SURE-tools 2.2.14__tar.gz → 2.2.17__tar.gz

{sure_tools-2.2.14 → sure_tools-2.2.17}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.2.14
+Version: 2.2.17
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.2.14 → sure_tools-2.2.17}/SURE/DensityFlow.py

@@ -62,9 +62,9 @@ class DensityFlow(nn.Module):
                  supervised_mode: bool = False,
                  z_dim: int = 10,
                  z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'gumbel',
-                 loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'negbinomial',
+                 loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'multinomial',
                  inverse_dispersion: float = 10.0,
-                 use_zeroinflate: bool = True,
+                 use_zeroinflate: bool = False,
                  hidden_layers: list = [500],
                  hidden_layer_activation: Literal['relu','softplus','leakyrelu','linear'] = 'relu',
                  nn_dropout: float = 0.1,
@@ -696,7 +696,7 @@ class DensityFlow(nn.Module):
         """
         Return the mean part of metacell codebook
         """
-        cb = self._get_metacell_coordinates()
+        cb = self._get_codebook()
         cb = tensor_to_numpy(cb)
         return cb
 
@@ -820,12 +820,12 @@ class DensityFlow(nn.Module):
             us_i = us[:,pert_idx].reshape(-1,1)
             
             # factor effect of xs 
-            dzs0 = self.get_cell_response(xs, factor_idx=pert_idx, perturb=us_i)
+            dzs0 = self.get_cell_response(zs, factor_idx=pert_idx, perturb=us_i)
             
             # perturbation effect 
             ps = np.ones_like(us_i)
             if np.sum(np.abs(ps-us_i))>=1:
-                dzs = self.get_cell_response(xs, factor_idx=pert_idx, perturb=ps)          
+                dzs = self.get_cell_response(zs, factor_idx=pert_idx, perturb=ps)          
                 zs = zs + dzs0 + dzs
             else:
                 zs = zs + dzs0
@@ -878,12 +878,6 @@ class DensityFlow(nn.Module):
         Z = np.concatenate(Z)
         return Z
     
-    def get_metacell_response(self, factor_idx, perturb):
-        zs = self._get_codebook()
-        ps = convert_to_tensor(perturb, device=self.get_device())         
-        ms = self.cell_factor_effect[factor_idx]([zs,ps])
-        return tensor_to_numpy(ms)
-    
     def _get_expression_response(self, delta_zs):
         return self.decoder_concentrate(delta_zs)
     

{sure_tools-2.2.14 → sure_tools-2.2.17}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.2.14
+Version: 2.2.17
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.2.14 → sure_tools-2.2.17}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.2.14',
+    version='2.2.17',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",