SURE-tools 2.1.14__py3-none-any.whl → 2.1.16__py3-none-any.whl

SURE/PerturbFlow.py

@@ -835,6 +835,44 @@ class PerturbFlow(nn.Module):
         R = np.concatenate(R)
         return R
     
+    def _count(self,concentrate):
+        if self.loss_func == 'bernoulli':
+            counts = self.sigmoid(concentrate)
+        else:
+            counts = concentrate.exp()
+        return counts
+    
+    def _count_sample(self,concentrate):
+        if self.loss_func == 'bernoulli':
+            logits = concentrate
+            counts = dist.Bernoulli(logits=logits).to_event(1).sample()
+        else:
+            counts = self._count(concentrate=concentrate)
+            counts = dist.Poisson(rate=counts).to_event(1).sample()
+        return counts
+    
+    def get_counts(self, zs, 
+                        batch_size: int = 1024, 
+                        use_sampler: bool = False):
+
+        zs = convert_to_tensor(zs, device=self.get_device())
+        dataset = CustomDataset(zs)
+        dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=False)
+        
+        E = []
+        with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
+            for Z_batch, _ in dataloader:
+                concentrate = self._expression(Z_batch)
+                if use_sampler:
+                    counts = self._count_sample(concentrate)
+                else:
+                    counts = self._count(concentrate)
+                E.append(tensor_to_numpy(counts))
+                pbar.update(1)
+        
+        E = np.concatenate(E)
+        return E
+    
     def preprocess(self, xs, threshold=0):
         if self.loss_func == 'bernoulli':
             ad = sc.AnnData(xs)

SURE/utils/custom_mlp.py

@@ -85,6 +85,7 @@ class MLP(nn.Module):
         post_act_fct=lambda layer_ix, total_layers, layer: None,
         allow_broadcast=False,
         use_cuda=False,
+        bias=True,
     ):
         # init the module object
         super().__init__()
@@ -114,11 +115,12 @@ class MLP(nn.Module):
             assert type(layer_size) == int, "Hidden layer sizes must be ints"
 
             # get our nn layer module (in this case nn.Linear by default)
-            cur_linear_layer = nn.Linear(last_layer_size, layer_size)
+            cur_linear_layer = nn.Linear(last_layer_size, layer_size, bias=bias)
 
             # for numerical stability -- initialize the layer properly
             cur_linear_layer.weight.data.normal_(0, 0.001)
-            cur_linear_layer.bias.data.normal_(0, 0.001)
+            if bias:
+                cur_linear_layer.bias.data.normal_(0, 0.001)
 
             # use GPUs to share data during training (if available)
             if use_cuda:
@@ -160,7 +162,7 @@ class MLP(nn.Module):
         ), "output_size must be int, list, tuple"
 
         if type(output_size) == int:
-            all_modules.append(nn.Linear(last_layer_size, output_size))
+            all_modules.append(nn.Linear(last_layer_size, output_size, bias=bias))
             if output_activation is not None:
                 all_modules.append(
                     call_nn_op(output_activation)
@@ -179,7 +181,7 @@ class MLP(nn.Module):
                 split_layer = []
 
                 # we have an activation function
-                split_layer.append(nn.Linear(last_layer_size, out_size))
+                split_layer.append(nn.Linear(last_layer_size, out_size, bias=bias))
 
                 # then we get our output activation (either we repeat all or we index into a same sized array)
                 act_out_fct = (

{sure_tools-2.1.14.dist-info → sure_tools-2.1.16.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.14
+Version: 2.1.16
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.14.dist-info → sure_tools-2.1.16.dist-info}/RECORD

@@ -1,4 +1,4 @@
-SURE/PerturbFlow.py,sha256=eW_RUuNd-D4UUY-YhCHklWm0TMdOdfyuzfvwRWwfwAc,49553
+SURE/PerturbFlow.py,sha256=NSNXAct139286O8f8k_NaONIPYB_2sdFmtQ19gtwO6Y,50925
 SURE/SURE.py,sha256=xMD6VBYsgk-bZ_xBWzpdGyxEAleonNRoPkZAxAX467s,47444
 SURE/SURE2.py,sha256=8wlnMwb1xuf9QUksNkWdWx5ZWq-xIy9NLx8RdUnE82o,48501
 SURE/__init__.py,sha256=NOJI_K-eCqPgStXXvgl3wIEMp6d8saMTDYLJ7Ga9MqE,293
@@ -16,12 +16,12 @@ SURE/flow/quiver.py,sha256=_euFqSaRrDoZ_oOabOx20LOoUTJ__XPhLW-vzLNQfAo,1859
 SURE/perturb/__init__.py,sha256=ouxShhbxZM4r5Gf7GmKiutrsmtyq7QL8rHjhgF0BU08,32
 SURE/perturb/perturb.py,sha256=CqO3xPfNA3cG175tadDidKvGsTu_yKfJRRLn_93awKM,3303
 SURE/utils/__init__.py,sha256=Htqv4KqVKcRiaaTBsR-6yZ4LSlbhbzutjNKXGD9-uds,660
-SURE/utils/custom_mlp.py,sha256=07TYX1HgxfEjb_3i5MpiZfNhOhx3dKntuwGkrpteWiM,7036
+SURE/utils/custom_mlp.py,sha256=n0GJj8GKSAqvyokCL_6LugbeedzqLdfBijq24B_I9dA,7113
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-sure_tools-2.1.14.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.1.14.dist-info/METADATA,sha256=b19udVA1bQF9_lsgyWblCnvlp1P3gX-kd_iB7E64hLE,2651
-sure_tools-2.1.14.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.1.14.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.1.14.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.1.14.dist-info/RECORD,,
+sure_tools-2.1.16.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.16.dist-info/METADATA,sha256=Va8l2Qh9jLwOLeiCUDF6Oudx_MqPzN-Opxd6-IMjnRs,2651
+sure_tools-2.1.16.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.16.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.16.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.16.dist-info/RECORD,,