SURE-tools 2.1.28__tar.gz → 2.1.29__tar.gz

{sure_tools-2.1.28 → sure_tools-2.1.29}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.28
+Version: 2.1.29
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.28 → sure_tools-2.1.29}/SURE/PerturbFlow.py

@@ -73,6 +73,7 @@ class PerturbFlow(nn.Module):
                  config_enum: str = 'parallel',
                  use_cuda: bool = False,
                  seed: int = 42,
+                 bias: bool = False,
                  dtype = torch.float32, # type: ignore
                  ):
         super().__init__()
@@ -96,6 +97,7 @@ class PerturbFlow(nn.Module):
         self.post_layer_fct = post_layer_fct
         self.post_act_fct = post_act_fct
         self.hidden_layer_activation = hidden_layer_activation
+        self.bias = bias
         
         self.codebook_weights = None
 
@@ -196,16 +198,29 @@ 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(ZeroBiasMLP(
-                    [self.latent_dim+1] + self.decoder_hidden_layers + [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,
-                )
-                )
+                if self.bias:
+                    self.cell_factor_effect.append(MLP(
+                        [self.latent_dim+1] + self.decoder_hidden_layers + [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,
+                        )
+                    )
+                else:
+                    self.cell_factor_effect.append(MLP(
+                        [self.latent_dim+1] + self.decoder_hidden_layers + [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(
                 [self.latent_dim] + self.decoder_hidden_layers + [self.input_size],

{sure_tools-2.1.28 → sure_tools-2.1.29}/SURE/utils/custom_mlp.py

@@ -233,7 +233,7 @@ class ZeroBiasMLP(nn.Module):
                        post_act_fct=post_act_fct,
                        allow_broadcast=allow_broadcast,
                        use_cuda=use_cuda,
-                       bias=False)
+                       bias=True)
         
     # pass through our sequential for the output!
     def forward(self, x):

{sure_tools-2.1.28 → sure_tools-2.1.29}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.28
+Version: 2.1.29
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.28 → sure_tools-2.1.29}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.28',
+    version='2.1.29',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",