SURE-tools 2.0.10__py3-none-any.whl → 2.1.1__py3-none-any.whl

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
@@ -813,77 +796,6 @@ class SURE(nn.Module):
         A = np.concatenate(A)
         return A
     
-    def _cell_move(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])
-        
-        if perturb.ndim==2:
-            ms = self.cell_factor_effect[factor_idx]([zns, perturb])
-        else:
-            ms = self.cell_factor_effect[factor_idx]([zns, perturb.reshape(-1,1)])
-            
-        return ms 
-
-    def get_cell_move(self, 
-                             xs, 
-                             factor_idx,
-                             perturb,
-                             batch_size: int = 1024):
-        """
-        Return cells' changes in the latent space induced by specific perturbation of a factor
-
-        """
-        xs = self.preprocess(xs)
-        xs = convert_to_tensor(xs, device=self.get_device())
-        ps = convert_to_tensor(perturb, device=self.get_device())
-        dataset = CustomDataset2(xs,ps)
-        dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=False)
-
-        Z = []
-        with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
-            for X_batch, P_batch, _ in dataloader:
-                zns = self._cell_move(X_batch, factor_idx, P_batch)
-                Z.append(tensor_to_numpy(zns))
-                pbar.update(1)
-
-        Z = np.concatenate(Z)
-        return Z
-    
-    def get_metacell_move(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])
-            
-        ms = self.cell_factor_effect[factor_idx]([zs,ps])
-        return tensor_to_numpy(ms)
-    
-    def _get_expression_responses(self, delta_zs):
-        return self.decoder_concentrate(delta_zs)
-    
-    def get_expression_responses(self, 
-                             delta_zs, 
-                             batch_size: int = 1024):
-        """
-        Return cells' changes in the latent space induced by specific perturbation of a factor
-
-        """
-        delta_zs = convert_to_tensor(delta_zs, device=self.get_device())
-        dataset = CustomDataset(delta_zs)
-        dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=False)
-
-        R = []
-        with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
-            for delta_Z_batch, _ in dataloader:
-                r = self._cell_move(delta_Z_batch)
-                R.append(tensor_to_numpy(r))
-                pbar.update(1)
-
-        R = np.concatenate(R)
-        return R
-    
     def preprocess(self, xs, threshold=0):
         if self.loss_func == 'bernoulli':
             ad = sc.AnnData(xs)

SURE/__init__.py

@@ -1,10 +1,11 @@
 from .SURE import SURE
-from .SURE2 import SURE2
+from .PerturbFlow import PerturbFlow
 
 from . import utils 
 from . import codebook
 from . import SURE
+from . import PerturbFlow
 from . import atac
 from . import flow 
 
-__all__ = ['SURE', 'flow', 'atac', 'utils', 'codebook']
+__all__ = ['SURE', 'PerturbFlow', 'flow', 'atac', 'utils', 'codebook']

{sure_tools-2.0.10.dist-info → sure_tools-2.1.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.0.10
+Version: 2.1.1
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.0.10.dist-info → sure_tools-2.1.1.dist-info}/RECORD

@@ -1,6 +1,7 @@
-SURE/SURE.py,sha256=DzuRXp9AtnwoezsR-zTkm6PxlfOV8sdmu3mYwkapYQs,51875
+SURE/PerturbFlow.py,sha256=RQoIhYQJdQpHdY_sMeDuqurbwvm6IX1XH7SVWG6SmS0,51658
+SURE/SURE.py,sha256=_ZOymj24DLQju0Lb90lKspHPmqIUDDzjIEr9t4qgqCI,48364
 SURE/SURE2.py,sha256=8wlnMwb1xuf9QUksNkWdWx5ZWq-xIy9NLx8RdUnE82o,48501
-SURE/__init__.py,sha256=mxdLoWa2fPEM4-WkJetMfcecpzqJ8YsM4lOoKHSLTrU,207
+SURE/__init__.py,sha256=xV10iBbh69g4mjBMb1cQxjuHe8e3Aq7pDzkZmx5G754,260
 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
@@ -15,9 +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-2.0.10.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.0.10.dist-info/METADATA,sha256=_64vkwUxRdYs5xvh76oYB34PUDpEnCN5Inl5tlGhe38,2651
-sure_tools-2.0.10.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.0.10.dist-info/entry_points.txt,sha256=u12payZYgCBy5FCwRHP6AlSQhKCiWSEDwj68r1DVdn8,40
-sure_tools-2.0.10.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.0.10.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,,

sure_tools-2.1.1.dist-info/entry_points.txt

@@ -0,0 +1,3 @@
+[console_scripts]
+PerturbFlow = PerturbFlow.PerturbFlow:main
+SURE = SURE.SURE:main

sure_tools-2.0.10.dist-info/entry_points.txt

@@ -1,2 +0,0 @@
-[console_scripts]
-SURE = SURE.SURE:main