SURE-tools 2.1.21__tar.gz → 2.1.24__tar.gz

{sure_tools-2.1.21 → sure_tools-2.1.24}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.21
+Version: 2.1.24
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.21 → sure_tools-2.1.24}/SURE/PerturbFlow.py

@@ -196,7 +196,7 @@ 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.cell_factor_effect.append(ZeroBiasMLP(
                     [self.latent_dim+1] + hidden_sizes + [self.latent_dim],
                     activation=activate_fct,
                     output_activation=None,

{sure_tools-2.1.21 → sure_tools-2.1.24}/SURE/SURE.py

@@ -10,7 +10,7 @@ from torch.distributions.utils import logits_to_probs, probs_to_logits, clamp_pr
 from torch.distributions import constraints
 from torch.distributions.transforms import SoftmaxTransform
 
-from .utils.custom_mlp import MLP, Exp
+from .utils.custom_mlp import MLP, Exp, ZeroBiasMLP
 from .utils.utils import CustomDataset, CustomDataset2, CustomDataset4, tensor_to_numpy, convert_to_tensor
 
 
@@ -232,7 +232,7 @@ class SURE(nn.Module):
         )
 
         if self.cell_factor_size>0:
-            self.cell_factor_effect = MLP(
+            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,

{sure_tools-2.1.21 → sure_tools-2.1.24}/SURE/utils/custom_mlp.py

@@ -212,3 +212,33 @@ class MLP(nn.Module):
 
 
 
+
+class ZeroBiasMLP(nn.Module):
+    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__()
+        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)
+        
+    # pass through our sequential for the output!
+    def forward(self, x):
+        y = self.mlp(x)
+        mask = torch.zeros_like(y)
+        mask[x[1][:,0]>0,:] = 1
+        return y*mask
+        

{sure_tools-2.1.21 → sure_tools-2.1.24}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.21
+Version: 2.1.24
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.21 → sure_tools-2.1.24}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.21',
+    version='2.1.24',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",