SURE-tools 2.3.1__tar.gz → 2.3.2__tar.gz

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Files changed (31) hide show
  1. {sure_tools-2.3.1 → sure_tools-2.3.2}/PKG-INFO +1 -1
  2. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/DensityFlow.py +11 -4
  3. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE_tools.egg-info/PKG-INFO +1 -1
  4. {sure_tools-2.3.1 → sure_tools-2.3.2}/setup.py +1 -1
  5. {sure_tools-2.3.1 → sure_tools-2.3.2}/LICENSE +0 -0
  6. {sure_tools-2.3.1 → sure_tools-2.3.2}/README.md +0 -0
  7. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/PerturbE.py +0 -0
  8. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/SURE.py +0 -0
  9. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/__init__.py +0 -0
  10. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/assembly/__init__.py +0 -0
  11. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/assembly/assembly.py +0 -0
  12. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/assembly/atlas.py +0 -0
  13. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/atac/__init__.py +0 -0
  14. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/atac/utils.py +0 -0
  15. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/codebook/__init__.py +0 -0
  16. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/codebook/codebook.py +0 -0
  17. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/flow/__init__.py +0 -0
  18. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/flow/flow_stats.py +0 -0
  19. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/flow/plot_quiver.py +0 -0
  20. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/perturb/__init__.py +0 -0
  21. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/perturb/perturb.py +0 -0
  22. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/utils/__init__.py +0 -0
  23. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/utils/custom_mlp.py +0 -0
  24. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/utils/queue.py +0 -0
  25. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/utils/utils.py +0 -0
  26. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE_tools.egg-info/SOURCES.txt +0 -0
  27. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE_tools.egg-info/dependency_links.txt +0 -0
  28. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE_tools.egg-info/entry_points.txt +0 -0
  29. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE_tools.egg-info/requires.txt +0 -0
  30. {sure_tools-2.3.1 → sure_tools-2.3.2}/SURE_tools.egg-info/top_level.txt +0 -0
  31. {sure_tools-2.3.1 → sure_tools-2.3.2}/setup.cfg +0 -0
{sure_tools-2.3.1 → sure_tools-2.3.2}/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: 2.3.1
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+ Version: 2.3.2
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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-2.3.1 → sure_tools-2.3.2}/SURE/DensityFlow.py RENAMED
@@ -396,7 +396,8 @@ class DensityFlow(nn.Module):
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  else:
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  pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
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  elif self.loss_func == 'multinomial':
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- pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
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+ #pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
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+ pyro.sample('x', dist.Multinomial(total_count=int(1e8), logits=concentrate), obs=xs)
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  elif self.loss_func == 'bernoulli':
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  if self.use_zeroinflate:
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  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
@@ -480,7 +481,8 @@ class DensityFlow(nn.Module):
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  else:
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  pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
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  elif self.loss_func == 'multinomial':
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- pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
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+ #pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
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+ pyro.sample('x', dist.Multinomial(total_count=int(1e8), logits=concentrate), obs=xs)
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  elif self.loss_func == 'bernoulli':
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  if self.use_zeroinflate:
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  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
@@ -576,7 +578,8 @@ class DensityFlow(nn.Module):
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  else:
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  pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
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  elif self.loss_func == 'multinomial':
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- pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
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+ #pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
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+ pyro.sample('x', dist.Multinomial(total_count=int(1e8), logits=concentrate), obs=xs)
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  elif self.loss_func == 'bernoulli':
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  if self.use_zeroinflate:
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  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
@@ -682,7 +685,8 @@ class DensityFlow(nn.Module):
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  else:
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  pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
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  elif self.loss_func == 'multinomial':
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- pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
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+ #pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
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+ pyro.sample('x', dist.Multinomial(total_count=int(1e8), logits=concentrate), obs=xs)
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  elif self.loss_func == 'bernoulli':
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  if self.use_zeroinflate:
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  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
@@ -946,6 +950,9 @@ class DensityFlow(nn.Module):
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  if self.loss_func == 'bernoulli':
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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 == 'multinomial':
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+ theta = dist.Multinomial(total_count=int(1e8), logits=concentrate).mean
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+ counts = theta * library_size
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  else:
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  rate = concentrate.exp()
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  theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
{sure_tools-2.3.1 → sure_tools-2.3.2}/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: 2.3.1
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+ Version: 2.3.2
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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-2.3.1 → sure_tools-2.3.2}/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='2.3.1',
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+ version='2.3.2',
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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-2.3.1 → sure_tools-2.3.2}/LICENSE RENAMED
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{sure_tools-2.3.1 → sure_tools-2.3.2}/README.md RENAMED
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{sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/PerturbE.py RENAMED
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{sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/SURE.py RENAMED
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{sure_tools-2.3.1 → sure_tools-2.3.2}/SURE/__init__.py RENAMED
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{sure_tools-2.3.1 → sure_tools-2.3.2}/setup.cfg RENAMED
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