├── .DS_Store ├── .gitignore ├── DSPIN_matlab ├── learn_hvec_adam.m ├── learn_jmat_adam.m ├── para_mean.m ├── para_moments.m ├── redblue.m ├── samp_mean.m ├── samp_moments.m ├── summarize_hvec.m ├── train_hvector.m ├── train_hvector_local.m └── train_network.m ├── DSPIN_matlab_beta ├── adam_optimizer.m ├── compute_relative_response.m ├── learn_jmat_adam.asv ├── learn_jmat_adam.m ├── learn_jmat_adam.m~ ├── matlab_metadata.mat ├── mean_field_grad.asv ├── mean_field_grad.m ├── mle_grad.m ├── para_moments.m ├── pseudo_grad.m ├── redblue.m └── train_network.m ├── LICENSE ├── README.md ├── README_PyPI.md ├── __pycache__ ├── __init__.cpython-310.pyc ├── __init__.cpython-37.pyc ├── compute.cpython-310.pyc ├── compute.cpython-37.pyc ├── dspin_abstract.cpython-310.pyc ├── plot.cpython-310.pyc └── plotting.cpython-37.pyc ├── data ├── HSC_simulation │ ├── hsc_simulation_with_perturbations.h5ad │ └── refNetwork.csv └── thomsonlab_signaling │ └── network.mat ├── deploy.sh ├── dist ├── dspin-1.5.0-py3-none-any.whl └── dspin-1.5.0.tar.gz ├── dspin.egg-info ├── PKG-INFO ├── SOURCES.txt ├── dependency_links.txt ├── requires.txt └── top_level.txt ├── dspin ├── __init__.py ├── __pycache__ │ ├── __init__.cpython-37.pyc │ ├── __init__.cpython-39.pyc │ ├── annotate.cpython-37.pyc │ ├── annotate.cpython-39.pyc │ ├── compute.cpython-37.pyc │ ├── compute.cpython-39.pyc │ ├── dspin.cpython-37.pyc │ ├── dspin.cpython-39.pyc │ ├── dspin_abstract.cpython-39.pyc │ ├── plot.cpython-37.pyc │ └── plot.cpython-39.pyc ├── annotate.py ├── compute.py ├── dspin.py └── plot.py ├── figure └── readme │ ├── Figure2_immune_dictionary.png │ ├── Figure3_program_network.png │ └── Overview_20250523.png ├── requirements.txt ├── setup.py └── todo.md /.DS_Store: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/JialongJiang/DSPIN/HEAD/.DS_Store -------------------------------------------------------------------------------- /.gitignore: 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