SURE-tools 3.6.11__tar.gz → 3.6.13__tar.gz

{sure_tools-3.6.11 → sure_tools-3.6.13}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 3.6.11
+Version: 3.6.13
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-3.6.11 → sure_tools-3.6.13}/SURE/SURE_nsf.py

@@ -168,7 +168,7 @@ class SURENF(nn.Module):
         self.use_mask = False 
         self.mask_ratio = 0
 
-        self.kmeans = None
+        self.kmeans = KMeans(n_clusters=codebook_size)
         self.seed = seed
         
         set_random_seed(seed)
@@ -593,8 +593,8 @@ class SURENF(nn.Module):
         return A
     
     def predict_cluster(self, xs, batch_size=1024, show_progress=True):
-        ns = self.hard_assignments(xs, batch_size=batch_size, show_progress=show_progress)
-        return np.argmax(ns, axis=1)
+        zs = self.get_cell_embedding(xs, batch_size=batch_size, show_progress=show_progress)
+        return self.kmeans.predict(zs)
     
     def predict(self, xs, cs, batch_size=1024, show_progress=True):
         """
@@ -1013,9 +1013,8 @@ class SURENF(nn.Module):
                     print("Restored model and optimizer states from best epoch.")
                     
         zs = self.get_cell_embedding(xs, show_progress=False)
-        ns = self.soft_assignments(xs, show_progress=False).T
-        ns = ns / np.sum(ns, axis=1, keepdims=True)
-        self.codebook_loc = ns @ zs
+        self.kmeans.fit(zs)
+        self.codebook_loc = self.kmeans.cluster_centers_
 
     def get_model_and_optimizer_state(self, scheduler=None):
         """获取模型和优化器的完整状态"""

{sure_tools-3.6.11 → sure_tools-3.6.13}/SURE/SURE_vae.py

@@ -169,7 +169,7 @@ class SUREVAE(nn.Module):
         self.transforms = transforms
         self.flow_hidden_layers = flow_hidden_layers
         
-        self.kmeans = None
+        self.kmeans = KMeans(n_clusters=codebook_size)
         self.seed = seed
 
         set_random_seed(seed)
@@ -593,10 +593,9 @@ class SUREVAE(nn.Module):
                 X_batch = X_batch.to(self.get_device())
                 C_batch = cs[idx].to(self.get_device())
                 
-                #_,ind = self._hard_assignments(X_batch)
-                #z_basal = cb_loc[ind.squeeze()]
-                ns = self._soft_assignments(X_batch)
-                z_basal = torch.matmul(ns, cb_loc)
+                #ns = self._soft_assignments(X_batch)
+                #z_basal = torch.matmul(ns, cb_loc)
+                z_basal = self._get_cell_embedding(X_batch)
                 dzs = self.condition_effect([C_batch,z_basal])
                 
                 A.append(tensor_to_numpy(dzs))
@@ -606,8 +605,8 @@ class SUREVAE(nn.Module):
         return A
         
     def predict_cluster(self, xs, batch_size=1024, show_progress=True):
-        ns = self.hard_assignments(xs, batch_size=batch_size, show_progress=show_progress)
-        return np.argmax(ns, axis=1)
+        zs = self.get_cell_embedding(xs, batch_size=batch_size, show_progress=show_progress)
+        return self.kmeans.predict(zs)
     
     def predict(self, xs, cs, batch_size=1024, show_progress=True):
         """
@@ -945,9 +944,8 @@ class SUREVAE(nn.Module):
                     print("Restored model and optimizer states from best epoch.")
         
         zs = self.get_cell_embedding(xs, show_progress=False)        
-        ns = self.soft_assignments(xs, show_progress=False).T
-        ns = ns / np.sum(ns, axis=1, keepdims=True)
-        self.codebook_loc = ns @ zs
+        self.kmeans.fit(zs)
+        self.codebook_loc = self.kmeans.cluster_centers_
 
     def get_model_and_optimizer_state(self, scheduler=None):
         """获取模型和优化器的完整状态"""

{sure_tools-3.6.11 → sure_tools-3.6.13}/SURE_tools.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 3.6.11
+Version: 3.6.13
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-3.6.11 → sure_tools-3.6.13}/setup.py

@@ -5,7 +5,7 @@ with open("README.md", "r") as fh:
 
 setup(
     name='SURE-tools',
-    version='3.6.11',
+    version='3.6.13',
     description='Succinct Representation of Single Cells',
     long_description=long_description,
     long_description_content_type="text/markdown",