SURE-tools 3.7.0__tar.gz → 3.7.2__tar.gz

{sure_tools-3.7.0 → sure_tools-3.7.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 3.7.0
+Version: 3.7.2
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-3.7.0 → sure_tools-3.7.2}/SURE/SURE_vae.py

@@ -256,18 +256,32 @@ class SUREVAE(nn.Module):
         )
 
         if np.sum(self.condition_sizes)>0:
-            self.condition_effects = nn.ModuleList()
+            self.decoder_condition_effects = nn.ModuleList()
             for condition_size in self.condition_sizes:
-                self.condition_effects.append(ZeroBiasMLP3(
-                        [condition_size + self.latent_dim] + self.decoder_hidden_layers + [self.latent_dim],
+                self.decoder_condition_effects.append(ZeroBiasMLP3(
+                        [condition_size + self.latent_dim] + self.decoder_hidden_layers + [[self.latent_dim,self.latent_dim]],
                         activation=activate_fct,
-                        output_activation=None,
+                        output_activation=[None,Exp],
                         post_layer_fct=post_layer_fct,
                         post_act_fct=post_act_fct,
                         allow_broadcast=self.allow_broadcast,
                         use_cuda=self.use_cuda,
                     )
                 )
+            
+            '''self.encoder_condition_effects = nn.ModuleList()
+            for condition_size in self.condition_sizes:
+                self.encoder_condition_effects.append(ZeroBiasMLP3(
+                        [condition_size + self.latent_dim] + self.decoder_hidden_layers + [[self.latent_dim,self.latent_dim]],
+                        activation=activate_fct,
+                        output_activation=[None,Exp],
+                        post_layer_fct=post_layer_fct,
+                        post_act_fct=post_act_fct,
+                        allow_broadcast=self.allow_broadcast,
+                        use_cuda=self.use_cuda,
+                    )
+                )'''
+                
         if self.covariate_size>0:
             self.covariate_effect = ZeroBiasMLP2(
                 [self.covariate_size] + self.decoder_hidden_layers + [self.latent_dim],
@@ -409,7 +423,10 @@ class SUREVAE(nn.Module):
                 shift = 0
                 for i, condition_size in enumerate(self.condition_sizes):
                     cs_i = cs[:,shift:(shift+condition_size)]
-                    zcs += self.condition_effects[i]([cs_i,zns])
+                    l,s = self.decoder_condition_effects[i]([cs_i,zns])
+                    zcs_i = pyro.sample(f'zcs_{i}', dist.Normal(l, s).to_event(1))
+                    #zcs += self.condition_effects[i]([cs_i,zns])
+                    zcs += zcs_i
                     shift += condition_size
             else:
                 zcs = torch.zeros_like(zs)
@@ -458,6 +475,13 @@ class SUREVAE(nn.Module):
             zn_loc, zn_scale = self.encoder_zn(xs)
             zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
+            shift = 0
+            for i, condition_size in enumerate(self.condition_sizes):
+                cs_i = cs[:,shift:(shift+condition_size)]
+                l,s = self.decoder_condition_effects[i]([cs_i,zns])
+                zcs_i = pyro.sample(f'zcs_{i}', dist.Normal(l, s).to_event(1))
+                shift += condition_size
+                    
             #alpha = self.encoder_n(zns)
             alpha = self.encoder_alpha(zns)
             ns = pyro.sample('n', dist.OneHotCategorical(logits=alpha))
@@ -602,7 +626,7 @@ class SUREVAE(nn.Module):
                 C_batch = cs[idx].to(self.get_device())
                 
                 z_basal = self._get_cell_embedding(X_batch)
-                dzs = self.condition_effects[i]([C_batch,z_basal])
+                dzs,_ = self.decoder_condition_effects[i]([C_batch,z_basal])
                 
                 A.append(tensor_to_numpy(dzs))
                 pbar.update(1)
@@ -646,7 +670,8 @@ class SUREVAE(nn.Module):
                 shift = 0
                 for i, condition_size in enumerate(self.condition_sizes):
                     C_batch_i = C_batch[:, shift:(shift+condition_size)]
-                    zcs += self.condition_effects[i]([C_batch_i,z_basal])
+                    zcs_i,_ = self.decoder_condition_effects[i]([C_batch_i,z_basal])
+                    zcs += zcs_i
                     shift += condition_size
                     
                 zfs = torch.zeros_like(z_basal)

{sure_tools-3.7.0 → sure_tools-3.7.2}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 3.7.0
+Version: 3.7.2
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-3.7.0 → sure_tools-3.7.2}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='3.7.0',
+    version='3.7.2',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",