SURE-tools 2.1.18__py3-none-any.whl → 2.1.20__py3-none-any.whl

SURE/PerturbFlow.py

@@ -10,7 +10,7 @@ from torch.distributions.utils import logits_to_probs, probs_to_logits, clamp_pr
 from torch.distributions import constraints
 from torch.distributions.transforms import SoftmaxTransform
 
-from .utils.custom_mlp import MLP, Exp
+from .utils.custom_mlp import MLP, Exp, ZeroBiasMLP
 from .utils.utils import CustomDataset, CustomDataset2, CustomDataset4, tensor_to_numpy, convert_to_tensor
 
 
@@ -196,16 +196,20 @@ 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(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.decoder_concentrate = MLP(
@@ -663,15 +667,15 @@ class PerturbFlow(nn.Module):
         cb = tensor_to_numpy(cb)
         return cb
 
-    def _get_basis_embedding(self, xs):           
+    def _get_basal_embedding(self, xs):           
         zns, _ = self.encoder_zn(xs)
         return zns 
     
-    def get_basis_embedding(self, 
+    def get_basal_embedding(self, 
                              xs, 
                              batch_size: int = 1024):
         """
-        Return cells' basis latent representations
+        Return cells' basal latent representations
 
         Parameters
         ----------
@@ -692,7 +696,7 @@ class PerturbFlow(nn.Module):
         Z = []
         with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
             for X_batch, _ in dataloader:
-                zns = self._get_basis_embedding(X_batch)
+                zns = self._get_basal_embedding(X_batch)
                 Z.append(tensor_to_numpy(zns))
                 pbar.update(1)
 

SURE/utils/custom_mlp.py

@@ -209,3 +209,27 @@ class MLP(nn.Module):
     # pass through our sequential for the output!
     def forward(self, *args, **kwargs):
         return self.sequential_mlp.forward(*args, **kwargs)
+
+
+
+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-2.1.18.dist-info → sure_tools-2.1.20.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.18
+Version: 2.1.20
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.18.dist-info → sure_tools-2.1.20.dist-info}/RECORD

@@ -1,4 +1,4 @@
-SURE/PerturbFlow.py,sha256=WNOKfRsaK-TSIhOHY9DqbT_h8mxvbUEFnkevlsc4Kz8,50957
+SURE/PerturbFlow.py,sha256=f0GUWbud-XDc3j0S3QKiRiUKr4cvtO9acoFyzMTH9eI,51151
 SURE/SURE.py,sha256=6qjf9E9OMBkZQSNnmvornpEa4E203-_rtz5Hs8jNCJA,47472
 SURE/SURE2.py,sha256=8wlnMwb1xuf9QUksNkWdWx5ZWq-xIy9NLx8RdUnE82o,48501
 SURE/__init__.py,sha256=NOJI_K-eCqPgStXXvgl3wIEMp6d8saMTDYLJ7Ga9MqE,293
@@ -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=n0GJj8GKSAqvyokCL_6LugbeedzqLdfBijq24B_I9dA,7113
+SURE/utils/custom_mlp.py,sha256=R63nhhRIO0sIEPwq7gAaBSDn5I5KMv7uDXsW6xEZXHw,7823
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-sure_tools-2.1.18.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.1.18.dist-info/METADATA,sha256=0MihooSGgEzdqyMlqUufrBjjtGURijDa7auUyE9extA,2651
-sure_tools-2.1.18.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.1.18.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.1.18.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.1.18.dist-info/RECORD,,
+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,,