SURE-tools 2.1.34__tar.gz → 2.1.36__tar.gz

{sure_tools-2.1.34 → sure_tools-2.1.36}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.34
+Version: 2.1.36
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.34 → sure_tools-2.1.36}/SURE/PerturbFlow.py

@@ -423,12 +423,13 @@ class PerturbFlow(nn.Module):
                 zns = pyro.sample('zn', dist.Gumbel(zn_loc, zn_scale).to_event(1))
 
             if self.cell_factor_size>0:
-                zus = None
-                for i in np.arange(self.cell_factor_size):
-                    if i==0:
-                        zus = self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
-                    else:
-                        zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
+                #zus = None
+                #for i in np.arange(self.cell_factor_size):
+                #    if i==0:
+                #        zus = self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
+                #    else:
+                #        zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
+                zus = self._total_effects(zns, us)
                 zs = zns+zus
             else:
                 zs = zns
@@ -618,12 +619,13 @@ class PerturbFlow(nn.Module):
                     zns = pyro.sample('zn', dist.Gumbel(zn_loc, zn_scale).to_event(1), obs=embeds)
 
             if self.cell_factor_size>0:
-                zus = None
-                for i in np.arange(self.cell_factor_size):
-                    if i==0:
-                        zus = self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
-                    else:
-                        zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
+                #zus = None
+                #for i in np.arange(self.cell_factor_size):
+                #    if i==0:
+                #        zus = self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
+                #    else:
+                #        zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
+                zus = self._total_effects(zns, us)
                 zs = zns+zus
             else:
                 zs = zns
@@ -660,6 +662,15 @@ class PerturbFlow(nn.Module):
                 zn_loc, zn_scale = self.encoder_zn(xs)
                 zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
+    def _total_effects(self, zns, us):
+        zus = None
+        for i in np.arange(self.cell_factor_size):
+            if i==0:
+                zus = self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
+            else:
+                zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
+        return zus
+                        
     def _get_codebook(self):
         I = torch.eye(self.code_size, **self.options)
         if self.latent_dist=='studentt':

{sure_tools-2.1.34 → sure_tools-2.1.36}/SURE/SURE.py

@@ -111,7 +111,6 @@ class SURE(nn.Module):
                  config_enum: str = 'parallel',
                  use_cuda: bool = False,
                  seed: int = 42,
-                 zero_bias: bool = True,
                  dtype = torch.float32, # type: ignore
                  ):
         super().__init__()
@@ -135,7 +134,6 @@ class SURE(nn.Module):
         self.post_layer_fct = post_layer_fct
         self.post_act_fct = post_act_fct
         self.hidden_layer_activation = hidden_layer_activation
-        self.use_bias = not zero_bias
         
         self.codebook_weights = None
 
@@ -234,26 +232,16 @@ class SURE(nn.Module):
         )
 
         if self.cell_factor_size>0:
-            if self.use_bias:
-                self.cell_factor_effect = MLP(
-                    [self.latent_dim + self.cell_factor_size] + self.decoder_hidden_layers + [self.latent_dim],
-                    activation=activate_fct,
-                    output_activation=None,
-                    post_layer_fct=post_layer_fct,
-                    post_act_fct=post_act_fct,
-                    allow_broadcast=self.allow_broadcast,
-                    use_cuda=self.use_cuda,
-                )
-            else:
-                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,
-                    post_layer_fct=post_layer_fct,
-                    post_act_fct=post_act_fct,
-                    allow_broadcast=self.allow_broadcast,
-                    use_cuda=self.use_cuda,
-                )
+            self.cell_factor_effect = MLP(
+                [self.latent_dim + self.cell_factor_size] + self.decoder_hidden_layers + [self.latent_dim],
+                activation=activate_fct,
+                output_activation=None,
+                post_layer_fct=post_layer_fct,
+                post_act_fct=post_act_fct,
+                allow_broadcast=self.allow_broadcast,
+                use_cuda=self.use_cuda,
+            )
+
             
         self.decoder_concentrate = MLP(
                 [self.latent_dim] + self.decoder_hidden_layers + [self.input_size],

{sure_tools-2.1.34 → sure_tools-2.1.36}/SURE/perturb/perturb.py

@@ -8,7 +8,7 @@ class LabelMatrix:
     def __init__(self):
         self.labels_ = None
     
-    def fit_transform(self, labels, sep_pattern=r'[;_\-\s]', speedup: Literal['none','vectorize','parallel']='none'):
+    def fit_transform(self, labels, control_label, sep_pattern=r'[;_\-\s]', speedup: Literal['none','vectorize','parallel']='none'):
         if speedup=='none':
             mat, self.labels_ = label_to_matrix(labels=labels, sep_pattern=sep_pattern)
         elif speedup=='vectorize':
@@ -17,6 +17,10 @@ class LabelMatrix:
             mat, self.labels_ = parallel_label_to_matrix(labels=labels, sep_pattern=sep_pattern)
             
         self.labels_ = np.array(self.labels_)
+        
+        idx = np.where(self.labels_==control_label)[0]
+        mat = np.delete(mat, idx, axis=1)
+        self.labels_ = np.delete(self.labels_, idx)
         return mat
             
     def inverse_transform(self, matrix):

{sure_tools-2.1.34 → sure_tools-2.1.36}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.34
+Version: 2.1.36
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.34 → sure_tools-2.1.36}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.34',
+    version='2.1.36',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",