-
Notifications
You must be signed in to change notification settings - Fork 0
/
references.bib
3626 lines (3237 loc) · 130 KB
/
references.bib
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499
500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
554
555
556
557
558
559
560
561
562
563
564
565
566
567
568
569
570
571
572
573
574
575
576
577
578
579
580
581
582
583
584
585
586
587
588
589
590
591
592
593
594
595
596
597
598
599
600
601
602
603
604
605
606
607
608
609
610
611
612
613
614
615
616
617
618
619
620
621
622
623
624
625
626
627
628
629
630
631
632
633
634
635
636
637
638
639
640
641
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
665
666
667
668
669
670
671
672
673
674
675
676
677
678
679
680
681
682
683
684
685
686
687
688
689
690
691
692
693
694
695
696
697
698
699
700
701
702
703
704
705
706
707
708
709
710
711
712
713
714
715
716
717
718
719
720
721
722
723
724
725
726
727
728
729
730
731
732
733
734
735
736
737
738
739
740
741
742
743
744
745
746
747
748
749
750
751
752
753
754
755
756
757
758
759
760
761
762
763
764
765
766
767
768
769
770
771
772
773
774
775
776
777
778
779
780
781
782
783
784
785
786
787
788
789
790
791
792
793
794
795
796
797
798
799
800
801
802
803
804
805
806
807
808
809
810
811
812
813
814
815
816
817
818
819
820
821
822
823
824
825
826
827
828
829
830
831
832
833
834
835
836
837
838
839
840
841
842
843
844
845
846
847
848
849
850
851
852
853
854
855
856
857
858
859
860
861
862
863
864
865
866
867
868
869
870
871
872
873
874
875
876
877
878
879
880
881
882
883
884
885
886
887
888
889
890
891
892
893
894
895
896
897
898
899
900
901
902
903
904
905
906
907
908
909
910
911
912
913
914
915
916
917
918
919
920
921
922
923
924
925
926
927
928
929
930
931
932
933
934
935
936
937
938
939
940
941
942
943
944
945
946
947
948
949
950
951
952
953
954
955
956
957
958
959
960
961
962
963
964
965
966
967
968
969
970
971
972
973
974
975
976
977
978
979
980
981
982
983
984
985
986
987
988
989
990
991
992
993
994
995
996
997
998
999
1000
@article{abadi.tensor,
IDS = {Abadi2016},
author = {Abadi, Mart\'{i}n and Agarwal, Ashish and Barham, Paul and Brevdo, Eugene and Chen, Zhifeng and Citro, Craig and Corrado, Greg S and Davis, Andy and Dean, Jeffrey and Devin, Matthieu and Ghemawat, Sanjay and Goodfellow, Ian and Harp, Andrew and Irving, Geoffrey and Isard, Michael and Jia, Yangqing and Jozefowicz, Rafal and Kaiser, Lukasz and Kudlur, Manjunath and Levenberg, Josh and Mane, Dan and Monga, Rajat and Moore, Sherry and Murray, Derek and Olah, Chris and Schuster, Mike and Shlens, Jonathon and Steiner, Benoit and Sutskever, Ilya and Talwar, Kunal and Tucker, Paul and Vanhoucke, Vincent and Vasudevan, Vijay and Viegas, Fernanda and Vinyals, Oriol and Warden, Pete and Wattenberg, Martin and Wicke, Martin and Yu, Yuan and Zheng, Xiaoqiang},
journal = {arXiv},
title = {{TensorFlow}: large-scale machine learning on heterogeneous distributed systems},
year = {2016}
}
@article{abid.contrastive,
IDS = {Abid2019},
author = {Abid, Abubakar and Zou, James},
journal = {arXiv},
title = {Contrastive variational autoencoder enhances salient features},
year = {2019}
}
@article{abid.exploring,
IDS = {Abid2018},
author = {Abid, Abubakar and Zhang, Martin J. and Bagaria, Vivek K. and Zou, James},
journal = {Nature Communications},
title = {{Exploring patterns enriched in a dataset with contrastive principal component analysis}},
year = {2018}
}
@article{agapiou.importance,
IDS = {Agapiou2017},
author = {Agapiou, Sergios and Papaspiliopoulos, Omiros and Sanz-Alonso, Daniel and Stuart, Andrew},
journal = {Statistical Science},
title = {Importance sampling: Intrinsic dimension and computational cost},
year = {2017}
}
@inproceedings{ambrogioni.wasserstein,
IDS = {NIPS2018_7514},
author = {Ambrogioni, Luca and G\"{u}\c{c}l\"{u}, Umut and G\"{u}\c{c}l\"{u}t\"{u}rk, Ya\u{g}mur and Hinne, Max and van Gerven, Marcel A. J. and Maris, Eric},
booktitle = {Advances in Neural Information Processing Systems},
title = {Wasserstein variational inference},
year = {2018}
}
@inproceedings{amini.variational,
IDS = {amini2018variational,Amini2018},
author = {Amini, Alexander and Schwarting, Wilko and Rosman, Guy and Araki, Brandon and Karaman, Sertac and Rus, Daniela},
booktitle = {International Conference on Intelligent Robots and Systems},
title = {Variational autoencoder for end-to-end control of autonomous driving with novelty detection and training de-biasing},
year = {2018}
}
@inproceedings{amodio.aligning,
IDS = {amodio2018magan},
author = {Amodio, Matthew and Krishnaswamy, Smita},
booktitle = {International Conference on Machine Learning},
title = {{MAGAN: aligning biological manifolds}},
year = {2018}
}
@article{amodio.exploring,
IDS = {saucie,Amodio2019},
author = {Amodio, Matthew
and van Dijk, David
and Srinivasan, Krishnan
and Chen, William S.
and Mohsen, Hussein
and Moon, Kevin R.
and Campbell, Allison
and Zhao, Yujiao
and Wang, Xiaomei
and Venkataswamy, Manjunatha
and Desai, Anita
and Ravi, V.
and Kumar, Priti
and Montgomery, Ruth
and Wolf, Guy
and Krishnaswamy, Smita},
journal = {Nature Methods},
title = {Exploring single-cell data with deep multitasking neural networks},
year = {2019}
}
@article{andrews.dropout,
IDS = {m3drop},
author = {Andrews, Tallulah S and Hemberg, Martin},
doi = {10.1101/065094},
journal = {bioRxiv},
title = {{Dropout-based feature selection for scRNASeq}},
url = {https://www.biorxiv.org/content/early/2018/05/17/065094},
year = {2018}
}
@article{andrews.false,
IDS = {andrews2018false},
author = {Andrews, Tallulah S and Hemberg, Martin},
journal = {F1000Research},
title = {False signals induced by single-cell imputation},
year = {2018}
}
@article{andrieu.an,
IDS = {andrieu2003introduction},
author = {Andrieu, Christophe and De Freitas, Nando and Doucet, Arnaud and Jordan, Michael I},
journal = {Machine learning},
title = {An introduction to {MCMC} for machine learning},
year = {2003}
}
@article{angerer.single,
IDS = {Angerer2017,angerer,philipp.single},
author = {Angerer, Philipp and Simon, Lukas and Tritschler, Sophie and Wolf, F. Alexander and Fischer, David and Theis, Fabian J.},
journal = {Current Opinion in Systems Biology},
title = {Single cells make big data: New challenges and opportunities in transcriptomics},
year = {2017}
}
@inproceedings{arjovsky.wasserstein,
IDS = {Arjovsky2017},
author = {Arjovsky, Martin and Chintala, Soumith and Bottou, L\'{e}on},
booktitle = {International Conference on Machine Learning},
title = {Wasserstein generative adversarial networks},
year = {2017}
}
@book{art.monte,
IDS = {mcbook},
author = {Art B. Owen},
title = {Monte Carlo Theory, Methods and Examples},
year = {2013}
}
@inproceedings{ashish.learning,
IDS = {8099724},
author = {Ashish Shrivastava and Tomas Pfister and Oncel Tuzel and Josh Susskind and Wenda Wang and Russ Webb},
booktitle = {Conference on Computer Vision and Pattern Recognition},
title = {{Learning from simulated and unsupervised images through adversarial training}},
year = {2017}
}
@article{athinodoros.from,
IDS = {YALEB},
author = {Athinodoros S. Georghiades, Peter N. Belhumeur, David J. Kriegman},
journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
number = {6},
pages = {643-660},
title = {From few to many: Illumination cone models for face recognition under variable lighting and pose},
volume = {23},
year = {2001}
}
@article{bacher.cnorm,
IDS = {Bacher2017},
author = {Bacher, Rhonda and Chu, Li Fang and Leng, Ning and Gasch, Audrey P. and Thomson, James A. and Stewart, Ron M. and Newton, Michael and Kendziorski, Christina},
journal = {Nature Methods},
number = {6},
pages = {584--586},
title = {{SCnorm: Robust normalization of single-cell RNA-seq data}},
volume = {14},
year = {2017}
}
@inproceedings{balin.concrete,
IDS = {balin2019concrete},
author = {Bal{\i}n, Muhammed Fatih and Abid, Abubakar and Zou, James},
booktitle = {International Conference on Machine Learning},
title = {Concrete autoencoders: Differentiable feature selection and reconstruction},
year = {2019}
}
@article{baron.single,
IDS = {pancreasindrop},
author = {Baron, Maayan and Veres, Adrian and Wolock, Samuel L and Faust, Aubrey L and Gaujoux, Renaud and Vetere, Amedeo and Ryu, Jennifer Hyoje and Wagner, Bridget K and Shen-Orr, Shai S and Klein, Allon M and others},
journal = {Cell systems},
number = {4},
pages = {346--360},
title = {A single-cell transcriptomic map of the human and mouse pancreas reveals inter-and intra-cell population structure},
volume = {3},
year = {2016}
}
@article{battaglia.relational,
IDS = {Battaglia2018RelationalNetworks},
author = {Battaglia, Peter W. and Hamrick, Jessica B. and Bapst, Victor and Sanchez-Gonzalez, Alvaro and Zambaldi, Vinicius and Malinowski, Mateusz and Tacchetti, Andrea and Raposo, David and Santoro, Adam and Faulkner, Ryan and Gulcehre, Caglar and Song, Francis and Ballard, Andrew and Gilmer, Justin and Dahl, George and Vaswani, Ashish and Allen, Kelsey and Nash, Charles and Langston, Victoria and Dyer, Chris and Heess, Nicolas and Wierstra, Daan and Kohli, Pushmeet and Botvinick, Matt and Vinyals, Oriol and Li, Yujia and Pascanu, Razvan},
journal = {arXiv},
title = {Relational inductive biases, deep learning, and graph networks},
year = {2018}
}
@article{becht.dimensionality,
IDS = {Becht2018},
author = {Becht, Etienne
and McInnes, Leland
and Healy, John
and Dutertre, Charles-Antoine
and Kwok, Immanuel W. H.
and Ng, Lai Guan
and Ginhoux, Florent
and Newell, Evan W.},
day = {03},
journal = {Nature Biotechnology},
title = {Dimensionality reduction for visualizing single-cell data using UMAP},
volume = {37},
year = {2018}
}
@article{bellman.dynamic,
IDS = {bellman1966dynamic},
author = {Bellman, Richard},
journal = {Science},
title = {Dynamic programming},
year = {1966}
}
@article{kouw2019review,
title={A review of domain adaptation without target labels},
author={Kouw, Wouter Marco and Loog, Marco},
journal={IEEE transactions on pattern analysis and machine intelligence},
year={2019},
publisher={IEEE}
}
@inproceedings{bengio.generalized,
IDS = {Bengio2013},
author = {Bengio, Yoshua and Yao, Li and Alain, Guillaume and Vincent, Pascal},
booktitle = {Advances in Neural Information Processing Systems},
title = {Generalized Denoising Auto-Encoders as Generative Models},
year = {2013}
}
@article{bento.the,
IDS = {bento2014chembl},
author = {Bento, A Patr{\'i}cia and Gaulton, Anna and Hersey, Anne and Bellis, Louisa J and Chambers, Jon and Davies, Mark and Kr{\"u}ger, Felix A and Light, Yvonne and Mak, Lora and McGlinchey, Shaun and others},
journal = {Nucleic acids research},
title = {The {ChEMBL} bioactivity database: an update},
year = {2014}
}
@book{berger.statistical,
IDS = {berger2013statistical,Fienberg},
author = {Berger, James O},
publisher = {Springer Science \& Business Media},
title = {{Statistical Decision Theory and Bayesian Analysis}},
year = {2013}
}
@incollection{bergstra.algorithms,
IDS = {Bergstra2011,NIPS2011_4443},
author = {Bergstra, James S and Bardenet, R\'{e}mi and Bengio, Yoshua and K{\'{e}}gl, Bal\'{a}zs},
booktitle = {Advances in Neural Information Processing Systems},
editor = {Shawe-Taylor, J and Zemel, R S and Bartlett, P L and Pereira, F and Weinberger, K Q},
pages = {2546--2554},
title = {{Algorithms for hyper-parameter optimization}},
year = {2011}
}
@article{bingham.pyro,
IDS = {Bingham2018},
author = {Bingham, Eli and Chen, Jonathan P and Jankowiak, Martin and Obermeyer, Fritz and Pradhan, Neeraj and Karaletsos, Theofanis and Singh, Rohit and Szerlip, Paul and Horsfall, Paul and Goodman, Noah D},
journal = {Journal of Machine Learning Research},
title = {Pyro: Deep universal probabilistic programming},
year = {2019}
}
@book{bishop.pattern,
IDS = {Bishop:2006:PRM:1162264},
author = {Bishop, Christopher M.},
publisher = {Springer-Verlag},
title = {Pattern Recognition and Machine Learning},
year = {2006}
}
@article{blaschke.application,
IDS = {Blaschke2018},
author = {Blaschke, Thomas and Olivecrona, Marcus and Engkvist, Ola and Bajorath, Jürgen and Chen, Hongming},
doi = {10.1002/minf.201700123},
issn = {18681743},
journal = {Molecular Informatics},
keywords = {Autoencoder, chemoinformatics, de novo molecular design, deep learning, inverse QSAR},
month = {1},
number = {1-2},
pages = {1700123},
publisher = {John Wiley \& Sons, Ltd},
title = {{Application of Generative Autoencoder in De Novo Molecular Design}},
url = {http://doi.wiley.com/10.1002/minf.201700123},
volume = {37},
year = {2018}
}
@article{blei.build,
IDS = {Blei2014},
author = {Blei, David M.},
journal = {Annual Review of Statistics and Its Application},
title = {Build, compute, critique, repeat: Data analysis with latent variable models},
year = {2014}
}
@article{blei.latent,
IDS = {LDA},
author = {Blei, David M. and Ng, Andrew Y. and Jordan, Michael I.},
issn = {1532-4435},
journal = {{Journal of Machine Learning Research}},
pages = {993--1022},
title = {Latent Dirichlet allocation},
volume = {3},
year = {2003}
}
@article{blei.variational,
IDS = {blei2017variational,Blei2017},
author = {Blei, David M. and Kucukelbir, Alp and McAuliffe, Jon D.},
journal = {Journal of the American Statistical Association},
title = {Variational inference: A review for statisticians},
year = {2017}
}
@inproceedings{bornschein.reweighted,
IDS = {Bornschein2015},
author = {Bornschein, J{\"{o}}rg and Bengio, Yoshua},
booktitle = {International Conference on Learning Representations},
title = {Reweighted wake-sleep},
year = {2015}
}
@article{box.science,
IDS = {Box1976},
author = {Box, George E. P.},
journal = {Journal of the American Statistical Association},
title = {{Science and Statistics}},
year = {1976}
}
@article{box.useful,
IDS = {Box1962},
author = {Box, Georges E. P. and Hunter, William G.},
journal = {Technometrics},
title = {A useful method for model-building},
year = {1962}
}
@inproceedings{boyeau.deep,
IDS = {Boyeau794289},
author = {Boyeau, Pierre and Lopez, Romain and Regier, Jeffrey and Gayoso, Adam and Jordan, Michael I. and Yosef, Nir},
booktitle = {Machine Learning in Computational Biology},
title = {Deep Generative models for detecting differential expression in single cells},
year = {2019}
}
@article{brett.privacy,
IDS = {PPGAN},
author = {Brett K. Beaulieu-Jones and Zhiwei Steven Wu and Chris Williams and Ran Lee and Sanjeev P. Bhavnani and James Brian Byrd and Casey S. Greene },
journal = {Circulation: Cardiovascular Quality and Outcomes},
title = {Privacy-preserving generative deep neural networks support clinical data sharing},
year = {2019}
}
@article{brookes.conditioning,
IDS = {Brookes2019},
author = {Brookes, David H. and Park, Hahnbeom and Listgarten, Jennifer},
journal = {International Conference on Machine Learning},
title = {{Conditioning by adaptive sampling for robust design}},
year = {2019}
}
@article{buettner.computational,
IDS = {Florian2015},
author = {Buettner, Florian and Natarajan, Kedar N and Casale, F Paolo and Proserpio, Valentina and Scialdone, Antonio and Theis, Fabian J and Teichmann, Sarah A and Marioni, John C and Stegle, Oliver},
journal = {Nature Biotechnology},
number = {2},
pages = {155--160},
title = {{Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells}},
volume = {33},
year = {2015}
}
@article{burbea.the,
IDS = {burbea1984convexity},
author = {Burbea, Jacob},
journal = {Utilitas Mathematica},
title = {The convexity with respect to Gaussian distributions of divergences of order $\alpha$},
year = {1984}
}
@inproceedings{burda.importance,
IDS = {BurdaGS15,Burda2016},
arxivid = {1509.00519v4},
author = {Burda, Yuri and Grosse, Roger and Salakhutdinov, Ruslan},
booktitle = {International Conference on Learning Representations},
title = {{Importance weighted autoencoders}},
year = {2016}
}
@inproceedings{burgess.understanding,
IDS = {Burgess2018},
author = {Burgess, Christopher P and Higgins, Irina and Pal, Arka and Matthey, Loic and Watters, Nick and Desjardins, Guillaume and Lerchner, Alexander},
booktitle = {Learning Disentangled Representations, NIPS Workshop},
title = {{Understanding disentangling in $\beta$-VAE}},
year = {2017}
}
@article{butler.integrating,
IDS = {seurat},
author = {Butler, Andrew
and Hoffman, Paul
and Smibert, Peter
and Papalexi, Efthymia
and Satija, Rahul},
day = {02},
journal = {Nature Biotechnology},
pages = {411},
title = {Integrating single-cell transcriptomic data across different conditions, technologies, and species},
volume = {36},
year = {2018}
}
@article{carpenter.stan,
IDS = {Carpenter2017},
author = {Carpenter, Bob and Gelman, Andrew and Hoffman, Matthew D. and Lee, Daniel and Goodrich, Ben and Betancourt, Michael and Brubaker, Marcus and Guo, Jiqiang and Li, Peter and Riddell, Allen},
journal = {Journal of Statistical Software},
title = {Stan: A probabilistic programming language},
year = {2017}
}
@inproceedings{casale.gaussian,
IDS = {NIPS2018_8238},
author = {Casale, Francesco Paolo and Dalca, Adrian and Saglietti, Luca and Listgarten, Jennifer and Fusi, Nicolo},
booktitle = {Advances in Neural Information Processing Systems},
title = {Gaussian process prior variational autoencoders},
year = {2018}
}
@inproceedings{chan.likelihood,
IDS = {Chan2018},
arxivid = {1802.06153},
author = {Chan, Jeffrey and Perrone, Valerio and Spence, Jeffrey P. and Jenkins, Paul A. and Mathieson, Sara and Song, Yun S.},
booktitle = {Advances in Neural Information Processing Systems 31},
month = {2},
title = {{A likelihood-free inference framework for population genetic data using exchangeable neural networks}},
year = {2018}
}
@inproceedings{charles.weight,
IDS = {pmlr-v37-blundell15},
address = {Lille, France},
author = {Charles Blundell and Julien Cornebise and Koray Kavukcuoglu and Daan Wierstra},
booktitle = {Proceedings of the 32nd International Conference on Machine Learning},
month = {07--09 Jul},
pages = {1613--1622},
title = {Weight Uncertainty in Neural Network},
volume = {37},
year = {2015}
}
@article{chatterjee.the,
IDS = {Chatterjee2018,chatterjee2018sample},
author = {Chatterjee, Sourav and Diaconis, Persi},
journal = {The Annals of Applied Probability},
title = {{The sample size required in importance sampling}},
year = {2018}
}
@article{clark2018scnmt,
title={scNMT-seq enables joint profiling of chromatin accessibility DNA methylation and transcription in single cells},
author={Clark, Stephen J and Argelaguet, Ricard and Kapourani, Chantriolnt-Andreas and Stubbs, Thomas M and Lee, Heather J and Alda-Catalinas, Celia and Krueger, Felix and Sanguinetti, Guido and Kelsey, Gavin and Marioni, John C and others},
journal={Nature communications},
volume={9},
number={1},
pages={1--9},
year={2018},
publisher={Nature Publishing Group}
}
@article{wang2014clonal,
title={Clonal evolution in breast cancer revealed by single nucleus genome sequencing},
author={Wang, Yong and Waters, Jill and Leung, Marco L and Unruh, Anna and Roh, Whijae and Shi, Xiuqing and Chen, Ken and Scheet, Paul and Vattathil, Selina and Liang, Han and others},
journal={Nature},
volume={512},
number={7513},
pages={155--160},
year={2014},
publisher={Nature Publishing Group}
}
@article{ramskold2012full,
title={Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells},
author={Ramsk{\"o}ld, Daniel and Luo, Shujun and Wang, Yu-Chieh and Li, Robin and Deng, Qiaolin and Faridani, Omid R and Daniels, Gregory A and Khrebtukova, Irina and Loring, Jeanne F and Laurent, Louise C and others},
journal={Nature Biotechnology},
volume={30},
number={8},
pages={777--782},
year={2012},
publisher={Nature Publishing Group}
}
@inproceedings{chen.heterogeneous,
IDS = {Chen2018a},
author = {Chen, Yifeng and Sun, Wei and Wang, Haohan},
booktitle = {IEEE International Conference on Bioinformatics and Biomedicine},
title = {Heterogeneous {Hi-C} data super-resolution with a conditional generative adversarial network},
year = {2018}
}
@inproceedings{chen.info,
IDS = {Chen2016},
author = {Chen, Xi and Duan, Yan and Houthooft, Rein and Schulman, John and Sutskever, Ilya and Abbeel, Pieter},
booktitle = {Advances in Neural Information Processing Systems},
pages = {2172--2180},
title = {{InfoGAN: interpretable representation learning by information maximizing generative adversarial nets}},
year = {2016}
}
@incollection{chen.isolating,
IDS = {NIPS2018_7527},
author = {Chen, Tian Qi and Li, Xuechen and Grosse, Roger B and Duvenaud, David K},
booktitle = {Advances in Neural Information Processing Systems 31},
editor = {S. Bengio and H. Wallach and H. Larochelle and K. Grauman and N. Cesa-Bianchi and R. Garnett},
pages = {2610--2620},
publisher = {Curran Associates, Inc.},
title = {Isolating sources of disentanglement in variational autoencoders},
year = {2018}
}
@inproceedings{chen.learning,
IDS = {Chen2018},
author = {Chen, Jianbo and Song, Le and Wainwright, Martin J and Jordan, Michael I},
booktitle = {Proceedings of the 35th International Conference on Machine Learning},
pages = {882--891},
title = {{Learning to explain: an information-theoretic perspective on model interpretation}},
volume = {80},
year = {2018}
}
@inproceedings{chen.variational,
IDS = {chen2018variational,Chen2017},
author = {Chen, Xi and Kingma, Diederik P and Salimans, Tim and Duan, Yan and Dhariwal, Prafulla and Schulman, John and Sutskever, Ilya and Abbeel, Pieter},
booktitle = {International Conference on Learning Representations},
title = {{Variational loosy autoencoder}},
year = {2017}
}
@article{ching.opportunities,
IDS = {Ching2018},
author = {Ching, Travers and Himmelstein, Daniel S. and Beaulieu-Jones, Brett K. and Kalinin, Alexandr A. and Do, Brian T. and Way, Gregory P. and Ferrero, Enrico and Agapow, Paul-Michael and Zietz, Michael and Hoffman, Michael M. and Xie, Wei and Rosen, Gail L. and Lengerich, Benjamin J. and Israeli, Johnny and Lanchantin, Jack and Woloszynek, Stephen and Carpenter, Anne E. and Shrikumar, Avanti and Xu, Jinbo and Cofer, Evan M. and Lavender, Christopher A. and Turaga, Srinivas C. and Alexandari, Amr M. and Lu, Zhiyong and Harris, David J. and DeCaprio, Dave and Qi, Yanjun and Kundaje, Anshul and Peng, Yifan and Wiley, Laura K. and Segler, Marwin H. S. and Boca, Simina M. and Swamidass, S. Joshua and Huang, Austin and Gitter, Anthony and Greene, Casey S.},
journal = {Journal of The Royal Society Interface},
title = {Opportunities and obstacles for deep learning in biology and medicine},
year = {2018}
}
@inproceedings{choi.stargan,
IDS = {choi2018stargan},
author = {Choi, Yunjey and Choi, Minje and Kim, Munyoung and Ha, Jung-Woo and Kim, Sunghun and Choo, Jaegul},
booktitle = {Proceedings of the IEEE Conference on Computer Vision and Pattern Recognition},
pages = {8789--8797},
title = {Stargan: Unified generative adversarial networks for multi-domain image-to-image translation},
year = {2018}
}
@inproceedings{chuan.on,
IDS = {pmlr-v70-guo17a},
author = {Chuan Guo and Geoff Pleiss and Yu Sun and Kilian Q. Weinberger},
booktitle = {International Conference on Machine Learning},
title = {On calibration of modern neural networks},
year = {2017}
}
@inproceedings{clivio.detecting,
IDS = {AutoZI},
author = {Clivio, Oscar and Lopez, Romain and Regier, Jeffrey and Gayoso, Adam and Jordan, Michael I and Yosef, Nir},
booktitle = {Machine Learning in Computational Biology (MLCB)},
title = {Detecting zero-inflated genes in single-cell transcriptomics data},
year = {2019}
}
@article{codeluppi.spatial,
IDS = {Codeluppi2018a},
author = {Codeluppi, Simone and Borm, Lars E. and Zeisel, Amit and La Manno, Gioele and van Lunteren, Josina A. and Svensson, Camilla I. and Linnarsson, Sten},
journal = {Nature Methods},
title = {Spatial organization of the somatosensory cortex revealed by {osmFISH}},
year = {2018}
}
@article{cole.performance,
IDS = {Cole2017,SCONE},
author = {Cole, Michael B and Risso, Davide and Wagner, Allon and Purdom, Elizabeth and Cole, Michael B and Risso, Davide and Wagner, Allon and Detomaso, David and Ngai, John and Purdom, Elizabeth},
journal = {Cell Systems},
title = {Performance assessment and selection of normalization procedures for single-cell {RNA}-seq},
year = {2019}
}
@inproceedings{cortes.learning,
IDS = {Cortes2010},
author = {Cortes, Corinna and Mansour, Yishay and Mohri, Mehryar},
booktitle = {Advances in Neural Information Processing Systems},
title = {Learning bounds for importance weighting},
year = {2010}
}
@inproceedings{cremer.inference,
IDS = {pmlr-v80-cremer18a},
author = {Cremer, Chris and Li, Xuechen and Duvenaud, David},
booktitle = {International Conference on Machine Learning},
title = {Inference suboptimality in variational autoencoders},
year = {2018}
}
@article{crow.characterizing,
IDS = {metaneighbors},
author = {Crow, Megan
and Paul, Anirban
and Ballouz, Sara
and Huang, Z. Josh
and Gillis, Jesse},
doi = {10.1038/s41467-018-03282-0},
issn = {2041-1723},
journal = {Nature Communications},
number = {1},
pages = {884},
title = {Characterizing the replicability of cell types defined by single cell RNA-sequencing data using MetaNeighbor},
volume = {9},
year = {2018}
}
@article{crowell.on,
IDS = {Crowell713412},
author = {Crowell, Helena L. and Soneson, Charlotte and Germain, Pierre-Luc and Calini, Daniela and Collin, Ludovic and Raposo, Catarina and Malhotra, Dheeraj and Robinson, Mark D.},
journal = {bioRxiv},
title = {On the discovery of subpopulation-specific state transitions from multi-sample multi-condition single-cell {RNA} sequencing data},
year = {2020}
}
@article{cui.hmm,
IDS = {Cui2015},
author = {Cui, Shiqi and Guha, Subharup and Ferreira, Marco A. R. and Tegge, Allison N.},
journal = {The Annals of Applied Statistics},
title = {{hmmSeq}: A hidden {M}arkov model for detecting differentially expressed genes from {RNA}-seq data},
year = {2015}
}
@article{davis.the,
IDS = {davis2018encyclopedia},
author = {Davis, Carrie A and Hitz, Benjamin C and Sloan, Cricket A and Chan, Esther T and Davidson, Jean M and Gabdank, Idan and Hilton, Jason A and Jain, Kriti and Baymuradov, Ulugbek K and Narayanan, Aditi K and others},
journal = {Nucleic acids research},
title = {The Encyclopedia of {DNA} elements ({ENCODE}): data portal update},
year = {2018}
}
@article{deng.scalable,
IDS = {Deng2018},
author = {Deng, Yue and Bao, Feng and Dai, Qionghai and Wu, Lani F and Altschuler, Steven J},
journal = {Nature Methods},
title = {{Scalable analysis of cell-type composition from single-cell transcriptomics using deep recurrent learning}},
year = {2019}
}
@article{detomaso.fast,
IDS = {DeTomaso2016,fastproject},
author = {DeTomaso, David and Yosef, Nir},
journal = {BMC Bioinformatics},
number = {1},
pages = {315},
publisher = {BioMed Central},
title = {{FastProject}: A tool for low-dimensional analysis of single-cell {RNA}-seq data},
year = {2016}
}
@article{detomaso.functional,
IDS = {VISION,DeTomaso2019},
author = {DeTomaso, David and Jones, Matthew and Subramaniam, Meena and Ashuach, Tal and Ye, Chun J. and Yosef, Nir},
journal = {Nature Communications},
title = {Functional interpretation of single-cell similarity maps},
year = {2019}
}
@article{dieng.reweighted,
IDS = {ReweightedEM2019},
author = {{Dieng}, Adji B. and {Paisley}, John},
journal = {arXiv},
title = {{Reweighted expectation maximization}},
year = {2019}
}
@inproceedings{dieng.variational,
IDS = {NIPS2017_6866},
author = {Dieng, Adji Bousso and Tran, Dustin and Ranganath, Rajesh and Paisley, John and Blei, David},
booktitle = {Advances in Neural Information Processing Systems},
title = {Variational inference via chi-square upper bound minimization},
year = {2017}
}
@article{dillon.tensor,
IDS = {Dillon2017},
author = {Dillon, Joshua V. and Langmore, Ian and Tran, Dustin and Brevdo, Eugene and Vasudevan, Srinivas and Moore, Dave and Patton, Brian and Alemi, Alex and Hoffman, Matt and Saurous, Rif A.},
journal = {arXiv},
title = {{TensorFlow} distributions},
year = {2017}
}
@inproceedings{dincer.deep,
IDS = {Dincer2018a},
author = {Dincer, Ayse Berceste and Celik, Safiye and Hiranuma, Naozumi and Lee, Su-In},
booktitle = {ICML Workshop on Computational Biology},
title = {{DeepProfile}: Deep learning of cancer molecular profiles for precision medicine},
year = {2018}
}
@article{ding.deep,
IDS = {Ding853457},
author = {Ding, Jiarui and Regev, Aviv},
journal = {bioRxiv},
title = {{Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces}},
year = {2019}
}
@article{ding.interpretable,
IDS = {Ding2018,scvis},
author = {Ding, Jiarui and Condon, Anne and Shah, Sohrab P},
journal = {Nature communications},
title = {{Interpretable dimensionality reduction of single cell transcriptome data with deep generative models.}},
year = {2018}
}
@article{dixit.perturb,
IDS = {Dixit2016},
author = {Dixit, Atray and Parnas, Oren and Li, Biyu and Chen, Jenny and Fulco, Charles P. and Jerby-Arnon, Livnat and Marjanovic, Nemanja D. and Dionne, Danielle and Burks, Tyler and Raychowdhury, Raktima and Adamson, Britt and Norman, Thomas M. and Lander, Eric S. and Weissman, Jonathan S. and Friedman, Nir and Regev, Aviv},
journal = {Cell},
title = {{Perturb-Seq}: dissecting molecular circuits with scalable single-cell {RNA} profiling of pooled genetic screens},
year = {2016}
}
@inproceedings{dizaji.semi,
IDS = {Dizaji2018},
author = {Dizaji, Kamran Ghasedi and Wang, Xiaoqian and Huang, Heng},
booktitle = {KDD},
title = {Semi-Supervised Generative Adversarial Network for Gene Expression Inference},
year = {2018}
}
@inproceedings{domke.importance,
IDS = {NIPS2018_7699},
author = {Domke, Justin and Sheldon, Daniel R},
booktitle = {Advances in Neural Information Processing Systems},
title = {Importance weighting and variational inference},
year = {2018}
}
@inproceedings{donahue.adversarial,
IDS = {Donahue2017},
author = {Donahue, Jeff and Kr{\"{a}}henb{\"{u}}hl, Philipp and Darrell, Trevor},
booktitle = {International Conference on Learning Representations},
title = {Adversarial feature learning},
year = {2017}
}
@inproceedings{dosovitskiy.generating,
IDS = {Dosovitskiy2016},
author = {Dosovitskiy, Alexey and Brox, Thomas},
booktitle = {Advances in Neural Information Processing Systems},
pages = {658--666},
title = {{Generating images with perceptual similarity metrics based on deep networks}},
year = {2016}
}
@inproceedings{durrieu.lower,
IDS = {Durrieu2012},
author = {Durrieu, Jean-Louis and Thiran, Jean-Philippe and Kelly, Finnian},
booktitle = {IEEE International Conference on Acoustics, Speech and Signal Processing},
isbn = {9781467300469},
pages = {4833--4836},
title = {{Lower and upper bounds for approximation of the Kullback-Leibler divergence between Gaussian mixture models}},
year = {2012}
}
@article{duverle.cell,
IDS = {cell-tree},
author = {duVerle, David A.
and Yotsukura, Sohiya
and Nomura, Seitaro
and Aburatani, Hiroyuki
and Tsuda, Koji},
day = {13},
journal = {BMC Bioinformatics},
month = {Sep},
title = {{CellTree: an R/bioconductor package to infer the hierarchical structure of cell populations from single-cell RNA-seq data}},
year = {2016}
}
@inproceedings{dwork.differential,
IDS = {dwork2008differential},
author = {Dwork, Cynthia},
booktitle = {International conference on theory and applications of models of computation},
title = {Differential privacy: A survey of results},
year = {2008}
}
@article{dzmitry.neural,
IDS = {bahdanau2015},
author = {Dzmitry Bahdanau and Kyunghyun Cho and Yoshua Bengio},
journal = {International Conference on Learning Representations},
title = {Neural machine translation by jointly learning to align and translate},
year = {2015}
}
@article{ecker.the,
IDS = {ecker2017brain},
author = {Ecker, Joseph R and Geschwind, Daniel H and Kriegstein, Arnold R and Ngai, John and Osten, Pavel and Polioudakis, Damon and Regev, Aviv and Sestan, Nenad and Wickersham, Ian R and Zeng, Hongkui},
journal = {Neuron},
number = {3},
pages = {542--557},
publisher = {Elsevier},
title = {The BRAIN initiative cell census consortium: lessons learned toward generating a comprehensive brain cell atlas},
volume = {96},
year = {2017}
}
@article{economou.on,
IDS = {economou2016use},
author = {Economou, Theodoros and Stephenson, David B and Rougier, Jonathan C and Neal, Robert and Mylne, Ken R},
journal = {Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences},
title = {On the use of Bayesian decision theory for issuing natural hazard warnings},
year = {2016}
}
@article{efremova.computational,
IDS = {Efremova2020},
author = {Efremova, Mirjana
and Teichmann, Sarah A.},
journal = {Nature Methods},
title = {Computational methods for single-cell omics across modalities},
year = {2020}
}
@article{eraslan.deep,
IDS = {Eraslan2019},
author = {Eraslan, Gökcen and Avsec, Žiga and Gagneur, Julien and Theis, Fabian J.},
journal = {Nature Reviews Genetics},
title = {Deep learning: new computational modelling techniques for genomics},
year = {2019}
}
@article{eraslan.single,
IDS = {Eraslan2019b,dca},
author = {Eraslan, Gökcen and Simon, Lukas M. and Mircea, Maria and Mueller, Nikola S. and Theis, Fabian J.},
journal = {Nature Communications},
title = {{Single-cell RNA-seq denoising using a deep count autoencoder}},
year = {2019}
}
@inproceedings{ester.density,
IDS = {dbscan},
author = {Ester, Martin and Kriegel, Hans-Peter and Sander, J\"{o}rg and Xu, Xiaowei},
booktitle = {International Conference on Knowledge Discovery and Data Mining},
numpages = {6},
pages = {226--231},
title = {A density-based algorithm for discovering clusters a density-based algorithm for discovering clusters in large spatial databases with noise},
year = {1996}
}
@article{fan.characterizing,
IDS = {Fan2016},
author = {Fan, Jean and Salathia, Neeraj and Liu, Rui and Kaeser, Gwendolyn E and Yung, Yun C and Herman, Joseph L and Kaper, Fiona and Fan, Jian Bing and Zhang, Kun and Chun, Jerold and Kharchenko, Peter V},
journal = {Nature Methods},
month = {3},
number = {3},
pages = {241--244},
publisher = {NIH Public Access},
title = {{Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis}},
volume = {13},
year = {2016}
}
@inproceedings{figurnov.implicit,
IDS = {figurnov2018implicit},
author = {Figurnov, Mikhail and Mohamed, Shakir and Mnih, Andriy},
booktitle = {Advances in Neural Information Processing Systems},
title = {Implicit reparameterization gradients},
year = {2018}
}
@article{finak.flexible,
IDS = {mast},
author = {Finak, Greg and McDavid, Andrew and Yajima, Masanao and Deng, Jingyuan and Gersuk, Vivian and Shalek, Alex K and Slichter, Chloe K and Miller, Hannah W and McElrath, M Juliana and Prlic, Martin and others},
journal = {Genome Biology},
number = {1},
pages = {278},
title = {{MAST}: a flexible statistical framework for assessing transcriptional changes and characterizing heterogeneity in single-cell {RNA} sequencing data},
volume = {16},
year = {2015}
}
@inproceedings{flaxman.bayesian,
IDS = {Flaxman2016},
author = {Flaxman, Seth and Sejdinovic, Dino and Cunningham, John P and Filippi, Sarah},
booktitle = {Proceedings of the 32nd Conference on Uncertainty in Artificial Intelligence},
title = {{Bayesian learning of kernel embeddings}},
year = {2016}
}
@article{franziska.transcriptional,
IDS = {PAUL2015},
author = {Franziska Paul and Ya'ara Arkin and Amir Giladi and DiegoAdhemar Jaitin and Ephraim Kenigsberg and Hadas Keren-Shaul and Deborah Winter and David Lara-Astiaso and Meital Gury and Assaf Weiner and Eyal David and Nadav Cohen and FeliciaKathrineBratt Lauridsen and Simon Haas and Andreas Schlitzer and Alexander Mildner and Florent Ginhoux and Steffen Jung and Andreas Trumpp and BoTorben Porse and Amos Tanay and Ido Amit},
doi = {https://doi.org/10.1016/j.cell.2015.11.013},
issn = {0092-8674},
journal = {Cell},
number = {7},
pages = {1663 - 1677},
title = {Transcriptional heterogeneity and lineage commitment in myeloid progenitors},
volume = {163},
year = {2015}
}
@inproceedings{fu.cyclical,
IDS = {fu2019cyclical},
author = {Fu, Hao and Li, Chunyuan and Liu, Xiaodong and Gao, Jianfeng and Celikyilmaz, Asli and Carin, Lawrence},
booktitle = {North American Chapter of the Association for Computational Linguistics},
title = {Cyclical Annealing Schedule: A Simple Approach to Mitigating KL Vanishing},
year = {2019}
}
@inproceedings{fukumizu.kernel,
IDS = {NIPS2007_3340},
author = {Fukumizu, Kenji and Gretton, Arthur and Sun, Xiaohai and Sch{\"{o}}lkopf, Bernhard},
booktitle = {Advances in Neural Information Processing Systems},
title = {{Kernel measures of conditional dependence}},
year = {2008}
}
@inproceedings{futami.variational,
IDS = {futami2018variational},
author = {Futami, Futoshi and Sato, Issei and Sugiyama, Masashi},
booktitle = {International Conference on Artificial Intelligence and Statistics},
title = {Variational inference based on robust divergences},
year = {2018}
}
@article{gabriel.regularizing,
IDS = {DBLP:journals/corr/PereyraTCKH17},
author = {Gabriel Pereyra and
George Tucker and
Jan Chorowski and
Lukasz Kaiser and
Geoffrey E. Hinton},
journal = {arXiv},
title = {Regularizing Neural Networks by Penalizing Confident Output Distributions},
volume = {abs/1701.06548},
year = {2017}
}
@article{ganin.domain,
IDS = {ganin2016domain},
author = {Ganin, Yaroslav and Ustinova, Evgeniya and Ajakan, Hana and Germain, Pascal and Larochelle, Hugo and Laviolette, Fran{\c{c}}ois and Marchand, Mario and Lempitsky, Victor},
journal = {The Journal of Machine Learning Research},
number = {1},
pages = {2096--2030},
title = {Domain-adversarial training of neural networks},
volume = {17},
year = {2016}
}
@article{gaublomme.single,
IDS = {Gaublomme2015},
author = {Gaublomme, Jellert T. and Yosef, Nir and Lee, Youjin and Gertner, Rona S. and Yang, Li V. and Wu, Chuan and Pandolfi, Pier Paolo and Mak, Tak and Satija, Rahul and Shalek, Alex K. and Kuchroo, Vijay K. and Park, Hongkun and Regev, Aviv},
journal = {Cell},
title = {Single-cell genomics unveils critical regulators of {Th17} cell pathogenicity},
year = {2015}
}
@misc{gaussian,
IDS = {riushu},
title = {Gaussian mixture VAE: lessons in variational inference, generative models and deep nets},
url = {http://ruishu.io/2016/12/25/gmvae/},
year = {2016}
}
@book{gelman.data,
IDS = {GelmanHill:2007},
author = {Gelman, Andrew and Hill, Jennifer},
booktitle = {{Data Analysis Using Regression and Multilevel / Hierarchical Models}},
publisher = {Cambridge University Press},
title = {{Data Analysis Using Regression and Multilevel/Hierarchical Models}},
year = {2007}
}
@misc{genomics,
IDS = {10x},
title = {10x Genomics},
url = {https://support.10xgenomics.com/single-cell-gene-expression/datasets},
year = {2017}
}
@article{ghahramani.generative,
IDS = {Ghahramani2018},
author = {Ghahramani, Arsham and Watt, Fiona M and Luscombe, Nicholas M},
journal = {bioRxiv},
title = {{Generative adversarial networks simulate gene expression and predict perturbations in single cells}},
year = {2018}
}
@inproceedings{gilpin.explaining,
IDS = {gilpin2018explaining},
author = {Gilpin, Leilani H and Bau, David and Yuan, Ben Z and Bajwa, Ayesha and Specter, Michael and Kagal, Lalana},
booktitle = {IEEE International Conference on data science and advanced analytics},