SURE-tools 2.1.57__py3-none-any.whl → 2.1.59__py3-none-any.whl

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Files changed (7) hide show
  1. SURE/PerturbFlow.py +38 -134
  2. {sure_tools-2.1.57.dist-info → sure_tools-2.1.59.dist-info}/METADATA +1 -1
  3. {sure_tools-2.1.57.dist-info → sure_tools-2.1.59.dist-info}/RECORD +7 -7
  4. {sure_tools-2.1.57.dist-info → sure_tools-2.1.59.dist-info}/WHEEL +0 -0
  5. {sure_tools-2.1.57.dist-info → sure_tools-2.1.59.dist-info}/entry_points.txt +0 -0
  6. {sure_tools-2.1.57.dist-info → sure_tools-2.1.59.dist-info}/licenses/LICENSE +0 -0
  7. {sure_tools-2.1.57.dist-info → sure_tools-2.1.59.dist-info}/top_level.txt +0 -0
SURE/PerturbFlow.py CHANGED
@@ -62,7 +62,7 @@ class PerturbFlow(nn.Module):
62
62
  supervised_mode: bool = False,
63
63
  z_dim: int = 10,
64
64
  z_dist: Literal['normal','studentt','laplacian','cauchy','gumbel'] = 'normal',
65
- loss_func: Literal['negbinomial','poisson','multinomial','bernoulli','gamma-poisson'] = 'negbinomial',
65
+ loss_func: Literal['negbinomial','poisson','multinomial','bernoulli'] = 'multinomial',
66
66
  inverse_dispersion: float = 10.0,
67
67
  use_zeroinflate: bool = False,
68
68
  hidden_layers: list = [300],
@@ -225,28 +225,7 @@ class PerturbFlow(nn.Module):
225
225
  )
226
226
  )
227
227
 
228
- if self.loss_func == 'gamma-poisson':
229
- self.decoder_concentrate = MLP(
230
- [self.latent_dim] + self.decoder_hidden_layers + [[self.input_size,self.input_size]],
231
- activation=activate_fct,
232
- output_activation=[Exp,Exp],
233
- post_layer_fct=post_layer_fct,
234
- post_act_fct=post_act_fct,
235
- allow_broadcast=self.allow_broadcast,
236
- use_cuda=self.use_cuda,
237
- )
238
- #self.encoder_concentrate = MLP(
239
- # [self.latent_dim] + self.decoder_hidden_layers + [[self.input_size,self.input_size]],
240
- # activation=activate_fct,
241
- # output_activation=[Exp,Exp],
242
- # post_layer_fct=post_layer_fct,
243
- # post_act_fct=post_act_fct,
244
- # allow_broadcast=self.allow_broadcast,
245
- # use_cuda=self.use_cuda,
246
- # )
247
- #self.encoder_concentrate = self.decoder_concentrate
248
- else:
249
- self.decoder_concentrate = MLP(
228
+ self.decoder_concentrate = MLP(
250
229
  [self.latent_dim] + self.decoder_hidden_layers + [self.input_size],
251
230
  activation=activate_fct,
252
231
  output_activation=None,
@@ -338,8 +317,6 @@ class PerturbFlow(nn.Module):
338
317
  if self.loss_func=='negbinomial':
339
318
  total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
340
319
  xs.new_ones(self.input_size), constraint=constraints.positive)
341
- elif self.loss_func == 'multinomial':
342
- total_count = pyro.param('total_count', int(1e8), constraint=constraints.positive_integer)
343
320
 
344
321
  if self.use_zeroinflate:
345
322
  gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -373,19 +350,14 @@ class PerturbFlow(nn.Module):
373
350
  zns = pyro.sample('zn', dist.Gumbel(zn_loc, zn_scale).to_event(1))
374
351
 
375
352
  zs = zns
376
- if self.loss_func == 'gamma-poisson':
377
- con_alpha,con_beta = self.decoder_concentrate(zs)
378
- rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
353
+ concentrate = self.decoder_concentrate(zs)
354
+ if self.loss_func in ['bernoulli','negbinomial']:
355
+ log_theta = concentrate
379
356
  else:
380
- concentrate = self.decoder_concentrate(zs)
381
- if self.loss_func == 'bernoulli':
382
- log_theta = concentrate
383
- elif self.loss_func == 'negbinomial':
384
- log_theta = concentrate
385
- else:
386
- rate = concentrate.exp()
387
- if self.loss_func != 'poisson':
388
- theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
357
+ rate = concentrate.exp()
358
+ theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
359
+ if self.loss_func == 'poisson':
360
+ rate = theta * torch.sum(xs, dim=1, keepdim=True)
389
361
 
390
362
  if self.loss_func == 'negbinomial':
391
363
  if self.use_zeroinflate:
@@ -397,13 +369,8 @@ class PerturbFlow(nn.Module):
397
369
  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
398
370
  else:
399
371
  pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
400
- elif self.loss_func == 'gamma-poisson':
401
- if self.use_zeroinflate:
402
- pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
403
- else:
404
- pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
405
372
  elif self.loss_func == 'multinomial':
406
- pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
373
+ pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
407
374
  elif self.loss_func == 'bernoulli':
408
375
  if self.use_zeroinflate:
409
376
  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
@@ -418,10 +385,6 @@ class PerturbFlow(nn.Module):
418
385
 
419
386
  alpha = self.encoder_n(zns)
420
387
  ns = pyro.sample('n', dist.OneHotCategorical(logits=alpha))
421
-
422
- #if self.loss_func == 'gamma-poisson':
423
- # con_alpha,con_beta = self.encoder_concentrate(zns)
424
- # rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
425
388
 
426
389
  def model2(self, xs, us=None):
427
390
  pyro.module('PerturbFlow', self)
@@ -433,8 +396,6 @@ class PerturbFlow(nn.Module):
433
396
  if self.loss_func=='negbinomial':
434
397
  total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
435
398
  xs.new_ones(self.input_size), constraint=constraints.positive)
436
- elif self.loss_func == 'multinomial':
437
- total_count = pyro.param('total_count', int(1e8), constraint=constraints.positive_integer)
438
399
 
439
400
  if self.use_zeroinflate:
440
401
  gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -468,30 +429,19 @@ class PerturbFlow(nn.Module):
468
429
  zns = pyro.sample('zn', dist.Gumbel(zn_loc, zn_scale).to_event(1))
469
430
 
470
431
  if self.cell_factor_size>0:
471
- #zus = None
472
- #for i in np.arange(self.cell_factor_size):
473
- # if i==0:
474
- # zus = self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
475
- # else:
476
- # zus = zus + self.cell_factor_effect[i]([zns,us[:,i].reshape(-1,1)])
477
432
  zus = self._total_effects(zns, us)
478
433
  zs = zns+zus
479
434
  else:
480
435
  zs = zns
481
436
 
482
- if self.loss_func == 'gamma-poisson':
483
- con_alpha,con_beta = self.decoder_concentrate(zs)
484
- rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
437
+ concentrate = self.decoder_concentrate(zs)
438
+ if self.loss_func in ['bernoulli','negbinomial']:
439
+ log_theta = concentrate
485
440
  else:
486
- concentrate = self.decoder_concentrate(zs)
487
- if self.loss_func == 'bernoulli':
488
- log_theta = concentrate
489
- elif self.loss_func == 'negbinomial':
490
- log_theta = concentrate
491
- else:
492
- rate = concentrate.exp()
493
- if self.loss_func != 'poisson':
494
- theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
441
+ rate = concentrate.exp()
442
+ theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
443
+ if self.loss_func == 'poisson':
444
+ rate = theta * torch.sum(xs, dim=1, keepdim=True)
495
445
 
496
446
  if self.loss_func == 'negbinomial':
497
447
  if self.use_zeroinflate:
@@ -503,13 +453,8 @@ class PerturbFlow(nn.Module):
503
453
  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
504
454
  else:
505
455
  pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
506
- elif self.loss_func == 'gamma-poisson':
507
- if self.use_zeroinflate:
508
- pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
509
- else:
510
- pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
511
456
  elif self.loss_func == 'multinomial':
512
- pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
457
+ pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
513
458
  elif self.loss_func == 'bernoulli':
514
459
  if self.use_zeroinflate:
515
460
  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
@@ -524,10 +469,6 @@ class PerturbFlow(nn.Module):
524
469
 
525
470
  alpha = self.encoder_n(zns)
526
471
  ns = pyro.sample('n', dist.OneHotCategorical(logits=alpha))
527
-
528
- #if self.loss_func == 'gamma-poisson':
529
- # con_alpha,con_beta = self.encoder_concentrate(zns)
530
- # rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
531
472
 
532
473
  def model3(self, xs, ys, embeds=None):
533
474
  pyro.module('PerturbFlow', self)
@@ -539,8 +480,6 @@ class PerturbFlow(nn.Module):
539
480
  if self.loss_func=='negbinomial':
540
481
  total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
541
482
  xs.new_ones(self.input_size), constraint=constraints.positive)
542
- elif self.loss_func == 'multinomial':
543
- total_count = pyro.param('total_count', int(1e8), constraint=constraints.positive_integer)
544
483
 
545
484
  if self.use_zeroinflate:
546
485
  gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -591,19 +530,14 @@ class PerturbFlow(nn.Module):
591
530
 
592
531
  zs = zns
593
532
 
594
- if self.loss_func == 'gamma-poisson':
595
- con_alpha,con_beta = self.decoder_concentrate(zs)
596
- rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
533
+ concentrate = self.decoder_concentrate(zs)
534
+ if self.loss_func in ['bernoulli','negbinomial']:
535
+ log_theta = concentrate
597
536
  else:
598
- concentrate = self.decoder_concentrate(zs)
599
- if self.loss_func == 'bernoulli':
600
- log_theta = concentrate
601
- elif self.loss_func == 'negbinomial':
602
- log_theta = concentrate
603
- else:
604
- rate = concentrate.exp()
605
- if self.loss_func != 'poisson':
606
- theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
537
+ rate = concentrate.exp()
538
+ theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
539
+ if self.loss_func == 'poisson':
540
+ rate = theta * torch.sum(xs, dim=1, keepdim=True)
607
541
 
608
542
  if self.loss_func == 'negbinomial':
609
543
  if self.use_zeroinflate:
@@ -615,13 +549,8 @@ class PerturbFlow(nn.Module):
615
549
  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
616
550
  else:
617
551
  pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
618
- elif self.loss_func == 'gamma-poisson':
619
- if self.use_zeroinflate:
620
- pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
621
- else:
622
- pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
623
552
  elif self.loss_func == 'multinomial':
624
- pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
553
+ pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
625
554
  elif self.loss_func == 'bernoulli':
626
555
  if self.use_zeroinflate:
627
556
  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
@@ -636,10 +565,6 @@ class PerturbFlow(nn.Module):
636
565
  zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
637
566
  else:
638
567
  zns = embeds
639
-
640
- #if self.loss_func == 'gamma-poisson':
641
- # con_alpha,con_beta = self.encoder_concentrate(zns)
642
- # rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
643
568
 
644
569
  def model4(self, xs, us, ys, embeds=None):
645
570
  pyro.module('PerturbFlow', self)
@@ -651,8 +576,6 @@ class PerturbFlow(nn.Module):
651
576
  if self.loss_func=='negbinomial':
652
577
  total_count = pyro.param("inverse_dispersion", self.inverse_dispersion *
653
578
  xs.new_ones(self.input_size), constraint=constraints.positive)
654
- elif self.loss_func == 'multinomial':
655
- total_count = pyro.param('total_count', int(1e8), constraint=constraints.positive_integer)
656
579
 
657
580
  if self.use_zeroinflate:
658
581
  gate_logits = pyro.param("dropout_rate", xs.new_zeros(self.input_size))
@@ -713,19 +636,14 @@ class PerturbFlow(nn.Module):
713
636
  else:
714
637
  zs = zns
715
638
 
716
- if self.loss_func == 'gamma-poisson':
717
- con_alpha,con_beta = self.decoder_concentrate(zs)
718
- rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
639
+ concentrate = self.decoder_concentrate(zs)
640
+ if self.loss_func in ['bernoulli','negbinomial']:
641
+ log_theta = concentrate
719
642
  else:
720
- concentrate = self.decoder_concentrate(zs)
721
- if self.loss_func == 'bernoulli':
722
- log_theta = concentrate
723
- elif self.loss_func == 'negbinomial':
724
- log_theta = concentrate
725
- else:
726
- rate = concentrate.exp()
727
- if self.loss_func != 'poisson':
728
- theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
643
+ rate = concentrate.exp()
644
+ theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
645
+ if self.loss_func == 'poisson':
646
+ rate = theta * torch.sum(xs, dim=1, keepdim=True)
729
647
 
730
648
  if self.loss_func == 'negbinomial':
731
649
  if self.use_zeroinflate:
@@ -737,13 +655,8 @@ class PerturbFlow(nn.Module):
737
655
  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
738
656
  else:
739
657
  pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
740
- elif self.loss_func == 'gamma-poisson':
741
- if self.use_zeroinflate:
742
- pyro.sample('x', dist.ZeroInflatedDistribution(dist.Poisson(rate=rate),gate_logits=gate_logits).to_event(1), obs=xs.round())
743
- else:
744
- pyro.sample('x', dist.Poisson(rate=rate).to_event(1), obs=xs.round())
745
658
  elif self.loss_func == 'multinomial':
746
- pyro.sample('x', dist.Multinomial(total_count=total_count, probs=theta), obs=xs)
659
+ pyro.sample('x', dist.Multinomial(total_count=int(1e8), probs=theta), obs=xs)
747
660
  elif self.loss_func == 'bernoulli':
748
661
  if self.use_zeroinflate:
749
662
  pyro.sample('x', dist.ZeroInflatedDistribution(dist.Bernoulli(logits=log_theta),gate_logits=gate_logits).to_event(1), obs=xs)
@@ -758,10 +671,6 @@ class PerturbFlow(nn.Module):
758
671
  zns = pyro.sample('zn', dist.Normal(zn_loc, zn_scale).to_event(1))
759
672
  else:
760
673
  zns = embeds
761
-
762
- #if self.loss_func == 'gamma-poisson':
763
- # con_alpha,con_beta = self.encoder_concentrate(zns)
764
- # rate = pyro.sample('cs', dist.Gamma(con_alpha, con_beta).to_event(1))
765
674
 
766
675
  def _total_effects(self, zns, us):
767
676
  zus = None
@@ -940,12 +849,7 @@ class PerturbFlow(nn.Module):
940
849
  return tensor_to_numpy(ms)
941
850
 
942
851
  def _get_expression_response(self, delta_zs):
943
- if self.loss_func == 'gamma-poisson':
944
- alpha,beta = self.decoder_concentrate(delta_zs)
945
- xs = dist.Gamma(alpha,beta).to_event(1).mean
946
- else:
947
- xs = self.decoder_concentrate(delta_zs)
948
- return xs
852
+ return self.decoder_concentrate(delta_zs)
949
853
 
950
854
  def get_expression_response(self,
951
855
  delta_zs,
@@ -981,9 +885,9 @@ class PerturbFlow(nn.Module):
981
885
  counts = dist.NegativeBinomial(total_count=total_count, logits=concentrate).to_event(1).mean
982
886
  elif self.loss_func == 'poisson':
983
887
  rate = concentrate.exp()
888
+ theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
889
+ rate = theta * library_size
984
890
  counts = dist.Poisson(rate=rate).to_event(1).mean
985
- elif self.loss_func == 'gamma-poisson':
986
- counts = dist.Poisson(rate=concentrate).to_event(1).mean
987
891
  elif self.loss_func == 'multinomial':
988
892
  rate = concentrate.exp()
989
893
  theta = dist.DirichletMultinomial(total_count=1, concentration=rate).mean
@@ -1007,7 +911,7 @@ class PerturbFlow(nn.Module):
1007
911
  zs = convert_to_tensor(zs, device=self.get_device())
1008
912
  ls = zs
1009
913
 
1010
- if self.loss_func == 'multinomial':
914
+ if self.loss_func in ['multinomial','poisson']:
1011
915
  assert library_sizes!=None, 'Library sizes are required for multinomial!'
1012
916
 
1013
917
  if type(library_sizes) == list:
{sure_tools-2.1.57.dist-info → sure_tools-2.1.59.dist-info}/METADATA RENAMED
@@ -1,6 +1,6 @@
1
1
  Metadata-Version: 2.4
2
2
  Name: SURE-tools
3
- Version: 2.1.57
3
+ Version: 2.1.59
4
4
  Summary: Succinct Representation of Single Cells
5
5
  Home-page: https://github.com/ZengFLab/SURE
6
6
  Author: Feng Zeng
{sure_tools-2.1.57.dist-info → sure_tools-2.1.59.dist-info}/RECORD RENAMED
@@ -1,4 +1,4 @@
1
- SURE/PerturbFlow.py,sha256=emkyhDc99eTJQNkMdsHCp6VPg6468CRkc8lRHyA4P4o,59977
1
+ SURE/PerturbFlow.py,sha256=LoWyN1gcgCPtGsa69wyBCA2oMYcqmK2Eq3__Xy0u-aQ,54454
2
2
  SURE/SURE.py,sha256=ko15a9BhvUqHviogZ0YCdTQjM-2zqkO9OvHZSpnGbg0,47458
3
3
  SURE/__init__.py,sha256=NOJI_K-eCqPgStXXvgl3wIEMp6d8saMTDYLJ7Ga9MqE,293
4
4
  SURE/assembly/__init__.py,sha256=jxZLURXKPzXe21LhrZ09LgZr33iqdjlQy4oSEj5gR2Q,172
@@ -17,9 +17,9 @@ SURE/utils/__init__.py,sha256=YF5jB-PAHJQ40OlcZ7BCZbsN2q1JKuPT6EppilRXQqM,680
17
17
  SURE/utils/custom_mlp.py,sha256=C0EXLGYsWkUQpEL49AyBFPSzKmasb2hdvtnJfxbF-YU,9282
18
18
  SURE/utils/queue.py,sha256=E_5PA5EWcBoGAZj8BkKQnkCK0p4C-4-xcTPqdIXaPXU,1892
19
19
  SURE/utils/utils.py,sha256=IUHjDDtYaAYllCWsZyIzqQwaLul6fJRvHRH4vIYcR-c,8462
20
- sure_tools-2.1.57.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
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- sure_tools-2.1.57.dist-info/METADATA,sha256=Y1npoz3fb9597vOLCGFK4__9N85QgzBnX_zUra5E1Fg,2678
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- sure_tools-2.1.57.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
23
- sure_tools-2.1.57.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
24
- sure_tools-2.1.57.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
25
- sure_tools-2.1.57.dist-info/RECORD,,
20
+ sure_tools-2.1.59.dist-info/licenses/LICENSE,sha256=TFHKwmrAViXQbSX5W-NDItkWFjm45HWOeUniDrqmnu0,1065
21
+ sure_tools-2.1.59.dist-info/METADATA,sha256=6U4dnYcyfpZX3GOpU2cBG4EctQSK03XHxrCqAdiqIUg,2678
22
+ sure_tools-2.1.59.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
23
+ sure_tools-2.1.59.dist-info/entry_points.txt,sha256=-nJI8rVe_qqrR0HmfAODzj-JNfEqCcSsyVh6okSqyHk,83
24
+ sure_tools-2.1.59.dist-info/top_level.txt,sha256=BtFTebdiJeqra4r6mm-uEtwVRFLZ_IjYsQ7OnalrOvY,5
25
+ sure_tools-2.1.59.dist-info/RECORD,,