PathwayVI 0.1.0__tar.gz

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Files changed (20) hide show
  1. pathwayvi-0.1.0/PKG-INFO +61 -0
  2. pathwayvi-0.1.0/PathwayVI/PathwayVI.py +1310 -0
  3. pathwayvi-0.1.0/PathwayVI/__init__.py +8 -0
  4. pathwayvi-0.1.0/PathwayVI/dist/__init__.py +1 -0
  5. pathwayvi-0.1.0/PathwayVI/dist/negbinomial.py +415 -0
  6. pathwayvi-0.1.0/PathwayVI/gmt/__init__.py +1 -0
  7. pathwayvi-0.1.0/PathwayVI/gmt/gmt.py +193 -0
  8. pathwayvi-0.1.0/PathwayVI/utils/__init__.py +20 -0
  9. pathwayvi-0.1.0/PathwayVI/utils/custom_mlp.py +409 -0
  10. pathwayvi-0.1.0/PathwayVI/utils/label.py +215 -0
  11. pathwayvi-0.1.0/PathwayVI/utils/queue.py +50 -0
  12. pathwayvi-0.1.0/PathwayVI/utils/utils.py +308 -0
  13. pathwayvi-0.1.0/PathwayVI.egg-info/PKG-INFO +61 -0
  14. pathwayvi-0.1.0/PathwayVI.egg-info/SOURCES.txt +18 -0
  15. pathwayvi-0.1.0/PathwayVI.egg-info/dependency_links.txt +1 -0
  16. pathwayvi-0.1.0/PathwayVI.egg-info/requires.txt +18 -0
  17. pathwayvi-0.1.0/PathwayVI.egg-info/top_level.txt +1 -0
  18. pathwayvi-0.1.0/README.md +21 -0
  19. pathwayvi-0.1.0/setup.cfg +4 -0
  20. pathwayvi-0.1.0/setup.py +25 -0
pathwayvi-0.1.0/PKG-INFO ADDED
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+ Metadata-Version: 2.4
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+ Name: PathwayVI
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+ Version: 0.1.0
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+ Summary: Variational inference for pathway-based perturbation prediction
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+ Home-page: https://github.com/ZengFLab/PathwayVI
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+ Author: Feng Zeng
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+ Author-email: zengfeng@xmu.edu.cn
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+ Classifier: Programming Language :: Python :: 3
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+ Classifier: License :: OSI Approved :: MIT License
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+ Classifier: Operating System :: OS Independent
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+ Requires-Python: >=3.10
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+ Description-Content-Type: text/markdown
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+ Requires-Dist: dill==0.3.8
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+ Requires-Dist: scanpy
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+ Requires-Dist: pytorch-ignite
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+ Requires-Dist: datatable
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+ Requires-Dist: scipy
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+ Requires-Dist: numpy
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+ Requires-Dist: scikit-learn
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+ Requires-Dist: pandas
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+ Requires-Dist: pyro-ppl
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+ Requires-Dist: jax[cuda12]
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+ Requires-Dist: leidenalg
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+ Requires-Dist: python-igraph
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+ Requires-Dist: networkx
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+ Requires-Dist: matplotlib
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+ Requires-Dist: seaborn
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+ Requires-Dist: fa2-modified
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+ Requires-Dist: zuko
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+ Requires-Dist: plotly
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+ Dynamic: author
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+ Dynamic: author-email
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+ Dynamic: classifier
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+ Dynamic: description
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+ Dynamic: description-content-type
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+ Dynamic: home-page
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+ Dynamic: requires-dist
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+ Dynamic: requires-python
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+ Dynamic: summary
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+
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+ # Variational inference for pathway-based perturbation prediction
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+ Learning pathway-informed virtual cellular operations.
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+
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+ ## Installation
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+ 1. Create a virtual environment
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+ ```bash
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+ conda create -n PathwayVI python=3.10 scipy numpy pandas scikit-learn && conda activate PathwayVI
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+ ```
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+
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+ 2. Install [PyTorch](https://pytorch.org/get-started/locally/) following the official instruction.
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+ ```bash
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+ pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu126
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+ ```
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+
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+ 3. Install PathwayVI
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+ ```bash
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+ pip3 install PathwayVI
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+ ```
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+
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+
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+