SURE-tools 2.1.15__tar.gz → 2.1.17__tar.gz

{sure_tools-2.1.15 → sure_tools-2.1.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.15
+Version: 2.1.17
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.15 → sure_tools-2.1.17}/SURE/PerturbFlow.py

@@ -204,6 +204,7 @@ class PerturbFlow(nn.Module):
                     post_act_fct=post_act_fct,
                     allow_broadcast=self.allow_broadcast,
                     use_cuda=self.use_cuda,
+                    bias=False,
                 )
                 )
             

{sure_tools-2.1.15 → sure_tools-2.1.17}/SURE/utils/custom_mlp.py

@@ -85,6 +85,7 @@ class MLP(nn.Module):
         post_act_fct=lambda layer_ix, total_layers, layer: None,
         allow_broadcast=False,
         use_cuda=False,
+        bias=True,
     ):
         # init the module object
         super().__init__()
@@ -114,11 +115,12 @@ class MLP(nn.Module):
             assert type(layer_size) == int, "Hidden layer sizes must be ints"
 
             # get our nn layer module (in this case nn.Linear by default)
-            cur_linear_layer = nn.Linear(last_layer_size, layer_size)
+            cur_linear_layer = nn.Linear(last_layer_size, layer_size, bias=bias)
 
             # for numerical stability -- initialize the layer properly
             cur_linear_layer.weight.data.normal_(0, 0.001)
-            cur_linear_layer.bias.data.normal_(0, 0.001)
+            if bias:
+                cur_linear_layer.bias.data.normal_(0, 0.001)
 
             # use GPUs to share data during training (if available)
             if use_cuda:
@@ -160,7 +162,7 @@ class MLP(nn.Module):
         ), "output_size must be int, list, tuple"
 
         if type(output_size) == int:
-            all_modules.append(nn.Linear(last_layer_size, output_size))
+            all_modules.append(nn.Linear(last_layer_size, output_size, bias=bias))
             if output_activation is not None:
                 all_modules.append(
                     call_nn_op(output_activation)
@@ -179,7 +181,7 @@ class MLP(nn.Module):
                 split_layer = []
 
                 # we have an activation function
-                split_layer.append(nn.Linear(last_layer_size, out_size))
+                split_layer.append(nn.Linear(last_layer_size, out_size, bias=bias))
 
                 # then we get our output activation (either we repeat all or we index into a same sized array)
                 act_out_fct = (

{sure_tools-2.1.15 → sure_tools-2.1.17}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.15
+Version: 2.1.17
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.15 → sure_tools-2.1.17}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.15',
+    version='2.1.17',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",