ ├── flatflow.py │ │ └── loss.py │ │ ├── gan │ │ ├── __init__.py │ │ ├── bigbigan.py │ │ └── biggan.py │ │ ├── labels │ │ ├── __init__.py │ │ └── model.py │ │ ├── mlp │ │ ├── __init__.py │ │ └── models.py │ │ ├── sbert │ │ ├── __init__.py │ │ └── model.py │ │ └── 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