SURE-tools 2.1.0__py3-none-any.whl → 2.1.1__py3-none-any.whl

SURE/PerturbFlow.py

@@ -97,7 +97,6 @@ class PerturbFlow(nn.Module):
                  input_size: int,
                  codebook_size: int = 200,
                  cell_factor_size: int = 0,
-                 cell_factor_names: list = None,
                  supervised_mode: bool = False,
                  z_dim: int = 10,
                  z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'normal',
@@ -135,7 +134,6 @@ 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.cell_factor_names = cell_factor_names
         
         self.codebook_weights = None
 
@@ -813,11 +811,8 @@ class PerturbFlow(nn.Module):
         A = np.concatenate(A)
         return A
     
-    def _cell_state_response(self, xs, factor_idx, perturb):
-        zns,_ = self.encoder_zn(xs)
-        if type(factor_idx) == str:
-            factor_idx = int(np.where(self.cell_factor_names==factor_idx)[0])
-        
+    def _cell_response(self, xs, factor_idx, perturb):
+        zns,_ = self.encoder_zn(xs)       
         if perturb.ndim==2:
             ms = self.cell_factor_effect[factor_idx]([zns, perturb])
         else:
@@ -825,7 +820,7 @@ class PerturbFlow(nn.Module):
             
         return ms 
 
-    def get_cell_state_response(self, 
+    def get_cell_response(self, 
                              xs, 
                              factor_idx,
                              perturb,
@@ -843,7 +838,7 @@ class PerturbFlow(nn.Module):
         Z = []
         with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
             for X_batch, P_batch, _ in dataloader:
-                zns = self._cell_state_response(X_batch, factor_idx, P_batch)
+                zns = self._cell_response(X_batch, factor_idx, P_batch)
                 Z.append(tensor_to_numpy(zns))
                 pbar.update(1)
 
@@ -852,11 +847,7 @@ class PerturbFlow(nn.Module):
     
     def get_metacell_response(self, factor_idx, perturb):
         zs = self._get_codebook()
-        ps = convert_to_tensor(perturb, device=self.get_device())
-        
-        if type(factor_idx) == str:
-            factor_idx = int(np.where(self.cell_factor_names==factor_idx)[0])
-            
+        ps = convert_to_tensor(perturb, device=self.get_device())         
         ms = self.cell_factor_effect[factor_idx]([zs,ps])
         return tensor_to_numpy(ms)
     

SURE/SURE.py

@@ -97,7 +97,6 @@ class SURE(nn.Module):
                  input_size: int,
                  codebook_size: int = 200,
                  cell_factor_size: int = 0,
-                 cell_factor_names: list = None,
                  supervised_mode: bool = False,
                  z_dim: int = 10,
                  z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'normal',
@@ -135,7 +134,6 @@ class SURE(nn.Module):
         self.post_layer_fct = post_layer_fct
         self.post_act_fct = post_act_fct
         self.hidden_layer_activation = hidden_layer_activation
-        self.cell_factor_names = cell_factor_names
         
         self.codebook_weights = None
 
@@ -234,18 +232,15 @@ class SURE(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,
-                )
-                )
+            self.cell_factor_effect = MLP(
+                [self.z_dim + self.cell_factor_size] + self.decoder_hidden_layers + [self.z_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],
@@ -449,13 +444,7 @@ class SURE(nn.Module):
                 zns = pyro.sample('zn', dist.Gumbel(zn_loc, zn_scale).to_event(1))
 
             if self.cell_factor_size>0:
-                #zus = self.decoder_undesired([zns,us])
-                zus = None
-                for i in np.arange(self.cell_factor_size):
-                    if i==0:
-                        zus = self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
-                    else:
-                        zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
+                zus = self.cell_factor_effect([zns,us])
                 zs = zns+zus
             else:
                 zs = zns
@@ -645,13 +634,7 @@ class SURE(nn.Module):
                     zns = pyro.sample('zn', dist.Gumbel(zn_loc, zn_scale).to_event(1), obs=embeds)
 
             if self.cell_factor_size>0:
-                #zus = self.decoder_undesired([zns,us])
-                zus = None
-                for i in np.arange(self.cell_factor_size):
-                    if i==0:
-                        zus = self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
-                    else:
-                        zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
+                zus = self.decoder_undesired([zns,us])
                 zs = zns+zus
             else:
                 zs = zns

{sure_tools-2.1.0.dist-info → sure_tools-2.1.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.0
+Version: 2.1.1
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.0.dist-info → sure_tools-2.1.1.dist-info}/RECORD

@@ -1,5 +1,5 @@
-SURE/PerturbFlow.py,sha256=ko6DcOoO-IUEm736n689jmtJSHM_s2hafG-yUmflNSU,52019
-SURE/SURE.py,sha256=OmwmA8RnhwrirXgnzqJMxv1BCr1jmjfHitvlmBKhHNA,49245
+SURE/PerturbFlow.py,sha256=RQoIhYQJdQpHdY_sMeDuqurbwvm6IX1XH7SVWG6SmS0,51658
+SURE/SURE.py,sha256=_ZOymj24DLQju0Lb90lKspHPmqIUDDzjIEr9t4qgqCI,48364
 SURE/SURE2.py,sha256=8wlnMwb1xuf9QUksNkWdWx5ZWq-xIy9NLx8RdUnE82o,48501
 SURE/__init__.py,sha256=xV10iBbh69g4mjBMb1cQxjuHe8e3Aq7pDzkZmx5G754,260
 SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
@@ -16,9 +16,9 @@ SURE/utils/__init__.py,sha256=Htqv4KqVKcRiaaTBsR-6yZ4LSlbhbzutjNKXGD9-uds,660
 SURE/utils/custom_mlp.py,sha256=07TYX1HgxfEjb_3i5MpiZfNhOhx3dKntuwGkrpteWiM,7036
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-sure_tools-2.1.0.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.1.0.dist-info/METADATA,sha256=bH8ARqqdk2bnLC5rk8MvPgBVAb8kaEKnzuHwyyDXpvE,2650
-sure_tools-2.1.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.1.0.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.1.0.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.1.0.dist-info/RECORD,,
+sure_tools-2.1.1.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.1.dist-info/METADATA,sha256=ET1LmoMzkRak6WiRpuGf2dcoY7cLgGoZtNmMkcqi6DU,2650
+sure_tools-2.1.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.1.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.1.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.1.dist-info/RECORD,,