SURE-tools 2.1.59__tar.gz → 2.1.64__tar.gz

{sure_tools-2.1.59 → sure_tools-2.1.64}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.59
+Version: 2.1.64
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.59 → sure_tools-2.1.64}/SURE/PerturbFlow.py

@@ -351,7 +351,7 @@ class PerturbFlow(nn.Module):
 
             zs = zns
             concentrate = self.decoder_concentrate(zs)
-            if self.loss_func in ['bernoulli','negbinomial']:
+            if self.loss_func in ['bernoulli']:
                 log_theta = concentrate
             else:
                 rate = concentrate.exp()
@@ -361,9 +361,9 @@ class PerturbFlow(nn.Module):
 
             if self.loss_func == 'negbinomial':
                 if self.use_zeroinflate:
-                    pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
+                    pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, probs=theta),gate_logits=gate_logits).to_event(1), obs=xs)
                 else:
-                    pyro.sample('x', dist.NegativeBinomial(total_count=total_count, logits=log_theta).to_event(1), obs=xs)
+                    pyro.sample('x', dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1), obs=xs)
             elif self.loss_func == 'poisson':
                 if self.use_zeroinflate:
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
@@ -435,7 +435,7 @@ class PerturbFlow(nn.Module):
                 zs = zns
 
             concentrate = self.decoder_concentrate(zs)
-            if self.loss_func in ['bernoulli','negbinomial']:
+            if self.loss_func in ['bernoulli']:
                 log_theta = concentrate
             else:
                 rate = concentrate.exp()
@@ -445,9 +445,9 @@ class PerturbFlow(nn.Module):
 
             if self.loss_func == 'negbinomial':
                 if self.use_zeroinflate:
-                    pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
+                    pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, probs=theta),gate_logits=gate_logits).to_event(1), obs=xs)
                 else:
-                    pyro.sample('x', dist.NegativeBinomial(total_count=total_count, logits=log_theta).to_event(1), obs=xs)
+                    pyro.sample('x', dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1), obs=xs)
             elif self.loss_func == 'poisson':
                 if self.use_zeroinflate:
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
@@ -531,7 +531,7 @@ class PerturbFlow(nn.Module):
             zs = zns
 
             concentrate = self.decoder_concentrate(zs)
-            if self.loss_func in ['bernoulli','negbinomial']:
+            if self.loss_func in ['bernoulli']:
                 log_theta = concentrate
             else:
                 rate = concentrate.exp()
@@ -541,9 +541,9 @@ class PerturbFlow(nn.Module):
 
             if self.loss_func == 'negbinomial':
                 if self.use_zeroinflate:
-                    pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
+                    pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, probs=theta),gate_logits=gate_logits).to_event(1), obs=xs)
                 else:
-                    pyro.sample('x', dist.NegativeBinomial(total_count=total_count, logits=log_theta).to_event(1), obs=xs)
+                    pyro.sample('x', dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1), obs=xs)
             elif self.loss_func == 'poisson':
                 if self.use_zeroinflate:
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
@@ -637,7 +637,7 @@ class PerturbFlow(nn.Module):
                 zs = zns
 
             concentrate = self.decoder_concentrate(zs)
-            if self.loss_func in ['bernoulli','negbinomial']:
+            if self.loss_func in ['bernoulli']:
                 log_theta = concentrate
             else:
                 rate = concentrate.exp()
@@ -647,9 +647,9 @@ class PerturbFlow(nn.Module):
 
             if self.loss_func == 'negbinomial':
                 if self.use_zeroinflate:
-                    pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
+                    pyro.sample('x', dist.ZeroInflatedDistribution(dist.NegativeBinomial(total_count=total_count, probs=theta),gate_logits=gate_logits).to_event(1), obs=xs)
                 else:
-                    pyro.sample('x', dist.NegativeBinomial(total_count=total_count, logits=log_theta).to_event(1), obs=xs)
+                    pyro.sample('x', dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1), obs=xs)
             elif self.loss_func == 'poisson':
                 if self.use_zeroinflate:
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
@@ -909,16 +909,17 @@ class PerturbFlow(nn.Module):
                         use_sampler: bool = False):
 
         zs = convert_to_tensor(zs, device=self.get_device())
-        ls = zs 
         
         if self.loss_func in ['multinomial','poisson']:
-            assert library_sizes!=None, 'Library sizes are required for multinomial!'
+            assert library_sizes is not None, 'Library sizes are required for multinomial!'
             
             if type(library_sizes) == list:
                 library_sizes = np.array(library_sizes).view(-1,1)
             elif len(library_sizes.shape)==1:
                 library_sizes = library_sizes.view(-1,1)
             ls = convert_to_tensor(library_sizes, device=self.get_device)
+        else:
+            ls = zs
             
         dataset = CustomDataset2(zs,ls)
         dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=False)

{sure_tools-2.1.59 → sure_tools-2.1.64}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.59
+Version: 2.1.64
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.59 → sure_tools-2.1.64}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.59',
+    version='2.1.64',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",