SURE-tools 2.1.82__tar.gz → 2.1.83__tar.gz

{sure_tools-2.1.82 → sure_tools-2.1.83}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.82
+Version: 2.1.83
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.82 → sure_tools-2.1.83}/SURE/PerturbFlow.py

@@ -204,7 +204,7 @@ class PerturbFlow(nn.Module):
             for i in np.arange(self.cell_factor_size):
                 if self.use_bias[i]:
                     self.cell_factor_effect.append(MLP(
-                        [self.latent_dim+1] + self.decoder_hidden_layers + [self.latent_dim],
+                        [self.code_size+1] + self.decoder_hidden_layers + [self.latent_dim],
                         activation=activate_fct,
                         output_activation=None,
                         post_layer_fct=post_layer_fct,
@@ -215,7 +215,7 @@ class PerturbFlow(nn.Module):
                     )
                 else:
                     self.cell_factor_effect.append(ZeroBiasMLP(
-                        [self.latent_dim+1] + self.decoder_hidden_layers + [self.latent_dim],
+                        [self.code_size+1] + self.decoder_hidden_layers + [self.latent_dim],
                         activation=activate_fct,
                         output_activation=None,
                         post_layer_fct=post_layer_fct,
@@ -429,7 +429,7 @@ class PerturbFlow(nn.Module):
                 zns = pyro.sample('zn', dist.Gumbel(zn_loc, zn_scale).to_event(1))
 
             if self.cell_factor_size>0:
-                zus = self._total_effects(zn_loc, us)
+                zus = self._total_effects(ns, us)
                 zs = zns+zus
             else:
                 zs = zns
@@ -631,7 +631,7 @@ class PerturbFlow(nn.Module):
                 #        zus = self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
                 #    else:
                 #        zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
-                zus = self._total_effects(zn_loc, us)
+                zus = self._total_effects(ns, us)
                 zs = zns+zus
             else:
                 zs = zns
@@ -681,6 +681,9 @@ class PerturbFlow(nn.Module):
                 zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
         return zus
                         
+    def _get_codebook_identity(self):
+        return torch.eye(self.code_size, **self.options)
+    
     def _get_codebook(self):
         I = torch.eye(self.code_size, **self.options)
         if self.latent_dist=='studentt':
@@ -839,7 +842,8 @@ class PerturbFlow(nn.Module):
     
     def _cell_response(self, xs, factor_idx, perturb):
         #zns,_ = self.encoder_zn(xs)    
-        zns,_ = self._get_basal_embedding(xs)   
+        #zns,_ = self._get_basal_embedding(xs)   
+        zns = self._soft_assignments(xs)
         if perturb.ndim==2:
             ms = self.cell_factor_effect[factor_idx]([zns, perturb])
         else:
@@ -873,7 +877,8 @@ class PerturbFlow(nn.Module):
         return Z
     
     def get_metacell_response(self, factor_idx, perturb):
-        zs = self._get_codebook()
+        #zs = self._get_codebook()
+        zs = self._get_codebook_identity()
         ps = convert_to_tensor(perturb, device=self.get_device())         
         ms = self.cell_factor_effect[factor_idx]([zs,ps])
         return tensor_to_numpy(ms)

{sure_tools-2.1.82 → sure_tools-2.1.83}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.82
+Version: 2.1.83
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.82 → sure_tools-2.1.83}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.82',
+    version='2.1.83',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",