SURE-tools 2.1.51__py3-none-any.whl → 2.1.53__py3-none-any.whl

SURE/PerturbFlow.py

@@ -317,12 +317,14 @@ class PerturbFlow(nn.Module):
         if self.loss_func=='negbinomial':
             total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
                                      xs.new_ones(self.input_size), constraint=constraints.positive)
+        elif self.loss_func == 'multinomial':
+            total_count = pyro.param('total_count', int(1e8), constraint=constraints.positive_integer)
             
         if self.use_zeroinflate:
             gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
             
         acs_scale = pyro.param("codebook_scale", xs.new_ones(self.latent_dim), constraint=constraints.positive)
-
+        
         I = torch.eye(self.code_size)
         if self.latent_dist=='studentt':
             acs_dof,acs_loc = self.codebook(I)
@@ -369,7 +371,7 @@ class PerturbFlow(nn.Module):
                 else:
                     pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
             elif self.loss_func == 'multinomial':
-                pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
+                pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
             elif self.loss_func == 'bernoulli':
                 if self.use_zeroinflate:
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
@@ -395,6 +397,8 @@ class PerturbFlow(nn.Module):
         if self.loss_func=='negbinomial':
             total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
                                      xs.new_ones(self.input_size), constraint=constraints.positive)
+        elif self.loss_func == 'multinomial':
+            total_count = pyro.param('total_count', int(1e8), constraint=constraints.positive_integer)
             
         if self.use_zeroinflate:
             gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -458,7 +462,7 @@ class PerturbFlow(nn.Module):
                 else:
                     pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
             elif self.loss_func == 'multinomial':
-                pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
+                pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
             elif self.loss_func == 'bernoulli':
                 if self.use_zeroinflate:
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
@@ -484,6 +488,8 @@ class PerturbFlow(nn.Module):
         if self.loss_func=='negbinomial':
             total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
                                      xs.new_ones(self.input_size), constraint=constraints.positive)
+        elif self.loss_func == 'multinomial':
+            total_count = pyro.param('total_count', int(1e8), constraint=constraints.positive_integer)
             
         if self.use_zeroinflate:
             gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -553,7 +559,7 @@ class PerturbFlow(nn.Module):
                 else:
                     pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
             elif self.loss_func == 'multinomial':
-                pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
+                pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
             elif self.loss_func == 'bernoulli':
                 if self.use_zeroinflate:
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
@@ -577,6 +583,8 @@ class PerturbFlow(nn.Module):
         if self.loss_func=='negbinomial':
             total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
                                      xs.new_ones(self.input_size), constraint=constraints.positive)
+        elif self.loss_func == 'multinomial':
+            total_count = pyro.param('total_count', int(1e8), constraint=constraints.positive_integer)
             
         if self.use_zeroinflate:
             gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -656,7 +664,7 @@ class PerturbFlow(nn.Module):
                 else:
                     pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
             elif self.loss_func == 'multinomial':
-                pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
+                pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
             elif self.loss_func == 'bernoulli':
                 if self.use_zeroinflate:
                     pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
@@ -872,9 +880,18 @@ 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):

{sure_tools-2.1.51.dist-info → sure_tools-2.1.53.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.51
+Version: 2.1.53
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.51.dist-info → sure_tools-2.1.53.dist-info}/RECORD

@@ -1,4 +1,4 @@
-SURE/PerturbFlow.py,sha256=qQYCKLf50KA8xuPBffOen-e04wMEi3ASeDVv-BPbvxc,52680
+SURE/PerturbFlow.py,sha256=JS0TguFFewNU6lwFLI0rtJsPUkDcHWFpN2USuBB1dL8,53827
 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-2.1.51.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.1.51.dist-info/METADATA,sha256=xurQhmv-0FHHED3zJ-fQyuWfK4-kkxLhdlOvbeyc96Q,2678
-sure_tools-2.1.51.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.1.51.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.1.51.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.1.51.dist-info/RECORD,,
+sure_tools-2.1.53.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.53.dist-info/METADATA,sha256=wNhmVGxxzIeL38Nb2VXIAJC6zX_jK3SgFqnqCd56ajA,2678
+sure_tools-2.1.53.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.53.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.53.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.53.dist-info/RECORD,,