SURE-tools 2.1.69__tar.gz → 2.1.70__tar.gz

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  1. {sure_tools-2.1.69 → sure_tools-2.1.70}/PKG-INFO +1 -1
  2. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/PerturbFlow.py +6 -6
  3. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE_tools.egg-info/PKG-INFO +1 -1
  4. {sure_tools-2.1.69 → sure_tools-2.1.70}/setup.py +1 -1
  5. {sure_tools-2.1.69 → sure_tools-2.1.70}/LICENSE +0 -0
  6. {sure_tools-2.1.69 → sure_tools-2.1.70}/README.md +0 -0
  7. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/SURE.py +0 -0
  8. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/__init__.py +0 -0
  9. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/assembly/__init__.py +0 -0
  10. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/assembly/assembly.py +0 -0
  11. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/assembly/atlas.py +0 -0
  12. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/atac/__init__.py +0 -0
  13. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/atac/utils.py +0 -0
  14. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/codebook/__init__.py +0 -0
  15. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/codebook/codebook.py +0 -0
  16. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/flow/__init__.py +0 -0
  17. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/flow/flow_stats.py +0 -0
  18. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/flow/plot_quiver.py +0 -0
  19. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/perturb/__init__.py +0 -0
  20. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/perturb/perturb.py +0 -0
  21. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/utils/__init__.py +0 -0
  22. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/utils/custom_mlp.py +0 -0
  23. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/utils/queue.py +0 -0
  24. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/utils/utils.py +0 -0
  25. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE_tools.egg-info/SOURCES.txt +0 -0
  26. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE_tools.egg-info/dependency_links.txt +0 -0
  27. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE_tools.egg-info/entry_points.txt +0 -0
  28. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE_tools.egg-info/requires.txt +0 -0
  29. {sure_tools-2.1.69 → sure_tools-2.1.70}/SURE_tools.egg-info/top_level.txt +0 -0
  30. {sure_tools-2.1.69 → sure_tools-2.1.70}/setup.cfg +0 -0
{sure_tools-2.1.69 → sure_tools-2.1.70}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: SURE-tools
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- Version: 2.1.69
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+ Version: 2.1.70
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  Summary: Succinct Representation of Single Cells
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  Home-page: https://github.com/ZengFLab/SURE
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  Author: Feng Zeng
{sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/PerturbFlow.py RENAMED
@@ -61,8 +61,8 @@ class PerturbFlow(nn.Module):
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  cell_factor_size: int = 0,
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  supervised_mode: bool = False,
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  z_dim: int = 10,
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- z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'normal',
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- loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'multinomial',
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+ z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'gumbel',
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+ loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'poisson',
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  inverse_dispersion: float = 10.0,
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  use_zeroinflate: bool = False,
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  hidden_layers: list = [300],
@@ -877,12 +877,12 @@ class PerturbFlow(nn.Module):
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  #counts = self.sigmoid(concentrate)
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  counts = dist.Bernoulli(logits=concentrate).to_event(1).mean
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  elif self.loss_func == 'negbinomial':
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- #counts = concentrate.exp()
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- #rate = concentrate.exp()
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- #theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
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+ counts = concentrate.exp()
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+ rate = concentrate.exp()
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+ theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
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  total_count = pyro.param("inverse_dispersion")
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- counts = dist.NegativeBinomial(total_count=total_count, logits=concentrate).to_event(1).mean
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+ counts = dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1).mean
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  elif self.loss_func == 'poisson':
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  rate = concentrate.exp()
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  theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
{sure_tools-2.1.69 → sure_tools-2.1.70}/SURE_tools.egg-info/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: SURE-tools
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- Version: 2.1.69
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+ Version: 2.1.70
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  Summary: Succinct Representation of Single Cells
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  Home-page: https://github.com/ZengFLab/SURE
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  Author: Feng Zeng
{sure_tools-2.1.69 → sure_tools-2.1.70}/setup.py RENAMED
@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
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  setup(
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  name='SURE-tools',
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- version='2.1.69',
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+ version='2.1.70',
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  description='Succinct Representation of Single Cells',
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  long_description=long_description,
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  long_description_content_type="text/markdown",
{sure_tools-2.1.69 → sure_tools-2.1.70}/LICENSE RENAMED
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{sure_tools-2.1.69 → sure_tools-2.1.70}/README.md RENAMED
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{sure_tools-2.1.69 → sure_tools-2.1.70}/SURE/SURE.py RENAMED
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{sure_tools-2.1.69 → sure_tools-2.1.70}/setup.cfg RENAMED
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