SURE-tools 2.1.33__py3-none-any.whl → 2.1.35__py3-none-any.whl

SURE/PerturbFlow.py

@@ -423,12 +423,13 @@ class PerturbFlow(nn.Module):
                 zns = pyro.sample('zn', dist.Gumbel(zn_loc, zn_scale).to_event(1))
 
             if self.cell_factor_size>0:
-                zus = None
-                for i in np.arange(self.cell_factor_size):
-                    if i==0:
-                        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 = None
+                #for i in np.arange(self.cell_factor_size):
+                #    if i==0:
+                #        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)
                 zs = zns+zus
             else:
                 zs = zns
@@ -618,12 +619,13 @@ class PerturbFlow(nn.Module):
                     zns = pyro.sample('zn', dist.Gumbel(zn_loc, zn_scale).to_event(1), obs=embeds)
 
             if self.cell_factor_size>0:
-                zus = None
-                for i in np.arange(self.cell_factor_size):
-                    if i==0:
-                        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 = None
+                #for i in np.arange(self.cell_factor_size):
+                #    if i==0:
+                #        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)
                 zs = zns+zus
             else:
                 zs = zns
@@ -660,6 +662,15 @@ class PerturbFlow(nn.Module):
                 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):
+        zus = None
+        for i in np.arange(self.cell_factor_size):
+            if i==0:
+                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)])
+        return zus
+                        
     def _get_codebook(self):
         I = torch.eye(self.code_size, **self.options)
         if self.latent_dist=='studentt':

SURE/SURE.py

@@ -111,7 +111,6 @@ class SURE(nn.Module):
                  config_enum: str = 'parallel',
                  use_cuda: bool = False,
                  seed: int = 42,
-                 zero_bias: bool = True,
                  dtype = torch.float32, # type: ignore
                  ):
         super().__init__()
@@ -135,7 +134,6 @@ class SURE(nn.Module):
         self.post_layer_fct = post_layer_fct
         self.post_act_fct = post_act_fct
         self.hidden_layer_activation = hidden_layer_activation
-        self.use_bias = not zero_bias
         
         self.codebook_weights = None
 
@@ -234,26 +232,16 @@ class SURE(nn.Module):
         )
 
         if self.cell_factor_size>0:
-            if self.use_bias:
-                self.cell_factor_effect = MLP(
-                    [self.latent_dim + self.cell_factor_size] + self.decoder_hidden_layers + [self.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,
-                )
-            else:
-                self.cell_factor_effect = ZeroBiasMLP(
-                    [self.latent_dim + self.cell_factor_size] + self.decoder_hidden_layers + [self.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.cell_factor_effect = MLP(
+                [self.latent_dim + self.cell_factor_size] + self.decoder_hidden_layers + [self.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.decoder_concentrate = MLP(
                 [self.latent_dim] + self.decoder_hidden_layers + [self.input_size],

SURE/flow/flow_stats.py

@@ -8,26 +8,15 @@ class VectorFieldEval:
     def __init__(self):
         pass 
     
-    def directional_alignment(self, vectors, weighted=False):
-        if weighted:
-            return weighted_alignment(vectors=vectors)
-        else:
-            return directional_alignment(vectors=vectors)
+    def directional_alignment(self, vectors):
+        return weighted_alignment(vectors=vectors)
         
-    def flow_coherence(self, vectors, pca=False):
-        if pca:
-            return pca_based_coherence(vectors=vectors)
-        else:
-            return flow_coherence_index(vectors=vectors)
+    def flow_coherence(self, vectors):
+        return pca_based_coherence(vectors=vectors)
         
     def momentum_flow_metric(self, vectors, masses=None):
         return momentum_flow_metric(vectors=vectors, masses=masses)
-            
-    def multi_scale_coherence(self, vectors, positoins, scale_factors=[1.0, 0.5, 0.1]):
-        return multi_scale_coherence(vectors=vectors, positions=positoins, scale_factors=scale_factors)
-    
-    def vector_field_coherence_score(self, vectors, positions=None, weights=None):
-        return vector_field_coherence_score(vectors=vectors, positions=positions, weights=weights)
+
         
 def calculate_movement_stats(vectors):
     """

{sure_tools-2.1.33.dist-info → sure_tools-2.1.35.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.33
+Version: 2.1.35
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.33.dist-info → sure_tools-2.1.35.dist-info}/RECORD

@@ -1,5 +1,5 @@
-SURE/PerturbFlow.py,sha256=BoaNDubCKpsYJcwipZxrSCpol4nVvCttP28MizHffzY,51650
-SURE/SURE.py,sha256=ghagk4vO3xrAXwdyYTIv7y0X2KXr1R2baXH8lqvUl7k,48094
+SURE/PerturbFlow.py,sha256=4oz02P9kTRNJ897ITR1oOxKYGVw2sgvFKazz2FC-6f0,52118
+SURE/SURE.py,sha256=ko15a9BhvUqHviogZ0YCdTQjM-2zqkO9OvHZSpnGbg0,47458
 SURE/__init__.py,sha256=NOJI_K-eCqPgStXXvgl3wIEMp6d8saMTDYLJ7Ga9MqE,293
 SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
 SURE/assembly/assembly.py,sha256=6IMdelPOiRO4mUb4dC7gVCoF1Uvfw86-Map8P_jnUag,21477
@@ -9,7 +9,7 @@ SURE/atac/utils.py,sha256=m4NYwpy9O5T1pXTzgCOCcmlwrC6GTi-cQ5sm2wZu2O8,4354
 SURE/codebook/__init__.py,sha256=2T5gjp8JIaBayrXAnOJYSebQHsWprOs87difpR1OPNw,243
 SURE/codebook/codebook.py,sha256=ZlN6gRX9Gj2D2u3P5KeOsbZri0MoMAiJo9lNeL-MK-I,17117
 SURE/flow/__init__.py,sha256=rsAjYsh1xVIrxBCuwOE0Q_6N5th1wBgjJceV0ABPG3c,183
-SURE/flow/flow_stats.py,sha256=3F3waCuEbIQ7bsiGga4cUvJphYdWA307SyGwEh8EzM8,10514
+SURE/flow/flow_stats.py,sha256=cBBsPEDpWNMpbzlyQ3f0385RSrX6_5RCH2caOyi4ihM,9908
 SURE/flow/plot_quiver.py,sha256=UbmuScUcgbQHeMmjKmgqxjrIjHhiHx0VWct16UMMwuE,8110
 SURE/perturb/__init__.py,sha256=ouxShhbxZM4r5Gf7GmKiutrsmtyq7QL8rHjhgF0BU08,32
 SURE/perturb/perturb.py,sha256=CqO3xPfNA3cG175tadDidKvGsTu_yKfJRRLn_93awKM,3303
@@ -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-2.1.33.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
-sure_tools-2.1.33.dist-info/METADATA,sha256=7YvSZWWRKzRPZeSR8LwyIlWP1AeT-jtYvnn4FAQFjvE,2651
-sure_tools-2.1.33.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-sure_tools-2.1.33.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
-sure_tools-2.1.33.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
-sure_tools-2.1.33.dist-info/RECORD,,
+sure_tools-2.1.35.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
+sure_tools-2.1.35.dist-info/METADATA,sha256=YFpehlaqDEuAK-0FPQA8AivqA4PJM1kWcEppjSk-p50,2651
+sure_tools-2.1.35.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+sure_tools-2.1.35.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
+sure_tools-2.1.35.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
+sure_tools-2.1.35.dist-info/RECORD,,