SURE-tools 2.1.21__py3-none-any.whl → 2.1.24__py3-none-any.whl

SURE/PerturbFlow.py

@@ -196,7 +196,7 @@ 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):
-                self.cell_factor_effect.append(MLP(
+                self.cell_factor_effect.append(ZeroBiasMLP(
                     [self.latent_dim+1] + hidden_sizes + [self.latent_dim],
                     activation=activate_fct,
                     output_activation=None,

SURE/SURE.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
 
 
@@ -232,7 +232,7 @@ class SURE(nn.Module):
         )
 
         if self.cell_factor_size>0:
-            self.cell_factor_effect = MLP(
+            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,

SURE/utils/custom_mlp.py

@@ -212,3 +212,33 @@ class MLP(nn.Module):
 
 
 
+
+class ZeroBiasMLP(nn.Module):
+    def __init__(
+        self,
+        mlp_sizes,
+        activation=nn.ReLU,
+        output_activation=None,
+        post_layer_fct=lambda layer_ix, total_layers, layer: None,
+        post_act_fct=lambda layer_ix, total_layers, layer: None,
+        allow_broadcast=False,
+        use_cuda=False,
+    ):
+        # init the module object
+        super().__init__()
+        self.mlp = MLP(mlp_sizes=mlp_sizes,
+                       activation=activation,
+                       output_activation=output_activation,
+                       post_layer_fct=post_layer_fct,
+                       post_act_fct=post_act_fct,
+                       allow_broadcast=allow_broadcast,
+                       use_cuda=use_cuda,
+                       bias=False)
+        
+    # pass through our sequential for the output!
+    def forward(self, x):
+        y = self.mlp(x)
+        mask = torch.zeros_like(y)
+        mask[x[1][:,0]>0,:] = 1
+        return y*mask
+        

{sure_tools-2.1.21.dist-info → sure_tools-2.1.24.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.21
+Version: 2.1.24
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.21.dist-info → sure_tools-2.1.24.dist-info}/RECORD

@@ -1,6 +1,5 @@
-SURE/PerturbFlow.py,sha256=P5YebRbhyEIueyStdaMkFvLq43MJSBCcYd-pI09eTBQ,50938
-SURE/SURE.py,sha256=xMD6VBYsgk-bZ_xBWzpdGyxEAleonNRoPkZAxAX467s,47444
-SURE/SURE2.py,sha256=8wlnMwb1xuf9QUksNkWdWx5ZWq-xIy9NLx8RdUnE82o,48501
+SURE/PerturbFlow.py,sha256=gHrIHTAmFsG3FwS1ov7K3KwRMS0aw_IFQM-3HDIWnaA,50946
+SURE/SURE.py,sha256=AxYfuR86I4w3_pUQp--GmqKbWXeF6SaffP1yikN3M2k,47465
 SURE/__init__.py,sha256=NOJI_K-eCqPgStXXvgl3wIEMp6d8saMTDYLJ7Ga9MqE,293
 SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
 SURE/assembly/assembly.py,sha256=6IMdelPOiRO4mUb4dC7gVCoF1Uvfw86-Map8P_jnUag,21477
@@ -12,16 +11,15 @@ SURE/codebook/codebook.py,sha256=ZlN6gRX9Gj2D2u3P5KeOsbZri0MoMAiJo9lNeL-MK-I,171
 SURE/flow/__init__.py,sha256=rsAjYsh1xVIrxBCuwOE0Q_6N5th1wBgjJceV0ABPG3c,183
 SURE/flow/flow_stats.py,sha256=3F3waCuEbIQ7bsiGga4cUvJphYdWA307SyGwEh8EzM8,10514
 SURE/flow/plot_quiver.py,sha256=wC42yLKfXYOGrrd4u9AbZS_6QiPUJ9QBXaOso55LjdA,8110
-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=IlW5L_YEhtn0guHlGyvGLRjJ5JOIWs4qB7BPi1Dmq9U,7116
+SURE/utils/custom_mlp.py,sha256=PCnXhJdK_g6z51JJqCdrNGBoOU_SjN5XYAOhB_2BxNo,8105
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-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,,
+sure_tools-2.1.24.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.24.dist-info/METADATA,sha256=Tv1Ta5sY6IpoQvgJ8tc8vNCqosV8_DX13WN5VYLRuTo,2651
+sure_tools-2.1.24.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.24.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.24.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.24.dist-info/RECORD,,