SURE-tools 2.1.20__tar.gz → 2.1.22__tar.gz

{sure_tools-2.1.20 → sure_tools-2.1.22}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.20
+Version: 2.1.22
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.20 → sure_tools-2.1.22}/SURE/PerturbFlow.py

@@ -196,20 +196,15 @@ class PerturbFlow(nn.Module):
         if self.cell_factor_size>0:
             self.cell_factor_effect = nn.ModuleList()
             for i in np.arange(self.cell_factor_size):
-                #self.cell_factor_effect.append(MLP(
-                #    [self.latent_dim+1] + hidden_sizes + [self.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,
-                #    bias=False,
-                #)
-                #)
                 self.cell_factor_effect.append(ZeroBiasMLP(
-                    self.latent_dim+1, hidden_sizes, self.latent_dim,
-                    )
+                    [self.latent_dim+1] + hidden_sizes + [self.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.decoder_concentrate = MLP(

{sure_tools-2.1.20 → sure_tools-2.1.22}/SURE/SURE.py

@@ -240,7 +240,6 @@ class SURE(nn.Module):
                 post_act_fct=post_act_fct,
                 allow_broadcast=self.allow_broadcast,
                 use_cuda=self.use_cuda,
-                bias=False,
             )
             
         self.decoder_concentrate = MLP(

{sure_tools-2.1.20 → sure_tools-2.1.22}/SURE/utils/custom_mlp.py

@@ -212,24 +212,33 @@ class MLP(nn.Module):
 
 
 
+
 class ZeroBiasMLP(nn.Module):
-    def __init__(self, input_dim, hidden_dims, output_dim):
+    def __init__(
+        self,
+        mlp_sizes,
+        activation=nn.ReLU,
+        output_activation=None,
+        post_layer_fct=lambda layer_ix, total_layers, layer: None,
+        post_act_fct=lambda layer_ix, total_layers, layer: None,
+        allow_broadcast=False,
+        use_cuda=False,
+    ):
+        # init the module object
         super().__init__()
-        layers = []
-        dims = [input_dim] + hidden_dims + [output_dim]
+        self.mlp = MLP(mlp_sizes=mlp_sizes,
+                       activation=activation,
+                       output_activation=output_activation,
+                       post_layer_fct=post_layer_fct,
+                       post_act_fct=post_act_fct,
+                       allow_broadcast=allow_broadcast,
+                       use_cuda=use_cuda,
+                       bias=False)
         
-        # 构建线性层（强制所有偏置为0）
-        for i in range(len(dims)-1):
-            linear = nn.Linear(dims[i], dims[i+1])
-            nn.init.zeros_(linear.bias)  # 初始化偏置为0
-            layers.append(linear)
-            if i < len(dims)-2:
-                layers.append(nn.ReLU())  # 激活函数
-        
-        self.net = nn.Sequential(*layers)
-    
+    # pass through our sequential for the output!
     def forward(self, x):
-        if type(x) == list:
-            x = torch.concat(x, dim=1)
-        return self.net(x)
-
+        y = self.mlp(x)
+        mask = torch.zeros_like(y)
+        mask[x[1]>0,:] = 1
+        return y*mask
+        

{sure_tools-2.1.20 → sure_tools-2.1.22}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.20
+Version: 2.1.22
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.20 → sure_tools-2.1.22}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.20',
+    version='2.1.22',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",