SURE-tools 2.1.92__py3-none-any.whl → 2.2.23__py3-none-any.whl

SURE/{PerturbFlow.py → DensityFlow.py}

@@ -54,18 +54,19 @@ def set_random_seed(seed):
     # Set seed for Pyro
     pyro.set_rng_seed(seed)
 
-class PerturbFlow(nn.Module):
+class DensityFlow(nn.Module):
     def __init__(self,
                  input_size: int,
                  codebook_size: int = 200,
                  cell_factor_size: int = 0,
+                 turn_off_cell_specific: bool = False,
                  supervised_mode: bool = False,
                  z_dim: int = 10,
                  z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'gumbel',
-                 loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'poisson',
+                 loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'multinomial',
                  inverse_dispersion: float = 10.0,
                  use_zeroinflate: bool = False,
-                 hidden_layers: list = [300],
+                 hidden_layers: list = [500],
                  hidden_layer_activation: Literal['relu','softplus','leakyrelu','linear'] = 'relu',
                  nn_dropout: float = 0.1,
                  post_layer_fct: list = ['layernorm'],
@@ -102,6 +103,7 @@ class PerturbFlow(nn.Module):
         else:
             self.use_bias = [not zero_bias] * self.cell_factor_size
         #self.use_bias = not zero_bias
+        self.turn_off_cell_specific = turn_off_cell_specific
         
         self.codebook_weights = None
 
@@ -203,27 +205,51 @@ class PerturbFlow(nn.Module):
             self.cell_factor_effect = nn.ModuleList()
             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],
-                        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,
+                    if self.turn_off_cell_specific:
+                        self.cell_factor_effect.append(MLP(
+                            [1] + 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.append(MLP(
+                            [self.latent_dim+1] + 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.append(ZeroBiasMLP(
-                        [self.latent_dim+1] + 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,
+                    if self.turn_off_cell_specific:
+                        self.cell_factor_effect.append(ZeroBiasMLP(
+                            [1] + 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.append(ZeroBiasMLP(
+                            [self.latent_dim+1] + 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],
@@ -308,7 +334,7 @@ class PerturbFlow(nn.Module):
         return xs
 
     def model1(self, xs):
-        pyro.module('PerturbFlow', self)
+        pyro.module('DensityFlow', self)
 
         eps = torch.finfo(xs.dtype).eps
         batch_size = xs.size(0)
@@ -387,7 +413,7 @@ class PerturbFlow(nn.Module):
             ns = pyro.sample('n', dist.OneHotCategorical(logits=alpha))
 
     def model2(self, xs, us=None):
-        pyro.module('PerturbFlow', self)
+        pyro.module('DensityFlow', self)
 
         eps = torch.finfo(xs.dtype).eps
         batch_size = xs.size(0)
@@ -471,7 +497,7 @@ class PerturbFlow(nn.Module):
             ns = pyro.sample('n', dist.OneHotCategorical(logits=alpha))
 
     def model3(self, xs, ys, embeds=None):
-        pyro.module('PerturbFlow', self)
+        pyro.module('DensityFlow', self)
 
         eps = torch.finfo(xs.dtype).eps
         batch_size = xs.size(0)
@@ -567,7 +593,7 @@ class PerturbFlow(nn.Module):
                 zns = embeds
 
     def model4(self, xs, us, ys, embeds=None):
-        pyro.module('PerturbFlow', self)
+        pyro.module('DensityFlow', self)
 
         eps = torch.finfo(xs.dtype).eps
         batch_size = xs.size(0)
@@ -676,9 +702,17 @@ class PerturbFlow(nn.Module):
         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)])
+                #if self.turn_off_cell_specific:
+                #    zus = self.cell_factor_effect[i](us[:,i].reshape(-1,1))
+                #else:
+                #    zus = self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
+                zus = self._cell_response(zns, i, us[:,i].reshape(-1,1))
             else:
-                zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
+                #if self.turn_off_cell_specific:
+                #    zus = zus + self.cell_factor_effect[i](us[:,i].reshape(-1,1))
+                #else:
+                #    zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
+                zus = zus + self._cell_response(zns, i, us[:,i].reshape(-1,1))
         return zus
                         
     def _get_codebook_identity(self):
@@ -696,7 +730,7 @@ class PerturbFlow(nn.Module):
         """
         Return the mean part of metacell codebook
         """
-        cb = self._get_metacell_coordinates()
+        cb = self._get_codebook()
         cb = tensor_to_numpy(cb)
         return cb
 
@@ -820,13 +854,15 @@ class PerturbFlow(nn.Module):
             us_i = us[:,pert_idx].reshape(-1,1)
             
             # factor effect of xs 
-            dzs0 = self.get_cell_response(xs, factor_idx=pert_idx, perturb=us_i)
+            dzs0 = self.get_cell_response(zs, factor_idx=pert_idx, perturb=us_i)
             
             # perturbation effect 
             ps = np.ones_like(us_i)
-            dzs = self.get_cell_response(xs, factor_idx=pert_idx, perturb=ps)
-            
-            zs = zs + dzs0 + dzs
+            if np.sum(np.abs(ps-us_i))>=1:
+                dzs = self.get_cell_response(zs, factor_idx=pert_idx, perturb=ps)          
+                zs = zs + dzs0 + dzs
+            else:
+                zs = zs + dzs0
         
         if library_sizes is None:
             library_sizes = np.sum(xs, axis=1, keepdims=True)
@@ -840,47 +876,48 @@ class PerturbFlow(nn.Module):
         
         return counts, zs
     
-    def _cell_response(self, xs, factor_idx, perturb):
+    def _cell_response(self, zs, perturb_idx, perturb):
         #zns,_ = self.encoder_zn(xs)    
-        zns,_ = self._get_basal_embedding(xs)   
+        #zns,_ = self._get_basal_embedding(xs)   
+        zns = zs
         if perturb.ndim==2:
-            ms = self.cell_factor_effect[factor_idx]([zns, perturb])
+            if self.turn_off_cell_specific:
+                ms = self.cell_factor_effect[perturb_idx](perturb)
+            else:
+                ms = self.cell_factor_effect[perturb_idx]([zns, perturb])
         else:
-            ms = self.cell_factor_effect[factor_idx]([zns, perturb.reshape(-1,1)])
+            if self.turn_off_cell_specific:
+                ms = self.cell_factor_effect[perturb_idx](perturb.reshape(-1,1))
+            else:
+                ms = self.cell_factor_effect[perturb_idx]([zns, perturb.reshape(-1,1)])
             
         return ms 
 
     def get_cell_response(self, 
-                             xs, 
-                             factor_idx,
-                             perturb,
+                             zs, 
+                             perturb_idx,
+                             perturb_us,
                              batch_size: int = 1024):
         """
         Return cells' changes in the latent space induced by specific perturbation of a factor
 
         """
-        xs = self.preprocess(xs)
-        xs = convert_to_tensor(xs, device=self.get_device())
-        ps = convert_to_tensor(perturb, device=self.get_device())
-        dataset = CustomDataset2(xs,ps)
+        #xs = self.preprocess(xs)
+        zs = convert_to_tensor(zs, device=self.get_device())
+        ps = convert_to_tensor(perturb_us, device=self.get_device())
+        dataset = CustomDataset2(zs,ps)
         dataloader = DataLoader(dataset, batch_size=batch_size, shuffle=False)
 
         Z = []
         with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
-            for X_batch, P_batch, _ in dataloader:
-                zns = self._cell_response(X_batch, factor_idx, P_batch)
+            for Z_batch, P_batch, _ in dataloader:
+                zns = self._cell_response(Z_batch, perturb_idx, P_batch)
                 Z.append(tensor_to_numpy(zns))
                 pbar.update(1)
 
         Z = np.concatenate(Z)
         return Z
     
-    def get_metacell_response(self, factor_idx, perturb):
-        zs = self._get_codebook()
-        ps = convert_to_tensor(perturb, device=self.get_device())         
-        ms = self.cell_factor_effect[factor_idx]([zs,ps])
-        return tensor_to_numpy(ms)
-    
     def _get_expression_response(self, delta_zs):
         return self.decoder_concentrate(delta_zs)
     
@@ -905,7 +942,7 @@ class PerturbFlow(nn.Module):
         R = np.concatenate(R)
         return R
     
-    def _count(self,concentrate, library_size=None):
+    def _count(self, concentrate, library_size=None):
         if self.loss_func == 'bernoulli':
             #counts = self.sigmoid(concentrate)
             counts = dist.Bernoulli(logits=concentrate).to_event(1).mean
@@ -913,28 +950,17 @@ class PerturbFlow(nn.Module):
             rate = concentrate.exp()
             theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
             counts = theta * library_size
-            #counts = dist.Poisson(rate=rate).to_event(1).mean
-        return counts
-    
-    def _count_sample(self,concentrate):
-        if self.loss_func == 'bernoulli':
-            logits = concentrate
-            counts = dist.Bernoulli(logits=logits).to_event(1).sample()
-        else:
-            counts = self._count(concentrate=concentrate)
-            counts = dist.Poisson(rate=counts).to_event(1).sample()
         return counts
     
     def get_counts(self, zs, library_sizes,
-                        batch_size: int = 1024, 
-                        use_sampler: bool = False):
+                        batch_size: int = 1024):
 
         zs = convert_to_tensor(zs, device=self.get_device())
         
         if type(library_sizes) == list:
-            library_sizes = np.array(library_sizes).view(-1,1)
+            library_sizes = np.array(library_sizes).reshape(-1,1)
         elif len(library_sizes.shape)==1:
-            library_sizes = library_sizes.view(-1,1)
+            library_sizes = library_sizes.reshape(-1,1)
         ls = convert_to_tensor(library_sizes, device=self.get_device())
             
         dataset = CustomDataset2(zs,ls)
@@ -944,10 +970,7 @@ class PerturbFlow(nn.Module):
         with tqdm(total=len(dataloader), desc='', unit='batch') as pbar:
             for Z_batch, L_batch, _ in dataloader:
                 concentrate = self._get_expression_response(Z_batch)
-                if use_sampler:
-                    counts = self._count_sample(concentrate)
-                else:
-                    counts = self._count(concentrate, L_batch)
+                counts = self._count(concentrate, L_batch)
                 E.append(tensor_to_numpy(counts))
                 pbar.update(1)
         
@@ -970,7 +993,7 @@ class PerturbFlow(nn.Module):
             us = None, 
             ys = None,
             zs = None,
-            num_epochs: int = 200, 
+            num_epochs: int = 500, 
             learning_rate: float = 0.0001, 
             batch_size: int = 256, 
             algo: Literal['adam','rmsprop','adamw'] = 'adam', 
@@ -981,7 +1004,7 @@ class PerturbFlow(nn.Module):
             threshold: int = 0,
             use_jax: bool = True):
         """
-        Train the PerturbFlow model.
+        Train the DensityFlow model.
 
         Parameters
         ----------
@@ -1007,7 +1030,7 @@ class PerturbFlow(nn.Module):
             Parameter for optimization.
         use_jax
             If toggled on, Jax will be used for speeding up. CAUTION: This will raise errors because of unknown reasons when it is called in
-            the Python script or Jupyter notebook. It is OK if it is used when runing PerturbFlow in the shell command.
+            the Python script or Jupyter notebook. It is OK if it is used when runing DensityFlow in the shell command.
         """
         xs = self.preprocess(xs, threshold=threshold)
         xs = convert_to_tensor(xs, dtype=self.dtype, device=self.get_device())
@@ -1125,12 +1148,12 @@ class PerturbFlow(nn.Module):
 
         
 EXAMPLE_RUN = (
-    "example run: PerturbFlow --help"
+    "example run: DensityFlow --help"
 )
 
 def parse_args():
     parser = argparse.ArgumentParser(
-        description="PerturbFlow\n{}".format(EXAMPLE_RUN))
+        description="DensityFlow\n{}".format(EXAMPLE_RUN))
 
     parser.add_argument(
         "--cuda", action="store_true", help="use GPU(s) to speed up training"
@@ -1317,7 +1340,7 @@ def main():
     cell_factor_size = 0 if us is None else us.shape[1]
 
     ###########################################
-    perturbflow = PerturbFlow(
+    DensityFlow = DensityFlow(
         input_size=input_size,
         cell_factor_size=cell_factor_size,
         inverse_dispersion=args.inverse_dispersion,
@@ -1336,7 +1359,7 @@ def main():
         dtype=dtype,
     )
 
-    perturbflow.fit(xs, us=us, 
+    DensityFlow.fit(xs, us=us, 
              num_epochs=args.num_epochs,
              learning_rate=args.learning_rate,
              batch_size=args.batch_size,
@@ -1348,12 +1371,11 @@ def main():
 
     if args.save_model is not None:
         if args.save_model.endswith('gz'):
-            PerturbFlow.save_model(perturbflow, args.save_model, compression=True)
+            DensityFlow.save_model(DensityFlow, args.save_model, compression=True)
         else:
-            PerturbFlow.save_model(perturbflow, args.save_model)
+            DensityFlow.save_model(DensityFlow, args.save_model)
     
 
 
 if __name__ == "__main__":
-
     main()

SURE/SURE.py

@@ -99,17 +99,17 @@ class SURE(nn.Module):
                  cell_factor_size: int = 0,
                  supervised_mode: bool = False,
                  z_dim: int = 10,
-                 z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'normal',
-                 loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'negbinomial',
+                 z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'gumbel',
+                 loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'poisson',
                  inverse_dispersion: float = 10.0,
                  use_zeroinflate: bool = True,
-                 hidden_layers: list = [300],
+                 hidden_layers: list = [500],
                  hidden_layer_activation: Literal['relu','softplus','leakyrelu','linear'] = 'relu',
                  nn_dropout: float = 0.1,
                  post_layer_fct: list = ['layernorm'],
                  post_act_fct: list = None,
                  config_enum: str = 'parallel',
-                 use_cuda: bool = False,
+                 use_cuda: bool = True,
                  seed: int = 42,
                  dtype = torch.float32, # type: ignore
                  ):
@@ -817,7 +817,7 @@ class SURE(nn.Module):
             us = None, 
             ys = None,
             zs = None,
-            num_epochs: int = 200, 
+            num_epochs: int = 500, 
             learning_rate: float = 0.0001, 
             batch_size: int = 256, 
             algo: Literal['adam','rmsprop','adamw'] = 'adam', 
@@ -826,7 +826,7 @@ class SURE(nn.Module):
             decay_rate: float = 0.9,
             config_enum: str = 'parallel',
             threshold: int = 0,
-            use_jax: bool = False):
+            use_jax: bool = True):
         """
         Train the SURE model.
 

SURE/__init__.py

@@ -1,12 +1,12 @@
 from .SURE import SURE
-from .PerturbFlow import PerturbFlow
+from .DensityFlow import DensityFlow
 
 from . import utils 
 from . import codebook
 from . import SURE
-from . import PerturbFlow
+from . import DensityFlow
 from . import atac
 from . import flow 
 from . import perturb
 
-__all__ = ['SURE', 'PerturbFlow', 'flow', 'perturb', 'atac', 'utils', 'codebook']
+__all__ = ['SURE', 'DensityFlow', 'flow', 'perturb', 'atac', 'utils', 'codebook']

SURE/flow/flow_stats.py

@@ -41,6 +41,18 @@ class VectorFieldEval:
         divergence[np.isnan(divergence)] = 0
         
         return divergence
+    
+    def movement_stats(self,vectors):
+        return calculate_movement_stats(vectors)
+    
+    def direction_stats(self, vectors):
+        return calculate_direction_stats(vectors)
+    
+    def movement_energy(self, vectors, masses=None):
+        return calculate_movement_energy(vectors, masses)
+    
+    def movement_divergence(self, positions, vectors):
+        return calculate_movement_divergence(positions, vectors)
 
         
 def calculate_movement_stats(vectors):

SURE/perturb/perturb.py

@@ -1,5 +1,6 @@
 import re
 import numpy as np
+import pandas as pd
 from numba import njit
 from itertools import chain
 from joblib import Parallel, delayed
@@ -8,6 +9,8 @@ from typing import Literal
 class LabelMatrix:
     def __init__(self):
         self.labels_ = None
+        self.control_label = None 
+        self.sep_pattern = None
     
     def fit_transform(self, labels, control_label=None, sep_pattern=r'[,;_\s]', speedup: Literal['none','vectorize','parallel']='none'):
         if speedup=='none':
@@ -24,8 +27,31 @@ class LabelMatrix:
             mat = np.delete(mat, idx, axis=1)
             self.labels_ = np.delete(self.labels_, idx)
             
+        self.control_label = control_label
+        self.sep_pattern=sep_pattern
+        
         return mat
-            
+    
+    def transform(self, labels, speedup: Literal['none','vectorize','parallel']='none'):
+        sep_pattern = self.sep_pattern
+        if speedup=='none':
+            mat, labels_ = label_to_matrix(labels=labels, sep_pattern=sep_pattern)
+        elif speedup=='vectorize':
+            mat, labels_ = vectorized_label_to_matrix(labels=labels, sep_pattern=sep_pattern)
+        elif speedup=='parallel':
+            mat, labels_ = parallel_label_to_matrix(labels=labels, sep_pattern=sep_pattern)
+          
+        mat_df = pd.DataFrame(mat, columns=labels_)
+        
+        labels_valid = [x for x in labels_ if x in self.labels_]  
+        mat_df = mat_df[labels_valid]
+        
+        mat_valid = np.zeros([mat.shape[0], len(self.labels_)])
+        mat_valid_df = pd.DataFrame(mat_valid, columns=self.labels_)
+        mat_valid_df[labels_valid] = mat_df 
+        
+        return mat_valid_df.values
+        
     def inverse_transform(self, matrix):
         return matrix_to_labels(matrix=matrix, unique_labels=self.labels_)
 

{sure_tools-2.1.92.dist-info → sure_tools-2.2.23.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: SURE-tools
-Version: 2.1.92
+Version: 2.2.23
 Summary: Succinct Representation of Single Cells
 Home-page: https://github.com/ZengFLab/SURE
 Author: Feng Zeng

{sure_tools-2.1.92.dist-info → sure_tools-2.2.23.dist-info}/RECORD

@@ -1,6 +1,6 @@
-SURE/PerturbFlow.py,sha256=kVpEdVgW_AGvvv7d1KnnBydx_hGfpXUXmFg4t4dPlwY,54677
-SURE/SURE.py,sha256=g8EhovBxjfpbVJA0AkmVkQ_ZW_JFc8TtkTCg8FCybV4,47750
-SURE/__init__.py,sha256=NOJI_K-eCqPgStXXvgl3wIEMp6d8saMTDYLJ7Ga9MqE,293
+SURE/DensityFlow.py,sha256=p5Pt3KrsdF_NTLFx0p1cUPuXkIac6wQED1LsLJRG7mI,56124
+SURE/SURE.py,sha256=MXs7iuvcj-lU4dJ_MwKegpL2Rqk2HB4eFfAgHRA3RtA,47744
+SURE/__init__.py,sha256=NVp22RCHrhSwHNMomABC-eftoCYvt7vV1XOzim-UZHE,293
 SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
 SURE/assembly/assembly.py,sha256=6IMdelPOiRO4mUb4dC7gVCoF1Uvfw86-Map8P_jnUag,21477
 SURE/assembly/atlas.py,sha256=ALjmVWutm_tOHTcT1aqOxmuCEQw-XzrtDoMCV_8oXLk,21794
@@ -9,17 +9,17 @@ 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=_pF7m4-87SKlCHVtVmx3LG2bAGVXOnAfEgMzLhLx4Io,10910
+SURE/flow/flow_stats.py,sha256=6SzNMT59WRFRP1nC6bvpBPF7BugWnkIS_DSlr4S-Ez0,11338
 SURE/flow/plot_quiver.py,sha256=UbmuScUcgbQHeMmjKmgqxjrIjHhiHx0VWct16UMMwuE,8110
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