SURE-tools 2.1.81__py3-none-any.whl → 2.1.83__py3-none-any.whl

SURE/PerturbFlow.py

@@ -204,7 +204,7 @@ class PerturbFlow(nn.Module):
             for i in np.arange(self.cell_factor_size):
                 if self.use_bias[i]:
                     self.cell_factor_effect.append(MLP(
-                        [self.latent_dim+1] + self.decoder_hidden_layers + [self.latent_dim],
+                        [self.code_size+1] + self.decoder_hidden_layers + [self.latent_dim],
                         activation=activate_fct,
                         output_activation=None,
                         post_layer_fct=post_layer_fct,
@@ -215,7 +215,7 @@ class PerturbFlow(nn.Module):
                     )
                 else:
                     self.cell_factor_effect.append(ZeroBiasMLP(
-                        [self.latent_dim+1] + self.decoder_hidden_layers + [self.latent_dim],
+                        [self.code_size+1] + self.decoder_hidden_layers + [self.latent_dim],
                         activation=activate_fct,
                         output_activation=None,
                         post_layer_fct=post_layer_fct,
@@ -429,7 +429,7 @@ class PerturbFlow(nn.Module):
                 zns = pyro.sample('zn', dist.Gumbel(zn_loc, zn_scale).to_event(1))
 
             if self.cell_factor_size>0:
-                zus = self._total_effects(zns, us)
+                zus = self._total_effects(ns, us)
                 zs = zns+zus
             else:
                 zs = zns
@@ -631,7 +631,7 @@ class PerturbFlow(nn.Module):
                 #        zus = self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
                 #    else:
                 #        zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
-                zus = self._total_effects(zns, us)
+                zus = self._total_effects(ns, us)
                 zs = zns+zus
             else:
                 zs = zns
@@ -681,6 +681,9 @@ class PerturbFlow(nn.Module):
                 zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
         return zus
                         
+    def _get_codebook_identity(self):
+        return torch.eye(self.code_size, **self.options)
+    
     def _get_codebook(self):
         I = torch.eye(self.code_size, **self.options)
         if self.latent_dist=='studentt':
@@ -839,7 +842,8 @@ class PerturbFlow(nn.Module):
     
     def _cell_response(self, xs, factor_idx, perturb):
         #zns,_ = self.encoder_zn(xs)    
-        zns,_ = self._get_basal_embedding(xs)   
+        #zns,_ = self._get_basal_embedding(xs)   
+        zns = self._soft_assignments(xs)
         if perturb.ndim==2:
             ms = self.cell_factor_effect[factor_idx]([zns, perturb])
         else:
@@ -873,7 +877,8 @@ class PerturbFlow(nn.Module):
         return Z
     
     def get_metacell_response(self, factor_idx, perturb):
-        zs = self._get_codebook()
+        #zs = self._get_codebook()
+        zs = self._get_codebook_identity()
         ps = convert_to_tensor(perturb, device=self.get_device())         
         ms = self.cell_factor_effect[factor_idx]([zs,ps])
         return tensor_to_numpy(ms)

{sure_tools-2.1.81.dist-info → sure_tools-2.1.83.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.81
+Version: 2.1.83
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.81.dist-info → sure_tools-2.1.83.dist-info}/RECORD

@@ -1,4 +1,4 @@
-SURE/PerturbFlow.py,sha256=Hi7oF9S_eImo2Q-Oxu0mW461DHOG0O05TIE_pUW3uJo,54577
+SURE/PerturbFlow.py,sha256=5HzS8oB06iSR3JM5AalGfYi-quxbjkTZeTypjih-VBI,54759
 SURE/SURE.py,sha256=g8EhovBxjfpbVJA0AkmVkQ_ZW_JFc8TtkTCg8FCybV4,47750
 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-2.1.81.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.1.81.dist-info/METADATA,sha256=uEiJyslzIPEZ_4HfoTR9JLtBuIfmAPH-HIu2Ar2dKg0,2678
-sure_tools-2.1.81.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.1.81.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.1.81.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.1.81.dist-info/RECORD,,
+sure_tools-2.1.83.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.83.dist-info/METADATA,sha256=H-q3GA7c-UxJp8C3OfR-f7YpSkhqaSQD3oZ_qcg9OJo,2678
+sure_tools-2.1.83.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.83.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.83.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.83.dist-info/RECORD,,