updated the vae, betatcvae, wgangp, michigan, ppca, gmm implementations

welch-lab · Apr 4, 2021 · bc8524d · bc8524d
1 parent 5437ac5
commit bc8524d
Show file tree

Hide file tree

Showing 34 changed files with 5,128 additions and 5 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git a/FunctionProgramExamples/.DS_Store b/FunctionProgramExamples/.DS_Store
diff --git a/Adam_prediction.py → FunctionProgramExamples/Adam_prediction.py b/Adam_prediction.py → FunctionProgramExamples/Adam_prediction.py
diff --git a/examples/MichiGAN_mean.py → ...ProgramExamples/examples/MichiGAN_mean.py b/examples/MichiGAN_mean.py → ...ProgramExamples/examples/MichiGAN_mean.py
diff --git a/examples/MichiGAN_sample.py → ...ogramExamples/examples/MichiGAN_sample.py b/examples/MichiGAN_sample.py → ...ogramExamples/examples/MichiGAN_sample.py
diff --git a/examples/beta_tcvae.py → ...ionProgramExamples/examples/beta_tcvae.py b/examples/beta_tcvae.py → ...ionProgramExamples/examples/beta_tcvae.py
diff --git a/examples/example_InfoWGAN_GP.ipynb → ...amples/examples/example_InfoWGAN_GP.ipynb b/examples/example_InfoWGAN_GP.ipynb → ...amples/examples/example_InfoWGAN_GP.ipynb
diff --git a/examples/example_MichiGAN_mean.ipynb → ...ples/examples/example_MichiGAN_mean.ipynb b/examples/example_MichiGAN_mean.ipynb → ...ples/examples/example_MichiGAN_mean.ipynb
diff --git a/examples/example_MichiGAN_sample.ipynb → ...es/examples/example_MichiGAN_sample.ipynb b/examples/example_MichiGAN_sample.ipynb → ...es/examples/example_MichiGAN_sample.ipynb
diff --git a/examples/example_VAE.ipynb → ...rogramExamples/examples/example_VAE.ipynb b/examples/example_VAE.ipynb → ...rogramExamples/examples/example_VAE.ipynb
diff --git a/examples/example_WGAN_GP.ipynb → ...amExamples/examples/example_WGAN_GP.ipynb b/examples/example_WGAN_GP.ipynb → ...amExamples/examples/example_WGAN_GP.ipynb
diff --git a/examples/example_beta_TCVAE.ipynb → ...xamples/examples/example_beta_TCVAE.ipynb b/examples/example_beta_TCVAE.ipynb → ...xamples/examples/example_beta_TCVAE.ipynb
diff --git a/examples/infowgangp.py → ...ionProgramExamples/examples/infowgangp.py b/examples/infowgangp.py → ...ionProgramExamples/examples/infowgangp.py
diff --git a/examples/vae.py → FunctionProgramExamples/examples/vae.py b/examples/vae.py → FunctionProgramExamples/examples/vae.py
diff --git a/examples/wgangp.py → FunctionProgramExamples/examples/wgangp.py b/examples/wgangp.py → FunctionProgramExamples/examples/wgangp.py
diff --git a/lib.py → FunctionProgramExamples/lib.py b/lib.py → FunctionProgramExamples/lib.py
diff --git a/nets.py → FunctionProgramExamples/nets.py b/nets.py → FunctionProgramExamples/nets.py
diff --git a/README.md b/README.md
@@ -1,14 +1,14 @@
 # MichiGAN: Learning disentangled representations of single-cell data for high-quality generation
 
-## Predicting unobserved cell states from disentangled representations of single-cell data using generative adversarial networks
+## Sampling from disentangled representations of single-cell data using generative adversarial networks
 
-The current folder contains files for implementing **VAE/beta-TCVAE, WGAN-GP, InfoWGAN-GP, and MichiGAN** on single-cell RNA-seq data. See our preprint for details:  
-[Predicting unobserved cell states from disentangled representations of single-cell data using generative adversarial networks](https://www.biorxiv.org/content/10.1101/2021.01.15.426872v1) (Yu and Welch, 2020+).
+The current folder contains files for implementing **PCA, GMM, VAE/beta-TCVAE, WGAN-GP, InfoWGAN-GP, ssInfoWGAN-GP, CWGAN-GP and MichiGAN** on single-cell RNA-seq data. See our preprint for details:  
+[Sampling from disentangled representations of single-cell data using generative adversarial networks](https://www.biorxiv.org/content/10.1101/2021.01.15.426872v1) (Yu and Welch, 2021+). We have a [presentation video](https://youtu.be/5tsccPMPzLQ) for [Learning Meaningful Representations of Life Workshop](https://www.lmrl.org/) at NeurIPS 2020, where we named our framework as `DRGAN` and changed the name to `MichiGAN` afterwards.   
 
 ## List of Files:
 
 1) `/data` is the folder containing the real scRNA-seq dataset of Tabula Muris heart data. Users can download the SCANPY-processed data on https://www.dropbox.com/sh/xseb0u6p01te3vr/AACuskVfswUFn5MroEFrqI-Xa?dl=0. 
-2) `/examples` is the folder for the experiments of\
+2) `/FunctionProgramExamples/examples` is the folder for the experiments of\
   (1) `vae.py`: VAE; \
   (2) `beta_tcvae.py`: beta-TCVAE;\
   (3) `wgangp.py`: WGAN-GP;\

diff --git a/data/README.md b/data/README.md
@@ -1,4 +1,4 @@
-The folder has the Tabula Muris heart data that are currently stored on dropbox and can be accessed via https://www.dropbox.com/sh/xseb0u6p01te3vr/AACuskVfswUFn5MroEFrqI-Xa?dl=0
+The folder has the Tabula Muris heart data that are currently stored on dropbox and can be accessed [here](https://www.dropbox.com/sh/xseb0u6p01te3vr/AACuskVfswUFn5MroEFrqI-Xa?dl=0). 
 
 List of Files:
 1) `TabulaMurisHeart_Processed.npy` is the SCANPY-processed Tabula Muris heart data (4221 cells/rows by 4062 genes/columns)