SURE-tools 2.1.73__tar.gz → 2.1.76__tar.gz

{sure_tools-2.1.73 → sure_tools-2.1.76}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.73
+Version: 2.1.76
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.73 → sure_tools-2.1.76}/SURE/PerturbFlow.py

@@ -104,6 +104,7 @@ class PerturbFlow(nn.Module):
         #self.use_bias = not zero_bias
         
         self.codebook_weights = None
+        self.total_count = None
 
         set_random_seed(seed)
         self.setup_networks()
@@ -317,6 +318,7 @@ class PerturbFlow(nn.Module):
         if self.loss_func=='negbinomial':
             total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
                                      xs.new_ones(self.input_size), constraint=constraints.positive)
+            self.total_count = total_count
             
         if self.use_zeroinflate:
             gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -396,6 +398,7 @@ class PerturbFlow(nn.Module):
         if self.loss_func=='negbinomial':
             total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
                                      xs.new_ones(self.input_size), constraint=constraints.positive)
+            self.total_count = total_count
             
         if self.use_zeroinflate:
             gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -480,6 +483,7 @@ class PerturbFlow(nn.Module):
         if self.loss_func=='negbinomial':
             total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
                                      xs.new_ones(self.input_size), constraint=constraints.positive)
+            self.total_count = total_count
             
         if self.use_zeroinflate:
             gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -576,6 +580,7 @@ class PerturbFlow(nn.Module):
         if self.loss_func=='negbinomial':
             total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
                                      xs.new_ones(self.input_size), constraint=constraints.positive)
+            self.total_count = total_count
             
         if self.use_zeroinflate:
             gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -880,7 +885,8 @@ class PerturbFlow(nn.Module):
             rate = concentrate.exp()
             theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
             
-            total_count = pyro.param("inverse_dispersion")
+            total_count = self.total_count
+            #total_count = pyro.param("inverse_dispersion")
             #store = pyro.get_param_store()
             #total_count = store['inverse_dispersion']
             counts = dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1).mean
@@ -1077,6 +1083,8 @@ class PerturbFlow(nn.Module):
                 # Update progress bar
                 pbar.set_postfix({'loss': str_loss})
                 pbar.update(1)
+                
+        self.total_count = pyro.param('inverse_dispersion')
 
     @classmethod
     def save_model(cls, model, file_path, compression=False):

{sure_tools-2.1.73 → sure_tools-2.1.76}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.73
+Version: 2.1.76
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.73 → sure_tools-2.1.76}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.73',
+    version='2.1.76',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",