SURE-tools 2.1.30__py3-none-any.whl → 2.1.32__py3-none-any.whl

SURE/PerturbFlow.py

@@ -73,7 +73,7 @@ class PerturbFlow(nn.Module):
                  config_enum: str = 'parallel',
                  use_cuda: bool = False,
                  seed: int = 42,
-                 bias: bool = False,
+                 zero_bias: bool = True,
                  dtype = torch.float32, # type: ignore
                  ):
         super().__init__()
@@ -97,7 +97,7 @@ class PerturbFlow(nn.Module):
         self.post_layer_fct = post_layer_fct
         self.post_act_fct = post_act_fct
         self.hidden_layer_activation = hidden_layer_activation
-        self.bias = bias
+        self.use_bias = not zero_bias
         
         self.codebook_weights = None
 
@@ -198,7 +198,7 @@ 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):
-                if self.bias:
+                if self.use_bias:
                     self.cell_factor_effect.append(MLP(
                         [self.latent_dim+1] + self.decoder_hidden_layers + [self.latent_dim],
                         activation=activate_fct,
@@ -207,11 +207,10 @@ class PerturbFlow(nn.Module):
                         post_act_fct=post_act_fct,
                         allow_broadcast=self.allow_broadcast,
                         use_cuda=self.use_cuda,
-                        bias=True,
                         )
                     )
                 else:
-                    self.cell_factor_effect.append(MLP(
+                    self.cell_factor_effect.append(ZeroBiasMLP(
                         [self.latent_dim+1] + self.decoder_hidden_layers + [self.latent_dim],
                         activation=activate_fct,
                         output_activation=None,
@@ -219,7 +218,6 @@ class PerturbFlow(nn.Module):
                         post_act_fct=post_act_fct,
                         allow_broadcast=self.allow_broadcast,
                         use_cuda=self.use_cuda,
-                        bias=False,
                         )
                     )
             

SURE/SURE.py

@@ -111,6 +111,7 @@ 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__()
@@ -134,6 +135,7 @@ 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
 
@@ -232,15 +234,26 @@ class SURE(nn.Module):
         )
 
         if self.cell_factor_size>0:
-            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,
-            )
+            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.decoder_concentrate = MLP(
                 [self.latent_dim] + self.decoder_hidden_layers + [self.input_size],

{sure_tools-2.1.30.dist-info → sure_tools-2.1.32.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.30
+Version: 2.1.32
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.30.dist-info → sure_tools-2.1.32.dist-info}/RECORD

@@ -1,5 +1,5 @@
-SURE/PerturbFlow.py,sha256=ppQWF2uipUdBkJGverqrz79P_vF2BmP2G7WdKPGSrsA,51692
-SURE/SURE.py,sha256=hVEjJtFVQkk_rX3KEaQgWoDTfxpDHf1p6j38UJjNkyY,47457
+SURE/PerturbFlow.py,sha256=BoaNDubCKpsYJcwipZxrSCpol4nVvCttP28MizHffzY,51650
+SURE/SURE.py,sha256=ghagk4vO3xrAXwdyYTIv7y0X2KXr1R2baXH8lqvUl7k,48094
 SURE/__init__.py,sha256=NOJI_K-eCqPgStXXvgl3wIEMp6d8saMTDYLJ7Ga9MqE,293
 SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
 SURE/assembly/assembly.py,sha256=6IMdelPOiRO4mUb4dC7gVCoF1Uvfw86-Map8P_jnUag,21477
@@ -17,9 +17,9 @@ SURE/utils/__init__.py,sha256=QJUOfrXzdWSmoM0P3LH8oKEHttzCWqpDy2UF0F0dtN4,673
 SURE/utils/custom_mlp.py,sha256=rHnx9jEef02zfCUdbYVCmbuHcDdIBmRgt__wpdpZvYg,8104
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-sure_tools-2.1.30.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.1.30.dist-info/METADATA,sha256=z-nDqP8GwHK8xSdxzKV5yhnDbPMTDNYbqEppdL-gaKk,2651
-sure_tools-2.1.30.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.1.30.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.1.30.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.1.30.dist-info/RECORD,,
+sure_tools-2.1.32.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.32.dist-info/METADATA,sha256=MdjeArB0rKjnH3MbWPA51badwykP2QQHvM3iAYldQFk,2651
+sure_tools-2.1.32.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.32.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.32.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.32.dist-info/RECORD,,