SURE-tools 2.1.31__tar.gz → 2.1.33__tar.gz

{sure_tools-2.1.31 → sure_tools-2.1.33}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.31
+Version: 2.1.33
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.31 → sure_tools-2.1.33}/SURE/PerturbFlow.py

@@ -207,7 +207,6 @@ class PerturbFlow(nn.Module):
                         post_act_fct=post_act_fct,
                         allow_broadcast=self.allow_broadcast,
                         use_cuda=self.use_cuda,
-                        bias=True,
                         )
                     )
                 else:

{sure_tools-2.1.31 → sure_tools-2.1.33}/SURE/SURE.py

@@ -111,6 +111,7 @@ class SURE(nn.Module):
                  config_enum: str = 'parallel',
                  use_cuda: bool = False,
                  seed: int = 42,
+                 zero_bias: bool = True,
                  dtype = torch.float32, # type: ignore
                  ):
         super().__init__()
@@ -134,6 +135,7 @@ class SURE(nn.Module):
         self.post_layer_fct = post_layer_fct
         self.post_act_fct = post_act_fct
         self.hidden_layer_activation = hidden_layer_activation
+        self.use_bias = not zero_bias
         
         self.codebook_weights = None
 
@@ -232,15 +234,26 @@ class SURE(nn.Module):
         )
 
         if self.cell_factor_size>0:
-            self.cell_factor_effect = MLP(
-                [self.latent_dim + self.cell_factor_size] + 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.use_bias:
+                self.cell_factor_effect = MLP(
+                    [self.latent_dim + self.cell_factor_size] + 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,
+                )
+            else:
+                self.cell_factor_effect = ZeroBiasMLP(
+                    [self.latent_dim + self.cell_factor_size] + 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-2.1.31 → sure_tools-2.1.33}/SURE/flow/plot_quiver.py

@@ -7,7 +7,7 @@ from matplotlib.colors import ListedColormap
 
 def plot_quiver(z_points, delta_z, method='pca', figsize=(6,4), dpi=200, 
                 subsample=None, color_by=None, colormap='viridis', 
-                arrow_scale=1.0, arrow_width=0.005, alpha=0.8):
+                arrow_scale=1.0, arrow_width=0.002, alpha=0.8):
     """
     优化后的quiver可视化函数
     

{sure_tools-2.1.31 → sure_tools-2.1.33}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.31
+Version: 2.1.33
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.31 → sure_tools-2.1.33}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.31',
+    version='2.1.33',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",