SURE-tools 2.1.43__tar.gz → 2.1.44__tar.gz

{sure_tools-2.1.43 → sure_tools-2.1.44}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.43
+Version: 2.1.44
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.43 → sure_tools-2.1.44}/SURE/PerturbFlow.py

@@ -189,10 +189,29 @@ class PerturbFlow(nn.Module):
                 use_cuda=self.use_cuda,
             )
 
-        self.encoder_zn = MLP(
-            [self.input_size] + hidden_sizes + [[latent_dim, latent_dim]],
+        #self.encoder_zn = MLP(
+        #    [self.input_size] + hidden_sizes + [[latent_dim, 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,
+        #)
+        
+        self.encoder_zn_loc = MLP(
+            [self.input_size] + hidden_sizes + [self.input_size * latent_dim],
+            activation=activate_fct,
+            output_activation=None,
+            post_layer_fct=post_layer_fct,
+            post_act_fct=post_act_fct,
+            allow_broadcast=self.allow_broadcast,
+            use_cuda=self.use_cuda,
+        )
+        self.encoder_zn_scale = MLP(
+            [self.input_size] + hidden_sizes + [latent_dim],
             activation=activate_fct,
-            output_activation=[None, Exp],
+            output_activation=Exp,
             post_layer_fct=post_layer_fct,
             post_act_fct=post_act_fct,
             allow_broadcast=self.allow_broadcast,
@@ -378,7 +397,11 @@ class PerturbFlow(nn.Module):
 
     def guide1(self, xs):
         with pyro.plate('data'):
-            zn_loc, zn_scale = self.encoder_zn(xs)
+            batch_size = xs.shape[0]
+            #zn_loc, zn_scale = self.encoder_zn(xs)
+            zn_loc, zn_scale = self.encoder_zn_loc(xs), self.encoder_zn_scale(xs)
+            zn_loc_3d = zn_loc.view(batch_size, self.input_size, self.latent_dim)
+            zn_loc = zn_loc_3d.sum(dim=1)
             zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
             alpha = self.encoder_n(zns)
@@ -466,7 +489,11 @@ class PerturbFlow(nn.Module):
 
     def guide2(self, xs, us=None):
         with pyro.plate('data'):
-            zn_loc, zn_scale = self.encoder_zn(xs)
+            batch_size = xs.shape[0]
+            #zn_loc, zn_scale = self.encoder_zn(xs)
+            zn_loc, zn_scale = self.encoder_zn_loc(xs), self.encoder_zn_scale(xs)
+            zn_loc_3d = zn_loc.view(batch_size, self.input_size, self.latent_dim)
+            zn_loc = zn_loc_3d.sum(dim=1)
             zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
             alpha = self.encoder_n(zns)
@@ -561,7 +588,11 @@ class PerturbFlow(nn.Module):
     def guide3(self, xs, ys, embeds=None):
         with pyro.plate('data'):
             if embeds is None:
-                zn_loc, zn_scale = self.encoder_zn(xs)
+                batch_size = xs.shape[0]
+                #zn_loc, zn_scale = self.encoder_zn(xs)
+                zn_loc, zn_scale = self.encoder_zn_loc(xs), self.encoder_zn_scale(xs)
+                zn_loc_3d = zn_loc.view(batch_size, self.input_size, self.latent_dim)
+                zn_loc = zn_loc_3d.sum(dim=1)
                 zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
     def model4(self, xs, us, ys, embeds=None):
@@ -663,7 +694,11 @@ class PerturbFlow(nn.Module):
     def guide4(self, xs, us, ys, embeds=None):
         with pyro.plate('data'):
             if embeds is None:
-                zn_loc, zn_scale = self.encoder_zn(xs)
+                batch_size = xs.shape[0]
+                #zn_loc, zn_scale = self.encoder_zn(xs)
+                zn_loc, zn_scale = self.encoder_zn_loc(xs), self.encoder_zn_scale(xs)
+                zn_loc_3d = zn_loc.view(batch_size, self.input_size, self.latent_dim)
+                zn_loc = zn_loc_3d.sum(dim=1)
                 zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
     def _total_effects(self, zns, us):
@@ -692,7 +727,11 @@ class PerturbFlow(nn.Module):
         return cb
 
     def _get_basal_embedding(self, xs):           
-        zns, _ = self.encoder_zn(xs)
+        #zns, _ = self.encoder_zn(xs)
+        batch_size = xs.shape[0]
+        zns = self.encoder_zn_loc(xs)
+        zns_3d = zns.view(batch_size, self.input_size, self.latent_dim)
+        zns = zns_3d.sum(dim=1)
         return zns 
     
     def get_basal_embedding(self, 
@@ -731,7 +770,8 @@ class PerturbFlow(nn.Module):
         if self.supervised_mode:
             alpha = self.encoder_n(xs)
         else:
-            zns,_ = self.encoder_zn(xs)
+            #zns,_ = self.encoder_zn(xs)
+            zns = self._get_basal_embedding(xs)
             alpha = self.encoder_n(zns)
         return alpha
     
@@ -801,7 +841,8 @@ class PerturbFlow(nn.Module):
         return A
     
     def _cell_response(self, xs, factor_idx, perturb):
-        zns,_ = self.encoder_zn(xs)       
+        #zns,_ = self.encoder_zn(xs)    
+        zns = self._get_basal_embedding(xs)   
         if perturb.ndim==2:
             ms = self.cell_factor_effect[factor_idx]([zns, perturb])
         else:

{sure_tools-2.1.43 → sure_tools-2.1.44}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.43
+Version: 2.1.44
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.43 → sure_tools-2.1.44}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.43',
+    version='2.1.44',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",