├── .gitignore ├── .pre-commit-config.yaml ├── LICENSE ├── README.md ├── conftest.py ├── contrastive_vi ├── __init__.py ├── data │ ├── __init__.py │ ├── dataloaders │ │ ├── __init__.py │ │ ├── contrastive_dataloader.py │ │ └── data_splitting.py │ ├── datasets │ │ ├── __init__.py │ │ ├── haber_2017.py │ │ ├── mcfarland_2020.py │ │ ├── norman_2019.py │ │ ├── papalexi_2021.py │ │ └── zheng_2017.py │ └── utils.py ├── model │ ├── __init__.py │ ├── base │ │ ├── __init__.py │ │ └── training_mixin.py │ ├── contrastive_vi.py │ └── total_contrastive_vi.py └── module │ ├── __init__.py │ ├── contrastive_vi.py │ ├── total_contrastive_vi.py │ └── utils.py ├── environment.yml ├── pyproject.toml ├── setup.cfg ├── sketch.png └── tests ├── __init__.py ├── data └── dataloaders │ ├── test_contrastive_dataloader.py │ └── test_data_splitting.py ├── model ├── __init__.py └── test_contrastive_vi.py ├── module ├── __init__.py └── test_contrastive_vi.py └── utils.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/.gitignore -------------------------------------------------------------------------------- /.pre-commit-config.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/.pre-commit-config.yaml -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/README.md -------------------------------------------------------------------------------- /conftest.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/conftest.py -------------------------------------------------------------------------------- /contrastive_vi/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/__init__.py -------------------------------------------------------------------------------- /contrastive_vi/data/__init__.py: -------------------------------------------------------------------------------- 1 | """Data preprocessing modules.""" 2 | -------------------------------------------------------------------------------- /contrastive_vi/data/dataloaders/__init__.py: -------------------------------------------------------------------------------- 1 | """Data loader modules for mini-batching.""" 2 | -------------------------------------------------------------------------------- /contrastive_vi/data/dataloaders/contrastive_dataloader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/data/dataloaders/contrastive_dataloader.py -------------------------------------------------------------------------------- /contrastive_vi/data/dataloaders/data_splitting.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/data/dataloaders/data_splitting.py -------------------------------------------------------------------------------- /contrastive_vi/data/datasets/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/data/datasets/__init__.py -------------------------------------------------------------------------------- /contrastive_vi/data/datasets/haber_2017.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/data/datasets/haber_2017.py -------------------------------------------------------------------------------- /contrastive_vi/data/datasets/mcfarland_2020.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/data/datasets/mcfarland_2020.py -------------------------------------------------------------------------------- /contrastive_vi/data/datasets/norman_2019.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/data/datasets/norman_2019.py -------------------------------------------------------------------------------- /contrastive_vi/data/datasets/papalexi_2021.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/data/datasets/papalexi_2021.py -------------------------------------------------------------------------------- /contrastive_vi/data/datasets/zheng_2017.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/data/datasets/zheng_2017.py -------------------------------------------------------------------------------- /contrastive_vi/data/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/data/utils.py -------------------------------------------------------------------------------- /contrastive_vi/model/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/model/__init__.py -------------------------------------------------------------------------------- /contrastive_vi/model/base/__init__.py: -------------------------------------------------------------------------------- 1 | """Reusable Model classes for inheritance.""" 2 | -------------------------------------------------------------------------------- /contrastive_vi/model/base/training_mixin.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/model/base/training_mixin.py -------------------------------------------------------------------------------- /contrastive_vi/model/contrastive_vi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/model/contrastive_vi.py -------------------------------------------------------------------------------- /contrastive_vi/model/total_contrastive_vi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/model/total_contrastive_vi.py -------------------------------------------------------------------------------- /contrastive_vi/module/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/module/__init__.py -------------------------------------------------------------------------------- /contrastive_vi/module/contrastive_vi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/module/contrastive_vi.py -------------------------------------------------------------------------------- /contrastive_vi/module/total_contrastive_vi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/module/total_contrastive_vi.py -------------------------------------------------------------------------------- /contrastive_vi/module/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/contrastive_vi/module/utils.py -------------------------------------------------------------------------------- /environment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/environment.yml -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/pyproject.toml -------------------------------------------------------------------------------- /setup.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/setup.cfg -------------------------------------------------------------------------------- /sketch.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/sketch.png -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/data/dataloaders/test_contrastive_dataloader.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/tests/data/dataloaders/test_contrastive_dataloader.py -------------------------------------------------------------------------------- /tests/data/dataloaders/test_data_splitting.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/tests/data/dataloaders/test_data_splitting.py -------------------------------------------------------------------------------- /tests/model/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/model/test_contrastive_vi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/tests/model/test_contrastive_vi.py -------------------------------------------------------------------------------- /tests/module/__init__.py: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /tests/module/test_contrastive_vi.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/tests/module/test_contrastive_vi.py -------------------------------------------------------------------------------- /tests/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/suinleelab/contrastiveVI/HEAD/tests/utils.py --------------------------------------------------------------------------------