SURE-tools 2.1.50__tar.gz → 2.1.52__tar.gz

{sure_tools-2.1.50 → sure_tools-2.1.52}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.50
+Version: 2.1.52
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.50 → sure_tools-2.1.52}/SURE/PerturbFlow.py

@@ -64,7 +64,7 @@ class PerturbFlow(nn.Module):
                  z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'normal',
                  loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'negbinomial',
                  inverse_dispersion: float = 10.0,
-                 use_zeroinflate: bool = True,
+                 use_zeroinflate: bool = False,
                  hidden_layers: list = [300],
                  hidden_layer_activation: Literal['relu','softplus','leakyrelu','linear'] = 'relu',
                  nn_dropout: float = 0.1,
@@ -872,9 +872,18 @@ class PerturbFlow(nn.Module):
     
     def _count(self,concentrate):
         if self.loss_func == 'bernoulli':
-            counts = self.sigmoid(concentrate)
-        else:
-            counts = concentrate.exp()
+            #counts = self.sigmoid(concentrate)
+            counts = dist.Bernoulli(logits=concentrate).to_event(1).mean
+        elif self.loss_func == 'negbinomial':
+            #counts = concentrate.exp()
+            rate = concentrate.exp()
+            theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
+            
+            total_count = pyro.param("inverse_dispersion")
+            counts = dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1)
+        elif self.loss_func == 'poisson':
+            rate = concentrate.exp()
+            counts = dist.Poisson(rate=rate).to_event(1)
         return counts
     
     def _count_sample(self,concentrate):
@@ -933,7 +942,7 @@ class PerturbFlow(nn.Module):
             decay_rate: float = 0.9,
             config_enum: str = 'parallel',
             threshold: int = 0,
-            use_jax: bool = False):
+            use_jax: bool = True):
         """
         Train the PerturbFlow model.
 

{sure_tools-2.1.50 → sure_tools-2.1.52}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.50
+Version: 2.1.52
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.50 → sure_tools-2.1.52}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.50',
+    version='2.1.52',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",