SURE-tools 2.1.20__tar.gz → 2.1.21__tar.gz

{sure_tools-2.1.20 → sure_tools-2.1.21}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.20
+Version: 2.1.21
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.20 → sure_tools-2.1.21}/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.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,
+                )
                 )
             
         self.decoder_concentrate = MLP(

{sure_tools-2.1.20 → sure_tools-2.1.21}/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-2.1.21}/SURE/utils/custom_mlp.py

@@ -212,24 +212,3 @@ class MLP(nn.Module):
 
 
 
-class ZeroBiasMLP(nn.Module):
-    def __init__(self, input_dim, hidden_dims, output_dim):
-        super().__init__()
-        layers = []
-        dims = [input_dim] + hidden_dims + [output_dim]
-        
-        # 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)
-    
-    def forward(self, x):
-        if type(x) == list:
-            x = torch.concat(x, dim=1)
-        return self.net(x)
-

{sure_tools-2.1.20 → sure_tools-2.1.21}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.20
+Version: 2.1.21
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.20 → sure_tools-2.1.21}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.20',
+    version='2.1.21',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",