SURE-tools 2.1.54__tar.gz → 2.1.55__tar.gz

{sure_tools-2.1.54 → sure_tools-2.1.55}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.54
+Version: 2.1.55
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.54 → sure_tools-2.1.55}/SURE/PerturbFlow.py

@@ -960,7 +960,7 @@ class PerturbFlow(nn.Module):
         R = np.concatenate(R)
         return R
     
-    def _count(self,concentrate):
+    def _count(self,concentrate, library_size=None):
         if self.loss_func == 'bernoulli':
             #counts = self.sigmoid(concentrate)
             counts = dist.Bernoulli(logits=concentrate).to_event(1).mean
@@ -976,6 +976,11 @@ class PerturbFlow(nn.Module):
             counts = dist.Poisson(rate=rate).to_event(1).mean
         elif self.loss_func == 'gamma-poisson':
             counts = dist.Poisson(rate=concentrate).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 = counts * library_size
         return counts
     
     def _count_sample(self,concentrate):
@@ -987,22 +992,35 @@ class PerturbFlow(nn.Module):
             counts = dist.Poisson(rate=counts).to_event(1).sample()
         return counts
     
-    def get_counts(self, zs, 
+    def get_counts(self, zs, library_sizes = None,
                         batch_size: int = 1024, 
                         use_sampler: bool = False):
 
         zs = convert_to_tensor(zs, device=self.get_device())
-        dataset = CustomDataset(zs)
+        ls = zs 
+        
+        if self.loss_func == 'multinomial':
+            assert library_sizes!=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)
+            
+        dataset = CustomDataset2(zs,ls)
         dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=False)
         
         E = []
         with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
-            for Z_batch, _ in dataloader:
+            for Z_batch, L_batch, _ in dataloader:
+                if self.loss_func != 'multinomial':
+                    L_batch = None
                 concentrate = self._get_expression_response(Z_batch)
                 if use_sampler:
                     counts = self._count_sample(concentrate)
                 else:
-                    counts = self._count(concentrate)
+                    counts = self._count(concentrate, L_batch)
                 E.append(tensor_to_numpy(counts))
                 pbar.update(1)
         

{sure_tools-2.1.54 → sure_tools-2.1.55}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.54
+Version: 2.1.55
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.54 → sure_tools-2.1.55}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.54',
+    version='2.1.55',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",