SURE-tools 2.1.56__py3-none-any.whl → 2.1.57__py3-none-any.whl

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Files changed (7) hide show
  1. SURE/PerturbFlow.py +19 -11
  2. {sure_tools-2.1.56.dist-info → sure_tools-2.1.57.dist-info}/METADATA +1 -1
  3. {sure_tools-2.1.56.dist-info → sure_tools-2.1.57.dist-info}/RECORD +7 -7
  4. {sure_tools-2.1.56.dist-info → sure_tools-2.1.57.dist-info}/WHEEL +0 -0
  5. {sure_tools-2.1.56.dist-info → sure_tools-2.1.57.dist-info}/entry_points.txt +0 -0
  6. {sure_tools-2.1.56.dist-info → sure_tools-2.1.57.dist-info}/licenses/LICENSE +0 -0
  7. {sure_tools-2.1.56.dist-info → sure_tools-2.1.57.dist-info}/top_level.txt +0 -0
SURE/PerturbFlow.py CHANGED
@@ -380,6 +380,8 @@ class PerturbFlow(nn.Module):
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  concentrate = self.decoder_concentrate(zs)
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  if self.loss_func == 'bernoulli':
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  log_theta = concentrate
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+ elif self.loss_func == 'negbinomial':
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+ log_theta = concentrate
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  else:
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  rate = concentrate.exp()
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  if self.loss_func != 'poisson':
@@ -387,9 +389,9 @@ class PerturbFlow(nn.Module):
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  if self.loss_func == 'negbinomial':
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  if self.use_zeroinflate:
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- pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, probs=theta),gate_logits=gate_logits).to_event(1), obs=xs)
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+ pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
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  else:
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- pyro.sample('x', dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1), obs=xs)
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+ pyro.sample('x', dist.NegativeBinomial(total_count=total_count, logits=log_theta).to_event(1), obs=xs)
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  elif self.loss_func == 'poisson':
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  if self.use_zeroinflate:
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  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
@@ -484,6 +486,8 @@ class PerturbFlow(nn.Module):
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  concentrate = self.decoder_concentrate(zs)
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  if self.loss_func == 'bernoulli':
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  log_theta = concentrate
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+ elif self.loss_func == 'negbinomial':
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+ log_theta = concentrate
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  else:
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  rate = concentrate.exp()
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  if self.loss_func != 'poisson':
@@ -491,9 +495,9 @@ class PerturbFlow(nn.Module):
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  if self.loss_func == 'negbinomial':
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  if self.use_zeroinflate:
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- pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, probs=theta),gate_logits=gate_logits).to_event(1), obs=xs)
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+ pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
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  else:
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- pyro.sample('x', dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1), obs=xs)
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+ pyro.sample('x', dist.NegativeBinomial(total_count=total_count, logits=log_theta).to_event(1), obs=xs)
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  elif self.loss_func == 'poisson':
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  if self.use_zeroinflate:
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  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
@@ -594,6 +598,8 @@ class PerturbFlow(nn.Module):
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  concentrate = self.decoder_concentrate(zs)
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  if self.loss_func == 'bernoulli':
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  log_theta = concentrate
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+ elif self.loss_func == 'negbinomial':
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+ log_theta = concentrate
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  else:
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  rate = concentrate.exp()
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  if self.loss_func != 'poisson':
@@ -601,9 +607,9 @@ class PerturbFlow(nn.Module):
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  if self.loss_func == 'negbinomial':
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  if self.use_zeroinflate:
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- pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, probs=theta),gate_logits=gate_logits).to_event(1), obs=xs)
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+ pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
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  else:
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- pyro.sample('x', dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1), obs=xs)
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+ pyro.sample('x', dist.NegativeBinomial(total_count=total_count, logits=log_theta).to_event(1), obs=xs)
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  elif self.loss_func == 'poisson':
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  if self.use_zeroinflate:
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  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
@@ -714,6 +720,8 @@ class PerturbFlow(nn.Module):
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  concentrate = self.decoder_concentrate(zs)
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  if self.loss_func == 'bernoulli':
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  log_theta = concentrate
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+ elif self.loss_func == 'negbinomial':
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+ log_theta = concentrate
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  else:
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  rate = concentrate.exp()
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  if self.loss_func != 'poisson':
@@ -721,9 +729,9 @@ class PerturbFlow(nn.Module):
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  if self.loss_func == 'negbinomial':
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  if self.use_zeroinflate:
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- pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, probs=theta),gate_logits=gate_logits).to_event(1), obs=xs)
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+ pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
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  else:
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- pyro.sample('x', dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1), obs=xs)
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+ pyro.sample('x', dist.NegativeBinomial(total_count=total_count, logits=log_theta).to_event(1), obs=xs)
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  elif self.loss_func == 'poisson':
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  if self.use_zeroinflate:
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  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
@@ -966,11 +974,11 @@ class PerturbFlow(nn.Module):
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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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+ #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, probs=theta).to_event(1).mean
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+ counts = dist.NegativeBinomial(total_count=total_count, logits=concentrate).to_event(1).mean
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  elif self.loss_func == 'poisson':
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  rate = concentrate.exp()
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  counts = dist.Poisson(rate=rate).to_event(1).mean
{sure_tools-2.1.56.dist-info → sure_tools-2.1.57.dist-info}/METADATA 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: 2.1.56
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+ Version: 2.1.57
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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-2.1.56.dist-info → sure_tools-2.1.57.dist-info}/RECORD RENAMED
@@ -1,4 +1,4 @@
1
- SURE/PerturbFlow.py,sha256=CvnmX1QVo4UK4rkmFQd0RR9YHrNjL1GCHM1aj-BHVqM,59536
1
+ SURE/PerturbFlow.py,sha256=emkyhDc99eTJQNkMdsHCp6VPg6468CRkc8lRHyA4P4o,59977
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  SURE/SURE.py,sha256=ko15a9BhvUqHviogZ0YCdTQjM-2zqkO9OvHZSpnGbg0,47458
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  SURE/__init__.py,sha256=NOJI_K-eCqPgStXXvgl3wIEMp6d8saMTDYLJ7Ga9MqE,293
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  SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
@@ -17,9 +17,9 @@ SURE/utils/__init__.py,sha256=YF5jB-PAHJQ40OlcZ7BCZbsN2q1JKuPT6EppilRXQqM,680
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  SURE/utils/custom_mlp.py,sha256=C0EXLGYsWkUQpEL49AyBFPSzKmasb2hdvtnJfxbF-YU,9282
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  SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
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  SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
20
- sure_tools-2.1.56.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
21
- sure_tools-2.1.56.dist-info/METADATA,sha256=kWBC-87jEjWE-JHxXGcrerFaxT9G5buo8zwZhkDxu9o,2678
22
- sure_tools-2.1.56.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
23
- sure_tools-2.1.56.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
24
- sure_tools-2.1.56.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
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- sure_tools-2.1.56.dist-info/RECORD,,
20
+ sure_tools-2.1.57.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
21
+ sure_tools-2.1.57.dist-info/METADATA,sha256=Y1npoz3fb9597vOLCGFK4__9N85QgzBnX_zUra5E1Fg,2678
22
+ sure_tools-2.1.57.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ sure_tools-2.1.57.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
24
+ sure_tools-2.1.57.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
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+ sure_tools-2.1.57.dist-info/RECORD,,