SURE-tools 2.1.44__py3-none-any.whl → 2.1.45__py3-none-any.whl

SURE/PerturbFlow.py

@@ -189,29 +189,10 @@ class PerturbFlow(nn.Module):
                 use_cuda=self.use_cuda,
             )
 
-        #self.encoder_zn = MLP(
-        #    [self.input_size] + hidden_sizes + [[latent_dim, latent_dim]],
-        #    activation=activate_fct,
-        #    output_activation=[None, Exp],
-        #    post_layer_fct=post_layer_fct,
-        #    post_act_fct=post_act_fct,
-        #    allow_broadcast=self.allow_broadcast,
-        #    use_cuda=self.use_cuda,
-        #)
-        
-        self.encoder_zn_loc = MLP(
-            [self.input_size] + hidden_sizes + [self.input_size * latent_dim],
-            activation=activate_fct,
-            output_activation=None,
-            post_layer_fct=post_layer_fct,
-            post_act_fct=post_act_fct,
-            allow_broadcast=self.allow_broadcast,
-            use_cuda=self.use_cuda,
-        )
-        self.encoder_zn_scale = MLP(
-            [self.input_size] + hidden_sizes + [latent_dim],
+        self.encoder_zn = MLP(
+            [self.input_size] + hidden_sizes + [[latent_dim, latent_dim]],
             activation=activate_fct,
-            output_activation=Exp,
+            output_activation=[None, Exp],
             post_layer_fct=post_layer_fct,
             post_act_fct=post_act_fct,
             allow_broadcast=self.allow_broadcast,
@@ -397,11 +378,7 @@ class PerturbFlow(nn.Module):
 
     def guide1(self, xs):
         with pyro.plate('data'):
-            batch_size = xs.shape[0]
-            #zn_loc, zn_scale = self.encoder_zn(xs)
-            zn_loc, zn_scale = self.encoder_zn_loc(xs), self.encoder_zn_scale(xs)
-            zn_loc_3d = zn_loc.view(batch_size, self.input_size, self.latent_dim)
-            zn_loc = zn_loc_3d.sum(dim=1)
+            zn_loc, zn_scale = self.encoder_zn(xs)
             zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
             alpha = self.encoder_n(zns)
@@ -489,11 +466,7 @@ class PerturbFlow(nn.Module):
 
     def guide2(self, xs, us=None):
         with pyro.plate('data'):
-            batch_size = xs.shape[0]
-            #zn_loc, zn_scale = self.encoder_zn(xs)
-            zn_loc, zn_scale = self.encoder_zn_loc(xs), self.encoder_zn_scale(xs)
-            zn_loc_3d = zn_loc.view(batch_size, self.input_size, self.latent_dim)
-            zn_loc = zn_loc_3d.sum(dim=1)
+            zn_loc, zn_scale = self.encoder_zn(xs)
             zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
             alpha = self.encoder_n(zns)
@@ -588,11 +561,7 @@ class PerturbFlow(nn.Module):
     def guide3(self, xs, ys, embeds=None):
         with pyro.plate('data'):
             if embeds is None:
-                batch_size = xs.shape[0]
-                #zn_loc, zn_scale = self.encoder_zn(xs)
-                zn_loc, zn_scale = self.encoder_zn_loc(xs), self.encoder_zn_scale(xs)
-                zn_loc_3d = zn_loc.view(batch_size, self.input_size, self.latent_dim)
-                zn_loc = zn_loc_3d.sum(dim=1)
+                zn_loc, zn_scale = self.encoder_zn(xs)
                 zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
     def model4(self, xs, us, ys, embeds=None):
@@ -694,11 +663,7 @@ class PerturbFlow(nn.Module):
     def guide4(self, xs, us, ys, embeds=None):
         with pyro.plate('data'):
             if embeds is None:
-                batch_size = xs.shape[0]
-                #zn_loc, zn_scale = self.encoder_zn(xs)
-                zn_loc, zn_scale = self.encoder_zn_loc(xs), self.encoder_zn_scale(xs)
-                zn_loc_3d = zn_loc.view(batch_size, self.input_size, self.latent_dim)
-                zn_loc = zn_loc_3d.sum(dim=1)
+                zn_loc, zn_scale = self.encoder_zn(xs)
                 zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
 
     def _total_effects(self, zns, us):
@@ -727,11 +692,7 @@ class PerturbFlow(nn.Module):
         return cb
 
     def _get_basal_embedding(self, xs):           
-        #zns, _ = self.encoder_zn(xs)
-        batch_size = xs.shape[0]
-        zns = self.encoder_zn_loc(xs)
-        zns_3d = zns.view(batch_size, self.input_size, self.latent_dim)
-        zns = zns_3d.sum(dim=1)
+        zns, _ = self.encoder_zn(xs)
         return zns 
     
     def get_basal_embedding(self, 

{sure_tools-2.1.44.dist-info → sure_tools-2.1.45.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.44
+Version: 2.1.45
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.44.dist-info → sure_tools-2.1.45.dist-info}/RECORD

@@ -1,4 +1,4 @@
-SURE/PerturbFlow.py,sha256=EbbEQBf9HQ6XeUw3g4DKFbe2IVCJRGmCwjQcHwCnQxU,54309
+SURE/PerturbFlow.py,sha256=EjBvHUNmQeyF41H-rzg7fSrcKo9_ts2za-JiMRp4y9M,52394
 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=QJUOfrXzdWSmoM0P3LH8oKEHttzCWqpDy2UF0F0dtN4,673
 SURE/utils/custom_mlp.py,sha256=rHnx9jEef02zfCUdbYVCmbuHcDdIBmRgt__wpdpZvYg,8104
 SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
 SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
-sure_tools-2.1.44.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.1.44.dist-info/METADATA,sha256=GOqZOvGRfh--3bd3Bgpkiv7E05gfRoDNflkE3c4Mt6s,2651
-sure_tools-2.1.44.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.1.44.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.1.44.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.1.44.dist-info/RECORD,,
+sure_tools-2.1.45.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.45.dist-info/METADATA,sha256=y0VumQ_zuHF_45Mo2MKKap2J_l4rGEzHiYLSxuq1isw,2651
+sure_tools-2.1.45.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.45.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.45.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.45.dist-info/RECORD,,