SURE-tools 2.1.46__tar.gz → 2.1.48__tar.gz

{sure_tools-2.1.46 → sure_tools-2.1.48}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.46
+Version: 2.1.48
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.46 → sure_tools-2.1.48}/SURE/PerturbFlow.py

@@ -378,7 +378,8 @@ class PerturbFlow(nn.Module):
 
     def guide1(self, xs):
         with pyro.plate('data'):
-            zn_loc, zn_scale = self.encoder_zn(xs)
+            #zn_loc, zn_scale = self.encoder_zn(xs)
+            zn_loc, zn_scale = self._get_basal_embedding(xs)
             zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
             alpha = self.encoder_n(zns)
@@ -466,7 +467,8 @@ class PerturbFlow(nn.Module):
 
     def guide2(self, xs, us=None):
         with pyro.plate('data'):
-            zn_loc, zn_scale = self.encoder_zn(xs)
+            #zn_loc, zn_scale = self.encoder_zn(xs)
+            zn_loc, zn_scale = self._get_basal_embedding(xs)
             zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
             alpha = self.encoder_n(zns)
@@ -561,7 +563,8 @@ class PerturbFlow(nn.Module):
     def guide3(self, xs, ys, embeds=None):
         with pyro.plate('data'):
             if embeds is None:
-                zn_loc, zn_scale = self.encoder_zn(xs)
+                #zn_loc, zn_scale = self.encoder_zn(xs)
+                zn_loc, zn_scale = self._get_basal_embedding(xs)
                 zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
     def model4(self, xs, us, ys, embeds=None):
@@ -663,7 +666,8 @@ class PerturbFlow(nn.Module):
     def guide4(self, xs, us, ys, embeds=None):
         with pyro.plate('data'):
             if embeds is None:
-                zn_loc, zn_scale = self.encoder_zn(xs)
+                #zn_loc, zn_scale = self.encoder_zn(xs)
+                zn_loc, zn_scale = self._get_basal_embedding(xs)
                 zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
     def _total_effects(self, zns, us):
@@ -692,8 +696,8 @@ class PerturbFlow(nn.Module):
         return cb
 
     def _get_basal_embedding(self, xs):           
-        zns, _ = self.encoder_zn(xs)
-        return zns 
+        loc, scale = self.encoder_zn(xs)
+        return loc, scale 
     
     def get_basal_embedding(self, 
                              xs, 
@@ -720,7 +724,7 @@ class PerturbFlow(nn.Module):
         Z = []
         with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
             for X_batch, _ in dataloader:
-                zns = self._get_basal_embedding(X_batch)
+                zns,_ = self._get_basal_embedding(X_batch)
                 Z.append(tensor_to_numpy(zns))
                 pbar.update(1)
 
@@ -732,7 +736,7 @@ class PerturbFlow(nn.Module):
             alpha = self.encoder_n(xs)
         else:
             #zns,_ = self.encoder_zn(xs)
-            zns = self._get_basal_embedding(xs)
+            zns,_ = self._get_basal_embedding(xs)
             alpha = self.encoder_n(zns)
         return alpha
     
@@ -803,7 +807,7 @@ class PerturbFlow(nn.Module):
     
     def _cell_response(self, xs, factor_idx, perturb):
         #zns,_ = self.encoder_zn(xs)    
-        zns = self._get_basal_embedding(xs)   
+        zns,_ = self._get_basal_embedding(xs)   
         if perturb.ndim==2:
             ms = self.cell_factor_effect[factor_idx]([zns, perturb])
         else:

{sure_tools-2.1.46 → sure_tools-2.1.48}/SURE/perturb/perturb.py

@@ -9,7 +9,7 @@ class LabelMatrix:
     def __init__(self):
         self.labels_ = None
     
-    def fit_transform(self, labels, control_label=None, sep_pattern=r'[;_\-\s]', speedup: Literal['none','vectorize','parallel']='none'):
+    def fit_transform(self, labels, control_label=None, sep_pattern=r'[,;_\s]', speedup: Literal['none','vectorize','parallel']='none'):
         if speedup=='none':
             mat, self.labels_ = label_to_matrix(labels=labels, sep_pattern=sep_pattern)
         elif speedup=='vectorize':

{sure_tools-2.1.46 → sure_tools-2.1.48}/SURE/utils/__init__.py

@@ -7,7 +7,7 @@ from .utils import find_partitions_greedy
 
 from .queue import PriorityQueue
 
-from .custom_mlp import MLP, Exp, ZeroBiasMLP
+from .custom_mlp import MLP, Exp, ZeroBiasMLP, HDMLP
 
 # Importing modules
 #from . import utils

{sure_tools-2.1.46 → sure_tools-2.1.48}/SURE/utils/custom_mlp.py

@@ -241,4 +241,38 @@ class ZeroBiasMLP(nn.Module):
         mask = torch.zeros_like(y)
         mask[x[1][:,0]>0,:] = 1
         return y*mask
-        
+        
+
+class HDMLP(nn.Module):
+    def __init__(
+        self,
+        input_size,
+        hidden_sizes,
+        output_depth,
+        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=[1] + hidden_sizes + [output_depth],
+                       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)
+        self.input_size=input_size
+        self.output_depth=output_depth
+        
+    # pass through our sequential for the output!
+    def forward(self, x):
+        batch_size, n = x.shape
+        x = x.view(batch_size * n, 1)
+        out = self.mlp(x)
+        out = out.view(batch_size, n, self.output_depth)
+        return out

{sure_tools-2.1.46 → sure_tools-2.1.48}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.46
+Version: 2.1.48
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.46 → sure_tools-2.1.48}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='2.1.46',
+    version='2.1.48',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",