SURE-tools 2.1.77__tar.gz → 2.1.78__tar.gz

{sure_tools-2.1.77 → sure_tools-2.1.78}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.77
+Version: 2.1.78
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.77 → sure_tools-2.1.78}/SURE/PerturbFlow.py

@@ -881,25 +881,11 @@ class PerturbFlow(nn.Module):
         if self.loss_func == 'bernoulli':
             #counts = self.sigmoid(concentrate)
             counts = dist.Bernoulli(logits=concentrate).to_event(1).mean
-        elif self.loss_func == 'negbinomial':
-            rate = concentrate.exp()
-            theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
-            
-            total_count = self.total_count
-            #total_count = pyro.param("inverse_dispersion")
-            #store = pyro.get_param_store()
-            #total_count = store['inverse_dispersion']
-            counts = dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1).mean
-        elif self.loss_func == 'poisson':
+        else:
             rate = concentrate.exp()
             theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
             counts = theta * library_size
             #counts = dist.Poisson(rate=rate).to_event(1).mean
-        elif self.loss_func == 'multinomial':
-            rate = concentrate.exp()
-            theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
-            #counts = dist.Multinomial(total_count=int(1e8), probs=theta).mean
-            counts = theta * library_size
         return counts
     
     def _count_sample(self,concentrate):
@@ -911,22 +897,17 @@ class PerturbFlow(nn.Module):
             counts = dist.Poisson(rate=counts).to_event(1).sample()
         return counts
     
-    def get_counts(self, zs, library_sizes = None,
+    def get_counts(self, zs, library_sizes,
                         batch_size: int = 1024, 
                         use_sampler: bool = False):
 
         zs = convert_to_tensor(zs, device=self.get_device())
         
-        if self.loss_func in ['multinomial','poisson']:
-            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
+        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())
             
         dataset = CustomDataset2(zs,ls)
         dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=False)

{sure_tools-2.1.77 → sure_tools-2.1.78}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.77
+Version: 2.1.78
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.77 → sure_tools-2.1.78}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.77',
+    version='2.1.78',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",