SURE-tools 2.1.52__tar.gz → 2.1.53__tar.gz

{sure_tools-2.1.52 → sure_tools-2.1.53}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.52
+Version: 2.1.53
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.52 → sure_tools-2.1.53}/SURE/PerturbFlow.py

@@ -317,12 +317,14 @@ class PerturbFlow(nn.Module):
         if self.loss_func=='negbinomial':
             total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
                                      xs.new_ones(self.input_size), constraint=constraints.positive)
+        elif self.loss_func == 'multinomial':
+            total_count = pyro.param('total_count', int(1e8), constraint=constraints.positive_integer)
             
         if self.use_zeroinflate:
             gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
             
         acs_scale = pyro.param("codebook_scale", xs.new_ones(self.latent_dim), constraint=constraints.positive)
-
+        
         I = torch.eye(self.code_size)
         if self.latent_dist=='studentt':
             acs_dof,acs_loc = self.codebook(I)
@@ -369,7 +371,7 @@ class PerturbFlow(nn.Module):
                 else:
                     pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
             elif self.loss_func == 'multinomial':
-                pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
+                pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
             elif self.loss_func == 'bernoulli':
                 if self.use_zeroinflate:
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
@@ -395,6 +397,8 @@ class PerturbFlow(nn.Module):
         if self.loss_func=='negbinomial':
             total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
                                      xs.new_ones(self.input_size), constraint=constraints.positive)
+        elif self.loss_func == 'multinomial':
+            total_count = pyro.param('total_count', int(1e8), constraint=constraints.positive_integer)
             
         if self.use_zeroinflate:
             gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -458,7 +462,7 @@ class PerturbFlow(nn.Module):
                 else:
                     pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
             elif self.loss_func == 'multinomial':
-                pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
+                pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
             elif self.loss_func == 'bernoulli':
                 if self.use_zeroinflate:
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
@@ -484,6 +488,8 @@ class PerturbFlow(nn.Module):
         if self.loss_func=='negbinomial':
             total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
                                      xs.new_ones(self.input_size), constraint=constraints.positive)
+        elif self.loss_func == 'multinomial':
+            total_count = pyro.param('total_count', int(1e8), constraint=constraints.positive_integer)
             
         if self.use_zeroinflate:
             gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -553,7 +559,7 @@ class PerturbFlow(nn.Module):
                 else:
                     pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
             elif self.loss_func == 'multinomial':
-                pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
+                pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
             elif self.loss_func == 'bernoulli':
                 if self.use_zeroinflate:
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
@@ -577,6 +583,8 @@ class PerturbFlow(nn.Module):
         if self.loss_func=='negbinomial':
             total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
                                      xs.new_ones(self.input_size), constraint=constraints.positive)
+        elif self.loss_func == 'multinomial':
+            total_count = pyro.param('total_count', int(1e8), constraint=constraints.positive_integer)
             
         if self.use_zeroinflate:
             gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -656,7 +664,7 @@ class PerturbFlow(nn.Module):
                 else:
                     pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
             elif self.loss_func == 'multinomial':
-                pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
+                pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
             elif self.loss_func == 'bernoulli':
                 if self.use_zeroinflate:
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)

{sure_tools-2.1.52 → sure_tools-2.1.53}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.52
+Version: 2.1.53
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.52 → sure_tools-2.1.53}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.52',
+    version='2.1.53',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",