SURE-tools 2.1.50__py3-none-any.whl → 2.1.52__py3-none-any.whl

SURE/PerturbFlow.py

@@ -64,7 +64,7 @@ class PerturbFlow(nn.Module):
                  z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'normal',
                  loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'negbinomial',
                  inverse_dispersion: float = 10.0,
-                 use_zeroinflate: bool = True,
+                 use_zeroinflate: bool = False,
                  hidden_layers: list = [300],
                  hidden_layer_activation: Literal['relu','softplus','leakyrelu','linear'] = 'relu',
                  nn_dropout: float = 0.1,
@@ -872,9 +872,18 @@ class PerturbFlow(nn.Module):
     
     def _count(self,concentrate):
         if self.loss_func == 'bernoulli':
-            counts = self.sigmoid(concentrate)
-        else:
-            counts = concentrate.exp()
+            #counts = self.sigmoid(concentrate)
+            counts = dist.Bernoulli(logits=concentrate).to_event(1).mean
+        elif self.loss_func == 'negbinomial':
+            #counts = concentrate.exp()
+            rate = concentrate.exp()
+            theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
+            
+            total_count = pyro.param("inverse_dispersion")
+            counts = dist.NegativeBinomial(total_count=total_count, probs=theta).to_event(1)
+        elif self.loss_func == 'poisson':
+            rate = concentrate.exp()
+            counts = dist.Poisson(rate=rate).to_event(1)
         return counts
     
     def _count_sample(self,concentrate):
@@ -933,7 +942,7 @@ class PerturbFlow(nn.Module):
             decay_rate: float = 0.9,
             config_enum: str = 'parallel',
             threshold: int = 0,
-            use_jax: bool = False):
+            use_jax: bool = True):
         """
         Train the PerturbFlow model.
 

{sure_tools-2.1.50.dist-info → sure_tools-2.1.52.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.50
+Version: 2.1.52
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.50.dist-info → sure_tools-2.1.52.dist-info}/RECORD

@@ -1,4 +1,4 @@
-SURE/PerturbFlow.py,sha256=LkJjaMgfklSIEOtC6AY7vOc097d3kHeb94cenuiQv3c,52680
+SURE/PerturbFlow.py,sha256=yt0kOW4buZKpJQ3Jn_8Zd2uEKUq29DZYkSzcgEP55EA,53211
 SURE/SURE.py,sha256=ko15a9BhvUqHviogZ0YCdTQjM-2zqkO9OvHZSpnGbg0,47458
 SURE/__init__.py,sha256=NOJI_K-eCqPgStXXvgl3wIEMp6d8saMTDYLJ7Ga9MqE,293
 SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
@@ -17,9 +17,9 @@ SURE/utils/__init__.py,sha256=YF5jB-PAHJQ40OlcZ7BCZbsN2q1JKuPT6EppilRXQqM,680
 SURE/utils/custom_mlp.py,sha256=C0EXLGYsWkUQpEL49AyBFPSzKmasb2hdvtnJfxbF-YU,9282
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-sure_tools-2.1.50.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.1.50.dist-info/METADATA,sha256=afFokguRAzf-MDZvkzmf-w5Uyj1RplSsJ8dHgNR7QXQ,2678
-sure_tools-2.1.50.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.1.50.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.1.50.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.1.50.dist-info/RECORD,,
+sure_tools-2.1.52.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.52.dist-info/METADATA,sha256=ARO36IQ9aKV9Sp4F9AkLR6zzXSsPnMGguljP7XU95Mk,2678
+sure_tools-2.1.52.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.52.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.52.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.52.dist-info/RECORD,,