SURE-tools 2.1.20__py3-none-any.whl → 2.1.21__py3-none-any.whl

SURE/PerturbFlow.py

@@ -196,20 +196,15 @@ 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] + hidden_sizes + [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,
-                #)
-                #)
-                self.cell_factor_effect.append(ZeroBiasMLP(
-                    self.latent_dim+1, hidden_sizes, self.latent_dim,
-                    )
+                self.cell_factor_effect.append(MLP(
+                    [self.latent_dim+1] + hidden_sizes + [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(

SURE/SURE.py

@@ -240,7 +240,6 @@ class SURE(nn.Module):
                 post_act_fct=post_act_fct,
                 allow_broadcast=self.allow_broadcast,
                 use_cuda=self.use_cuda,
-                bias=False,
             )
             
         self.decoder_concentrate = MLP(

SURE/utils/custom_mlp.py

@@ -212,24 +212,3 @@ class MLP(nn.Module):
 
 
 
-class ZeroBiasMLP(nn.Module):
-    def __init__(self, input_dim, hidden_dims, output_dim):
-        super().__init__()
-        layers = []
-        dims = [input_dim] + hidden_dims + [output_dim]
-        
-        # 构建线性层（强制所有偏置为0）
-        for i in range(len(dims)-1):
-            linear = nn.Linear(dims[i], dims[i+1])
-            nn.init.zeros_(linear.bias)  # 初始化偏置为0
-            layers.append(linear)
-            if i < len(dims)-2:
-                layers.append(nn.ReLU())  # 激活函数
-        
-        self.net = nn.Sequential(*layers)
-    
-    def forward(self, x):
-        if type(x) == list:
-            x = torch.concat(x, dim=1)
-        return self.net(x)
-

{sure_tools-2.1.20.dist-info → sure_tools-2.1.21.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.20
+Version: 2.1.21
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.20.dist-info → sure_tools-2.1.21.dist-info}/RECORD

@@ -1,5 +1,5 @@
-SURE/PerturbFlow.py,sha256=f0GUWbud-XDc3j0S3QKiRiUKr4cvtO9acoFyzMTH9eI,51151
-SURE/SURE.py,sha256=6qjf9E9OMBkZQSNnmvornpEa4E203-_rtz5Hs8jNCJA,47472
+SURE/PerturbFlow.py,sha256=P5YebRbhyEIueyStdaMkFvLq43MJSBCcYd-pI09eTBQ,50938
+SURE/SURE.py,sha256=xMD6VBYsgk-bZ_xBWzpdGyxEAleonNRoPkZAxAX467s,47444
 SURE/SURE2.py,sha256=8wlnMwb1xuf9QUksNkWdWx5ZWq-xIy9NLx8RdUnE82o,48501
 SURE/__init__.py,sha256=NOJI_K-eCqPgStXXvgl3wIEMp6d8saMTDYLJ7Ga9MqE,293
 SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
@@ -16,12 +16,12 @@ SURE/flow/quiver.py,sha256=_euFqSaRrDoZ_oOabOx20LOoUTJ__XPhLW-vzLNQfAo,1859
 SURE/perturb/__init__.py,sha256=ouxShhbxZM4r5Gf7GmKiutrsmtyq7QL8rHjhgF0BU08,32
 SURE/perturb/perturb.py,sha256=CqO3xPfNA3cG175tadDidKvGsTu_yKfJRRLn_93awKM,3303
 SURE/utils/__init__.py,sha256=Htqv4KqVKcRiaaTBsR-6yZ4LSlbhbzutjNKXGD9-uds,660
-SURE/utils/custom_mlp.py,sha256=R63nhhRIO0sIEPwq7gAaBSDn5I5KMv7uDXsW6xEZXHw,7823
+SURE/utils/custom_mlp.py,sha256=IlW5L_YEhtn0guHlGyvGLRjJ5JOIWs4qB7BPi1Dmq9U,7116
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-sure_tools-2.1.20.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.1.20.dist-info/METADATA,sha256=TWnbf7P62fec9iUnT2i8PZXuY9tMNL76_1uWS0j37rY,2651
-sure_tools-2.1.20.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.1.20.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.1.20.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.1.20.dist-info/RECORD,,
+sure_tools-2.1.21.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.21.dist-info/METADATA,sha256=5pPz0o1rpF7udNtmSfrCFE14qcuhl-86De2HkA_fUww,2651
+sure_tools-2.1.21.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.21.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.21.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.21.dist-info/RECORD,,