SURE-tools 2.2.19__py3-none-any.whl → 2.3.2__py3-none-any.whl

SURE/__init__.py

@@ -1,5 +1,6 @@
 from .SURE import SURE
 from .DensityFlow import DensityFlow
+from .PerturbE import PerturbE
 
 from . import utils 
 from . import codebook
@@ -9,4 +10,4 @@ from . import atac
 from . import flow 
 from . import perturb
 
-__all__ = ['SURE', 'DensityFlow', 'flow', 'perturb', 'atac', 'utils', 'codebook']
+__all__ = ['SURE', 'DensityFlow', 'PerturbE', 'flow', 'perturb', 'atac', 'utils', 'codebook']

SURE/utils/custom_mlp.py

@@ -240,12 +240,49 @@ class ZeroBiasMLP(nn.Module):
         y = self.mlp(x)
         mask = torch.zeros_like(y)
         if len(y.shape)==2:
-            mask[x[1][:,0]>0,:] = 1
+            if type(x)==list:
+                mask[x[1][:,0]>0,:] = 1
+            else:
+                mask[x[:,0]>0,:] = 1
         elif len(y.shape)==3:
-            mask[:,x[1][:,0]>0,:] = 1
+            if type(x)==list:
+                mask[:,x[1][:,0]>0,:] = 1
+            else:
+                mask[:,x[:,0]>0,:] = 1
         return y*mask
         
 
+
+class ZeroBiasMLP2(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=True)
+        
+    # pass through our sequential for the output!
+    def forward(self, x):
+        y = self.mlp(x)
+        mask = torch.zeros_like(y)
+        x_sum = torch.sum(x, dim=1)
+        mask[x_sum>0,:] = 1
+        return y*mask
+    
 class HDMLP(nn.Module):
     def __init__(
         self,

{sure_tools-2.2.19.dist-info → sure_tools-2.3.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.2.19
+Version: 2.3.2
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.2.19.dist-info → sure_tools-2.3.2.dist-info}/RECORD

@@ -1,6 +1,7 @@
-SURE/DensityFlow.py,sha256=FQ5LT-5xo_O3Qa5I0hxYBMq8f7HvapxfwTQj-oc3iyI,56086
+SURE/DensityFlow.py,sha256=YvaE9aPbAC2U7WhTye5i2AMtcw0BI_qS3gv9SP4aE0k,56676
+SURE/PerturbE.py,sha256=nomWc8nl4WkihhaITsAVXc-wTp1OTXfypQYP4kTz7JQ,51685
 SURE/SURE.py,sha256=MXs7iuvcj-lU4dJ_MwKegpL2Rqk2HB4eFfAgHRA3RtA,47744
-SURE/__init__.py,sha256=NVp22RCHrhSwHNMomABC-eftoCYvt7vV1XOzim-UZHE,293
+SURE/__init__.py,sha256=Q6J9HwAMxI42Boj8QCVbIDTAr0YyLY9Qj2ewTkM0uUw,336
 SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
 SURE/assembly/assembly.py,sha256=6IMdelPOiRO4mUb4dC7gVCoF1Uvfw86-Map8P_jnUag,21477
 SURE/assembly/atlas.py,sha256=ALjmVWutm_tOHTcT1aqOxmuCEQw-XzrtDoMCV_8oXLk,21794
@@ -14,12 +15,12 @@ SURE/flow/plot_quiver.py,sha256=UbmuScUcgbQHeMmjKmgqxjrIjHhiHx0VWct16UMMwuE,8110
 SURE/perturb/__init__.py,sha256=8TP1dSUhXiZzKpFebHZmm8XMMGbUz_OfQ10xu-6uPPY,43
 SURE/perturb/perturb.py,sha256=ey7cxsM1tO1MW4UaE_MLpLHK87CjvXzn2CBPtvv1VZ0,6116
 SURE/utils/__init__.py,sha256=YF5jB-PAHJQ40OlcZ7BCZbsN2q1JKuPT6EppilRXQqM,680
-SURE/utils/custom_mlp.py,sha256=HuNb7f8-6RFjsvfEu1XOuNpLrHZkGYHgf8TpJfPSNO0,9382
+SURE/utils/custom_mlp.py,sha256=Rn_PQouxPMSda-KKBYrwVVv3GFFuUmCLxp8cV5LszZo,10580
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-sure_tools-2.2.19.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.2.19.dist-info/METADATA,sha256=F2Obio0gRQMcBdPPcsyS8MhNnsy2J0px2twO4XlPtys,2678
-sure_tools-2.2.19.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.2.19.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.2.19.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.2.19.dist-info/RECORD,,
+sure_tools-2.3.2.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.3.2.dist-info/METADATA,sha256=NDI2_X4N1FIZkNSBdksNPATk-XtSAxUJJs7Hlx3OTSI,2677
+sure_tools-2.3.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.3.2.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.3.2.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.3.2.dist-info/RECORD,,