SURE-tools 2.1.27__py3-none-any.whl → 2.1.29__py3-none-any.whl

SURE/PerturbFlow.py

@@ -73,6 +73,7 @@ class PerturbFlow(nn.Module):
                  config_enum: str = 'parallel',
                  use_cuda: bool = False,
                  seed: int = 42,
+                 bias: bool = False,
                  dtype = torch.float32, # type: ignore
                  ):
         super().__init__()
@@ -96,6 +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.codebook_weights = None
 
@@ -196,16 +198,29 @@ 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):
-                self.cell_factor_effect.append(MLP(
-                    [self.latent_dim+1] + 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.bias:
+                    self.cell_factor_effect.append(MLP(
+                        [self.latent_dim+1] + 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,
+                        bias=False,
+                        )
+                    )
+                else:
+                    self.cell_factor_effect.append(MLP(
+                        [self.latent_dim+1] + 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/utils/custom_mlp.py

@@ -233,7 +233,7 @@ class ZeroBiasMLP(nn.Module):
                        post_act_fct=post_act_fct,
                        allow_broadcast=allow_broadcast,
                        use_cuda=use_cuda,
-                       bias=False)
+                       bias=True)
         
     # pass through our sequential for the output!
     def forward(self, x):

{sure_tools-2.1.27.dist-info → sure_tools-2.1.29.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.27
+Version: 2.1.29
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.27.dist-info → sure_tools-2.1.29.dist-info}/RECORD

@@ -1,4 +1,4 @@
-SURE/PerturbFlow.py,sha256=vNxcG3rYg7UqCoTmhYovvOagR8A4DWO1zXSm2FuLQGs,50952
+SURE/PerturbFlow.py,sha256=EDCZaQdz55_Jtxehi9n57wZndKkbXWudCIKB6gL74SQ,51657
 SURE/SURE.py,sha256=hVEjJtFVQkk_rX3KEaQgWoDTfxpDHf1p6j38UJjNkyY,47457
 SURE/__init__.py,sha256=NOJI_K-eCqPgStXXvgl3wIEMp6d8saMTDYLJ7Ga9MqE,293
 SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
@@ -14,12 +14,12 @@ SURE/flow/plot_quiver.py,sha256=wC42yLKfXYOGrrd4u9AbZS_6QiPUJ9QBXaOso55LjdA,8110
 SURE/perturb/__init__.py,sha256=ouxShhbxZM4r5Gf7GmKiutrsmtyq7QL8rHjhgF0BU08,32
 SURE/perturb/perturb.py,sha256=CqO3xPfNA3cG175tadDidKvGsTu_yKfJRRLn_93awKM,3303
 SURE/utils/__init__.py,sha256=QJUOfrXzdWSmoM0P3LH8oKEHttzCWqpDy2UF0F0dtN4,673
-SURE/utils/custom_mlp.py,sha256=PCnXhJdK_g6z51JJqCdrNGBoOU_SjN5XYAOhB_2BxNo,8105
+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-2.1.27.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.1.27.dist-info/METADATA,sha256=DBiRuz1tIyQ8Dp3wKjapiapkmXjajScDP-6xrFGGrew,2651
-sure_tools-2.1.27.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.1.27.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.1.27.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.1.27.dist-info/RECORD,,
+sure_tools-2.1.29.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.29.dist-info/METADATA,sha256=PZSER0TCcl7my4EAFNDTf3rECMT5m7tRrvMImKrF5b0,2651
+sure_tools-2.1.29.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.29.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.29.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.29.dist-info/RECORD,,