-
Notifications
You must be signed in to change notification settings - Fork 1
Expand file tree
/
Copy pathreferences.bib
More file actions
915 lines (821 loc) · 29.3 KB
/
references.bib
File metadata and controls
915 lines (821 loc) · 29.3 KB
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
@article{nesterov2005smooth,
title={Smooth minimization of non-smooth functions},
author={Nesterov, Yu},
journal={Mathematical Programming},
volume={103},
number= {1},
pages = {127--152},
year={2005}
}
@article{nesterov2005excessive,
title={Excessive gap technique in nonsmooth convex minimization},
author={Nesterov, Yu},
journal={SIAM Journal on Optimization},
volume={16},
number={1},
pages={235--249},
year={2005},
publisher={SIAM}
}
@article{schmidt2011convergence,
title={Convergence rates of inexact proximal-gradient methods for convex optimization},
author={Schmidt, Mark and Roux, Nicolas and Bach, Francis},
journal={Advances in neural information processing systems},
volume={24},
year={2011}
}
@article{maury2019epigenetics,
title={Epigenetics in forest trees: role in plasticity, adaptation and potential implications for breeding in a context of climate change (EPITREE).},
author={Maury, St{\'e}phane and Fichot, R{\'e}gis and Sow, MD and Delaunay, Alain and Le Jan, I and Laskar, G and Lesage Descauses, Marie-Claude and Buret, Corinne and Guerin, Vanina and Rogier, Odile and others},
year={2019}
}
@phdthesis{sow2019role,
title={R{\^o}le fonctionnel de l'{\'e}pig{\'e}n{\'e}tique (M{\'e}thylation de l’ADN) dans la r{\'e}ponse du peuplier {\`a} des variations de disponibilit{\'e} en eau du sol},
author={Sow, Mamadou Dia},
year={2019},
school={Universit{\'e} d'Orl{\'e}ans}
}
@book{akalin2020computational,
title={Computational Genomics with r},
author={Akalin, Altuna},
year={2020},
publisher={Chapman and Hall/CRC}
}
@article{aitchison1982statistical,
title={The statistical analysis of compositional data},
author={Aitchison, John},
journal={Journal of the Royal Statistical Society: Series B (Methodological)},
volume={44},
number={2},
pages={139--160},
year={1982},
publisher={Wiley Online Library}
}
@article{mcdonald2018american,
title={American gut: an open platform for citizen science microbiome research},
author={McDonald, Daniel and Hyde, Embriette and Debelius, Justine W and Morton, James T and Gonzalez, Antonio and Ackermann, Gail and Aksenov, Alexander A and Behsaz, Bahar and Brennan, Caitriona and Chen, Yingfeng and others},
journal={Msystems},
volume={3},
number={3},
pages={e00031--18},
year={2018},
publisher={Am Soc Microbiol}
}
@article{plomion2016forest,
title={Forest tree genomics: 10 achievements from the past 10 years and future prospects},
author={Plomion, Christophe and Bastien, Catherine and Bogeat-Triboulot, Marie-B{\'e}atrice and Bouffier, Laurent and D{\'e}jardin, Annabelle and Duplessis, S{\'e}bastien and Fady, Bruno and Heuertz, Myriam and Le Gac, Anne-Laure and Le Provost, Gr{\'e}goire and others},
journal={Annals of Forest Science},
volume={73},
number={1},
pages={77--103},
year={2016},
publisher={BioMed Central}
}
@article{amaral2020advances,
title={Advances and promises of epigenetics for forest trees},
author={Amaral, Joana and Ribeyre, Zo{\'e} and Vigneaud, Julien and Sow, Mamadou Dia and Fichot, R{\'e}gis and Messier, Christian and Pinto, Gloria and Nolet, Philippe and Maury, St{\'e}phane},
journal={Forests},
volume={11},
number={9},
pages={976},
year={2020},
publisher={MDPI}
}
@article{chateigner2020gene,
title={Gene expression predictions and networks in natural populations supports the omnigenic theory},
author={Chateigner, Aur{\'e}lien and Lesage-Descauses, Marie-Claude and Rogier, Odile and Jorge, V{\'e}ronique and Lepl{\'e}, Jean-Charles and Brunaud, V{\'e}ronique and Roux, Christine Paysant-Le and Soubigou-Taconnat, Ludivine and Martin-Magniette, Marie-Laure and Sanchez, L{\'e}opoldo and others},
journal={BMC genomics},
volume={21},
number={1},
pages={1--16},
year={2020},
publisher={BioMed Central}
}
@article{sow2018narrow,
title={Narrow-sense heritability and PST estimates of DNA methylation in three Populus nigra L. populations under contrasting water availability},
author={Sow, Mamadou Dia and Segura, Vincent and Chamaillard, Sylvain and Jorge, V{\'e}ronique and Delaunay, Alain and Lafon-Placette, Cl{\'e}ment and Fichot, R{\'e}gis and Faivre-Rampant, Patricia and Villar, Marc and Brignolas, Franck and others},
journal={Tree Genetics \& Genomes},
volume={14},
number={5},
pages={1--12},
year={2018},
publisher={Springer}
}
@incollection{akaike1998information,
title={Information theory and an extension of the maximum likelihood principle},
author={Akaike, Hirotogu},
booktitle={Selected papers of hirotugu akaike},
pages={199--213},
year={1998},
publisher={Springer}
}
@article{schwarz1978estimating,
title={Estimating the dimension of a model},
author={Schwarz, Gideon},
journal={The annals of statistics},
pages={461--464},
year={1978},
publisher={JSTOR}
}
@article{chakraborty2020biconvex,
title={Biconvex clustering},
author={Chakraborty, Saptarshi and Xu, Jason},
journal={arXiv preprint arXiv:2008.01760},
year={2020}
}
@article{petry2011pairwise,
title={Pairwise fused lasso},
author={Petry, Sebastian and Flexeder, Claudia and Tutz, Gerhard},
year={2011}
}
@book{hastie2009elements,
title={The elements of statistical learning: data mining, inference, and prediction},
author={Hastie, Trevor and Tibshirani, Robert and Friedman, Jerome H and Friedman, Jerome H},
volume={2},
year={2009},
publisher={Springer}
}
@article{rudin1992nonlinear,
title={Nonlinear total variation based noise removal algorithms},
author={Rudin, Leonid I and Osher, Stanley and Fatemi, Emad},
journal={Physica D: nonlinear phenomena},
volume={60},
number={1-4},
pages={259--268},
year={1992},
publisher={Elsevier}
}
@article{yang2012graphical,
title={Graphical models via generalized linear models},
author={Yang, Eunho and Allen, Genevera and Liu, Zhandong and Ravikumar, Pradeep},
journal={Advances in neural information processing systems},
volume={25},
year={2012}
}
@article{erdHos1960evolution,
title={On the evolution of random graphs},
author={Erd{\H{o}}s, Paul and R{\'e}nyi, Alfr{\'e}d and others},
journal={Publ. Math. Inst. Hung. Acad. Sci},
volume={5},
number={1},
pages={17--60},
year={1960}
}
@article{newman2001random,
title={Random graphs with arbitrary degree distributions and their applications},
author={Newman, Mark EJ and Strogatz, Steven H and Watts, Duncan J},
journal={Physical review E},
volume={64},
number={2},
pages={026118},
year={2001},
publisher={APS}
}
@article{fienberg1981categorical,
title={Categorical data analysis of single sociometric relations},
author={Fienberg, Stephen E and Wasserman, Stanley S},
journal={Sociological methodology},
volume={12},
pages={156--192},
year={1981},
publisher={JSTOR}
}
@article{yang2015fused,
title={Fused multiple graphical lasso},
author={Yang, Sen and Lu, Zhaosong and Shen, Xiaotong and Wonka, Peter and Ye, Jieping},
journal={SIAM Journal on Optimization},
volume={25},
number={2},
pages={916--943},
year={2015},
publisher={SIAM}
}
@article{chu2021adaptive,
title={Adaptive Convex Clustering of Generalized Linear Models With Application in Purchase Likelihood Prediction},
author={Chu, Shuyu and Jiang, Huijing and Xue, Zhengliang and Deng, Xinwei},
journal={Technometrics},
volume={63},
number={2},
pages={171--183},
year={2021},
publisher={Taylor \& Francis}
}
@article{dondelinger2020joint,
title={The joint lasso: high-dimensional regression for group structured data},
author={Dondelinger, Frank and Mukherjee, Sach and Alzheimer’s Disease Neuroimaging Initiative},
journal={Biostatistics},
volume={21},
number={2},
pages={219--235},
year={2020},
publisher={Oxford University Press}
}
@INPROCEEDINGS{Yao2019,
author={Yao, Tianyi and Allen, Genevera I.},
booktitle={2019 IEEE Data Science Workshop (DSW)},
title={Clustered Gaussian Graphical Model Via Symmetric Convex Clustering},
year={2019},
volume={},
number={},
pages={76-82},
doi={10.1109/DSW.2019.8755774}
}
@article{Kurtz2015,
doi = {10.1371/journal.pcbi.1004226},
author = {Kurtz, Zachary D. AND Müller, Christian L. AND Miraldi, Emily R. AND Littman, Dan R. AND Blaser, Martin J. AND Bonneau, Richard A.},
journal = {PLOS Computational Biology},
publisher = {Public Library of Science},
title = {Sparse and Compositionally Robust Inference of Microbial Ecological Networks},
year = {2015},
month = {05},
volume = {11},
url = {https://doi.org/10.1371/journal.pcbi.1004226},
pages = {1-25}
}
@article{hadjselem2018,
TITLE = {{Continuation of Nesterov's Smoothing for Regression with Structured Sparsity in High-Dimensional Neuroimaging}},
AUTHOR = {Hadj-Selem, Fouad and Lofstedt, Tommy and Dohmatob, Elvis and Frouin, Vincent and Dubois, Mathieu and Guillemot, Vincent and Duchesnay, Edouard},
URL = {https://hal-cea.archives-ouvertes.fr/cea-01883286},
JOURNAL = {{IEEE Transactions on Medical Imaging}},
PUBLISHER = {{Institute of Electrical and Electronics Engineers}},
VOLUME = {2018},
YEAR = {2018},
DOI = {10.1109/TMI.2018.2829802},
KEYWORDS = {Prediction ; Structured Sparsity ; schizophrenia ; structural MRI ; Machine Learning ; Convex Optimization E Duchesnay ; classification ; Neuroimaging},
PDF = {https://hal-cea.archives-ouvertes.fr/cea-01883286/file/HadjSelem-18_preprint-ieeetmi_conesta.pdf},
HAL_ID = {cea-01883286},
HAL_VERSION = {v1},
}
@inproceedings{hallac2015network,
title={Network lasso: Clustering and optimization in large graphs},
author={Hallac, David and Leskovec, Jure and Boyd, Stephen},
booktitle={Proceedings of the 21th ACM SIGKDD international conference on knowledge discovery and data mining},
pages={387--396},
year={2015}
}
@article{Devijver2018,
author = {Devijver, Emilie and Gallopin, M{\'{e}}lina},
doi = {10.1080/01621459.2016.1247002},
issn = {1537274X},
journal = {Journal of the American Statistical Association},
keywords = {Adaptive minimax theory,Graphical lasso,Network inference,Nonasymptotic model selection,Variable selection},
month = {jan},
number = {521},
pages = {306--314},
publisher = {American Statistical Association},
title = {{Block-Diagonal Covariance Selection for High-Dimensional Gaussian Graphical Models}},
volume = {113},
year = {2018}
}
@article{Cheng2017,
author = {Cheng, Lulu and Shan, Liang and Kim, Inyoung},
doi = {10.1016/j.jspi.2017.05.003},
journal = {Journal of Statistical Planning and Inference},
keywords = {Gaussian graphical model,Graphical LASSO,Pathway,Penalized likelihood,Sparse},
mendeley-groups = {Multilevel},
month = {nov},
pages = {1--14},
publisher = {Elsevier B.V.},
title = {{Multilevel Gaussian graphical model for multilevel networks}},
volume = {190},
year = {2017}
}
@article{Fan2016,
author = {Fan, Jianqing and Liao, Yuan and Liu, Han},
title = {An overview of the estimation of large covariance and precision matrices},
journal = {The Econometrics Journal},
volume = {19},
number = {1},
pages = {C1-C32},
keywords = {Approximate factor model, Elliptical distribution, Graphical model, Heavy-tailed, High-dimensionality, Low-rank matrix, Principal components, Rank-based methods, Sparse matrix, Thresholding},
doi = {https://doi.org/10.1111/ectj.12061},
url = {https://onlinelibrary.wiley.com/doi/abs/10.1111/ectj.12061},
eprint = {https://onlinelibrary.wiley.com/doi/pdf/10.1111/ectj.12061},
year = {2016}
}
@article{danaher2014joint,
title={The joint graphical lasso for inverse covariance estimation across multiple classes},
author={Danaher, Patrick and Wang, Pei and Witten, Daniela M},
journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
volume={76},
number={2},
pages={373--397},
year={2014},
publisher={Wiley Online Library}
}
@article{lin2020estimation,
title={Estimation of sparse Gaussian graphical models with hidden clustering structure},
author={Lin, Meixia and Sun, Defeng and Toh, Kim-Chuan and Wang, Chengjing},
journal={arXiv preprint arXiv:2004.08115},
year={2020}
}
@article{chiquet2011inferring,
title={Inferring multiple graphical structures},
author={Chiquet, Julien and Grandvalet, Yves and Ambroise, Christophe},
journal={Statistics and Computing},
volume={21},
number={4},
pages={537--553},
year={2011},
publisher={Springer}
}
@inproceedings{Grechkin2015,
author = {Grechkin, Maxim and Fazel, Maryam and Witten, Daniela and Lee, Su-In},
title = {Pathway Graphical Lasso},
year = {2015},
isbn = {0262511290},
publisher = {AAAI Press},
booktitle = {Proceedings of the Twenty-Ninth AAAI Conference on Artificial Intelligence},
pages = {2617–2623},
numpages = {7},
location = {Austin, Texas},
series = {AAAI'15}
}
@article{Tan2015,
author = {Kean Ming Tan and Daniela Witten},
title = {{Statistical properties of convex clustering}},
volume = {9},
journal = {Electronic Journal of Statistics},
number = {2},
publisher = {Institute of Mathematical Statistics and Bernoulli Society},
pages = {2324 -- 2347},
keywords = {$k$-means, Degrees of freedom, fusion penalty, hierarchical clustering, prediction error, single linkage},
year = {2015},
doi = {10.1214/15-EJS1074},
URL = {https://doi.org/10.1214/15-EJS1074}
}
@article{Hsieh2014,
author = {Cho-Jui Hsieh and M{{\'a}}ty{{\'a}}s A. Sustik and Inderjit S. Dhillon and Pradeep Ravikumar},
title = {QUIC: Quadratic Approximation for Sparse Inverse Covariance Estimation},
journal = {Journal of Machine Learning Research},
year = {2014},
volume = {15},
number = {83},
pages = {2911-2947},
url = {http://jmlr.org/papers/v15/hsieh14a.html}
}
@article{degras2021sparse,
title={Sparse group fused lasso for model segmentation: a hybrid approach},
author={Degras, David},
journal={Advances in Data Analysis and Classification},
volume={15},
number={3},
pages={625--671},
year={2021},
publisher={Springer}
}
@article{chen2010graph,
title={Graph-structured multi-task regression and an efficient optimization method for general fused lasso},
author={Chen, Xi and Kim, Seyoung and Lin, Qihang and Carbonell, Jaime G and Xing, Eric P},
journal={arXiv preprint arXiv:1005.3579},
year={2010}
}
@article{tibshirani2005sparsity,
title={Sparsity and smoothness via the fused lasso},
author={Tibshirani, Robert and Saunders, Michael and Rosset, Saharon and Zhu, Ji and Knight, Keith},
journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
volume={67},
number={1},
pages={91--108},
year={2005},
publisher={Wiley Online Library}
}
@misc{ganguly2014,
title={Local Neighborhood Fusion in Locally Constant Gaussian Graphical Models},
author={Apratim Ganguly and Wolfgang Polonik},
year={2014},
eprint={1410.8766},
archivePrefix={arXiv},
primaryClass={stat.ME}
}
@article{Tan2013,
author = {Tan, Kean Ming and Witten, Daniela and Shojaie, Ali},
month = {jul},
title = {{The Cluster Graphical Lasso for improved estimation of Gaussian graphical models}},
url = {http://arxiv.org/abs/1307.5339},
year = {2013}
}
@article{Buhlmann2012,
author = {B{\"{u}}hlmann, Peter and R{\"{u}}timann, Philipp and {Van De Geer}, Sara and Zhang, Cun-Hui},
eprint = {1209.5908v1},
title = {{Correlated variables in regression: clustering and sparse estimation}},
year = {2012}
}
@article{Mazumder2012,
author = {Rahul Mazumder and Trevor Hastie},
title = {{The graphical lasso: New insights and alternatives}},
volume = {6},
journal = {Electronic Journal of Statistics},
number = {none},
publisher = {Institute of Mathematical Statistics and Bernoulli Society},
pages = {2125 -- 2149},
keywords = {convex analysis/optimization, graphical lasso, positive definite matrices, precision matrix, semidefinite programming, sparse inverse covariance selection, Sparsity},
year = {2012},
doi = {10.1214/12-EJS740},
URL = {https://doi.org/10.1214/12-EJS740}
}
@article{baudry2012slope,
title={Slope heuristics: overview and implementation},
author={Baudry, Jean-Patrick and Maugis, Cathy and Michel, Bertrand},
journal={Statistics and Computing},
volume={22},
number={2},
pages={455--470},
year={2012},
publisher={Springer}
}
@article{zhao2012huge,
title={The huge package for high-dimensional undirected graph estimation in R},
author={Zhao, Tuo and Liu, Han and Roeder, Kathryn and Lafferty, John and Wasserman, Larry},
journal={The Journal of Machine Learning Research},
volume={13},
number={1},
pages={1059--1062},
year={2012},
publisher={JMLR. org}
}
@article{giraud2012graph,
title={Graph selection with GGMselect},
author={Giraud, Christophe and Huet, Sylvie and Verzelen, Nicolas},
journal={Statistical applications in genetics and molecular biology},
volume={11},
number={3},
year={2012},
publisher={De Gruyter}
}
@inproceedings{Hocking2011,
title={Clusterpath: an Algorithm for Clustering using Convex Fusion Penalties},
author={T. Hocking and Jean-Philippe Vert and F. Bach and Armand Joulin},
booktitle={ICML},
year={2011}
}
@article{Bach2011,
author = {Bach, Francis and Jenatton, Rodolphe and Mairal, Julien and Obozinski, Guillaume},
year = {2011},
month = {01},
pages = {},
title = {Convex Optimization with Sparsity-Inducing Norms}
}
@INPROCEEDINGS{Lindsten2011,
author={F. {Lindsten} and H. {Ohlsson} and L. {Ljung}},
booktitle={2011 IEEE Statistical Signal Processing Workshop (SSP)},
title={Clustering using sum-of-norms regularization: With application to particle filter output computation},
year={2011},
volume={},
number={},
pages={201-204},
doi={10.1109/SSP.2011.5967659}}
@article{Boyd2011,
author = {Boyd, Stephen and Parikh, Neal and Chu, Eric and Peleato, Borja and Eckstein, Jonathan},
title = {Distributed Optimization and Statistical Learning via the Alternating Direction Method of Multipliers},
year = {2011},
issue_date = {January 2011},
publisher = {Now Publishers Inc.},
address = {Hanover, MA, USA},
volume = {3},
number = {1},
issn = {1935-8237},
url = {https://doi.org/10.1561/2200000016},
doi = {10.1561/2200000016},
journal = {Found. Trends Mach. Learn.},
month = jan,
pages = {1–122},
numpages = {122}
}
@inproceedings{pelckmans2005convex,
title={Convex clustering shrinkage},
author={Pelckmans, Kristiaan and De Brabanter, Joseph and Suykens, Johan AK and De Moor, Bart},
booktitle={PASCAL workshop on statistics and optimization of clustering workshop},
year={2005}
}
@article{bien2011sparse,
title={Sparse estimation of a covariance matrix},
author={Bien, Jacob and Tibshirani, Robert J},
journal={Biometrika},
volume={98},
number={4},
pages={807--820},
year={2011},
publisher={Oxford University Press}
}
@article{Cai2011,
author = {Tony Cai and Weidong Liu and Xi Luo},
title = {A Constrained l1 Minimization Approach to Sparse Precision Matrix Estimation},
journal = {Journal of the American Statistical Association},
volume = {106},
number = {494},
pages = {594-607},
year = {2011},
publisher = {Taylor & Francis},
doi = {10.1198/jasa.2011.tm10155},
URL = {https://doi.org/10.1198/jasa.2011.tm10155},
eprint = {https://doi.org/10.1198/jasa.2011.tm10155}
}
@article{meinshausen2010stability,
title={Stability selection},
author={Meinshausen, Nicolai and B{\"u}hlmann, Peter},
journal={Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
volume={72},
number={4},
pages={417--473},
year={2010},
publisher={Wiley Online Library}
}
@article{foygel2010extended,
title={Extended Bayesian information criteria for Gaussian graphical models},
author={Foygel, Rina and Drton, Mathias},
journal={arXiv preprint arXiv:1011.6640},
year={2010}
}
@article{Liu2010,
author = {Liu, Han and Roeder, Kathryn and Wasserman, Larry},
isbn = {9781617823800},
issn = {1049-5258},
journal = {Advances in Neural Information Processing Systems 23: 24th Annual Conference on Neural Information Processing Systems 2010, NIPS 2010},
pages = {1--14},
pmid = {25152607},
title = {{Stability approach to regularization selection (StARS) for high dimensional graphical models}},
year = {2010}
}
@article{Hoefling2010,
author = {Holger Hoefling},
title = {A Path Algorithm for the Fused Lasso Signal Approximator},
journal = {Journal of Computational and Graphical Statistics},
volume = {19},
number = {4},
pages = {984-1006},
year = {2010},
publisher = {Taylor & Francis},
doi = {10.1198/jcgs.2010.09208},
URL = {https://doi.org/10.1198/jcgs.2010.0920},
eprint = {https://doi.org/10.1198/jcgs.2010.0920}
}
@article{Yuan2010,
author = {Ming Yuan},
title = {High Dimensional Inverse Covariance Matrix Estimation via Linear Programming},
journal = {Journal of Machine Learning Research},
year = {2010},
volume = {11},
number = {79},
pages = {2261-2286},
url = {http://jmlr.org/papers/v11/yuan10b.html}
}
@article{el2010safe,
title={Safe feature elimination in sparse supervised learning technical report no},
author={El Ghaoui, L and Viallon, V and Rabbani, T},
journal={Technical report, UCB/EECS-2010--126, EECS Department, University of California, Berkeley},
year={2010}
}
@article{Ambroise2009,
author = {Ambroise, Christophe and Chiquet, Julien and Matias, Catherine},
doi = {10.1214/08-EJS314},
eprint = {0810.3177},
issn = {19357524},
journal = {Electronic Journal of Statistics},
keywords = {Em algorithm,Gaussian graphical model,L1-penalization,Mixture model,Model selection,Variational inference},
mendeley-groups = {Gaussian GM},
month = {oct},
number = {0},
pages = {205--238},
title = {{Inferring sparse gaussian graphical models with latent structure}},
url = {http://arxiv.org/abs/0810.3177 http://dx.doi.org/10.1214/08-EJS314 http://projecteuclid.org/euclid.ejs/1238078905},
volume = {3},
year = {2009}
}
@article{Honorio2009,
title={Sparse and locally constant Gaussian graphical models},
author={Honorio, Jean and Samaras, Dimitris and Paragios, Nikos and Goldstein, Rita and Ortiz, Luis E},
journal={Advances in Neural Information Processing Systems},
volume={22},
pages={745--753},
year={2009}
}
@article{Koller2009,
author = {Koller, Daphne and Friedman, Nir},
doi = {10.2307/478142},
eprint = {arXiv:1011.1669v3},
isbn = {9780262013192},
issn = {00213020},
journal = {Italica},
mendeley-groups = {Books},
number = {3},
pages = {327},
pmid = {25246403},
title = {{Probabilistic Graphical Models: Principles}},
volume = {51},
year = {2009}
}
@article{Peng2009,
author = {Jie Peng and Pei Wang and Nengfeng Zhou and Ji Zhu},
title = {Partial Correlation Estimation by Joint Sparse Regression Models},
journal = {Journal of the American Statistical Association},
volume = {104},
number = {486},
pages = {735-746},
year = {2009},
publisher = {Taylor & Francis},
doi = {10.1198/jasa.2009.0126},
note ={PMID: 19881892},
URL = {https://doi.org/10.1198/jasa.2009.0126},
eprint = { https://doi.org/10.1198/jasa.2009.0126}
}
@article{chiquet2017fast,
title={Fast tree inference with weighted fusion penalties},
author={Chiquet, Julien and Gutierrez, Pierre and Rigaill, Guillem},
journal={Journal of Computational and Graphical Statistics},
volume={26},
number={1},
pages={205--216},
year={2017},
publisher={Taylor \& Francis}
}
@article{chi2015splitting,
title={Splitting methods for convex clustering},
author={Chi, Eric C and Lange, Kenneth},
journal={Journal of Computational and Graphical Statistics},
volume={24},
number={4},
pages={994--1013},
year={2015},
publisher={Taylor \& Francis}
}
@article{Beck2009,
author = {Beck, Amir and Teboulle, Marc},
year = {2009},
month = {01},
pages = {183-202},
title = {A Fast Iterative Shrinkage-Thresholding Algorithm for Linear Inverse Problems},
volume = {2},
journal = {SIAM J. Imaging Sciences},
doi = {10.1137/080716542}
}
@MISC{Rocha2008,
author = {Guilherme V. Rocha and Peng Zhao and Bin Yu},
title = {A path following algorithm for Sparse Pseudo-Likelihood Inverse Covariance Estimation (SPLICE)},
year = {2008}
}
@article{Rothman2008,
author = {Adam J. Rothman and Peter J. Bickel and Elizaveta Levina and Ji Zhu},
title = {{Sparse permutation invariant covariance estimation}},
volume = {2},
journal = {Electronic Journal of Statistics},
number = {none},
publisher = {Institute of Mathematical Statistics and Bernoulli Society},
pages = {494 -- 515},
keywords = {Cholesky decomposition, Covariance matrix, high dimension low sample size, large p small n, Lasso, Sparsity},
year = {2008},
doi = {10.1214/08-EJS176},
URL = {https://doi.org/10.1214/08-EJS176}
}
@article{Banerjee2008,
author = {Banerjee, Onureena and El Ghaoui, Laurent and d'Aspremont, Alexandre},
title = {Model Selection Through Sparse Maximum Likelihood Estimation for Multivariate Gaussian or Binary Data},
year = {2008},
issue_date = {6/1/2008},
publisher = {JMLR.org},
volume = {9},
issn = {1532-4435},
month = jun,
pages = {485–516},
numpages = {32}
}
@article{Park2007,
author = {Park, Mee Young and Hastie, Trevor and Tibshirani, Robert},
title = "{Averaged gene expressions for regression}",
journal = {Biostatistics},
volume = {8},
number = {2},
pages = {212-227},
year = {2006},
month = {05},
issn = {1465-4644},
doi = {10.1093/biostatistics/kxl002},
url = {https://doi.org/10.1093/biostatistics/kxl002},
eprint = {https://academic.oup.com/biostatistics/article-pdf/8/2/212/622669/kxl002.pdf},
}
@article{Yuan2007,
author = {Yuan, Ming and Lin, Yi},
title = "{Model selection and estimation in the Gaussian graphical model}",
journal = {Biometrika},
volume = {94},
number = {1},
pages = {19-35},
year = {2007},
month = {03},
issn = {0006-3444},
doi = {10.1093/biomet/asm018},
url = {https://doi.org/10.1093/biomet/asm018},
eprint = {https://academic.oup.com/biomet/article-pdf/94/1/19/617853/asm018.pdf},
}
@article{Friedman2007,
author = {Friedman, Jerome and Hastie, Trevor and Tibshirani, Robert},
file = {:Users/doedmond.sanou/Library/Application Support/Mendeley Desktop/Downloaded/Friedman, Hastie, Tibshirani - 2007 - Sparse inverse covariance estimation with the graphical lasso.pdf:pdf},
title = {{Sparse inverse covariance estimation with the graphical lasso}},
year = {2007}
}
@article{Yuan2006,
author = {Ming Yuan and Yi Lin},
title = {Model selection and estimation in regression with grouped variables},
journal = {JOURNAL OF THE ROYAL STATISTICAL SOCIETY, SERIES B},
year = {2006},
volume = {68},
pages = {49--67}
}
@article{Meinshausen2006,
author = {Meinshausen, Nicolai and B{\"{u}}hlmann, Peter},
doi = {10.1214/009053606000000281},
eprint = {0608017},
issn = {00905364},
journal = {Annals of Statistics},
keywords = {Covariance selection,Gaussian graphical models,Linear regression,Penalized regression},
month = {jun},
number = {3},
pages = {1436--1462},
primaryClass = {math},
publisher = {Institute of Mathematical Statistics},
title = {{High-dimensional graphs and variable selection with the Lasso}},
url = {http://projecteuclid.org/euclid.aos/1152540754},
volume = {34},
year = {2006}
}
@article{Tibshirani2005,
author = {Robert Tibshirani and Michael Saunders and Saharon Rosset and Ji Zhu and Keith Knight},
title = {Sparsity and smoothness via the fused lasso},
journal = {Journal of the Royal Statistical Society Series B},
year = {2005},
pages = {91--108}
}
@article{tibshirani1996,
added-at = {2009-04-04T18:01:35.000+0200},
author = {Tibshirani, R.},
biburl = {https://www.bibsonomy.org/bibtex/290e648276aa6cd3c601e7c0a54366233/dieudonnew},
interhash = {334927808d42a9a6bf8eae717fed41b3},
intrahash = {90e648276aa6cd3c601e7c0a54366233},
journal = {Journal of the Royal Statistical Society (Series B)},
keywords = {imported},
pages = {267-288},
timestamp = {2009-04-04T18:01:35.000+0200},
title = {Regression Shrinkage and Selection via the Lasso},
volume = 58,
year = 1996
}
@book{Lauritzen1996,
author = {Lauritzen, Steffen L.},
isbn = {9780198522195},
mendeley-groups = {Books},
pages = {298},
publisher = {Clarendon Press},
title = {{Graphical models}},
url = {https://global.oup.com/academic/product/graphical-models-9780198522195?cc=fr&lang=en&},
year = {1996}
}
@article{Dempster1972,
author = {Dempster, A. P.},
doi = {10.2307/2528966},
issn = {0006341X},
journal = {Biometrics},
mendeley-groups = {Gaussian GM},
month = {mar},
number = {1},
pages = {157},
publisher = {International Biometric Society},
title = {{Covariance Selection}},
url = {https://www.jstor.org/stable/2528966?origin=crossref},
volume = {28},
year = {1972}
}
@article{Hsieh,
author = {Hsieh, Cho-Jui and Sustik, M{\'{a}}ty{\'{a}}s A and Dhillon, Inderjit S and Ravikumar, Pradeep and Poldrack, Russell A},
title = {{BIG \& QUIC: Sparse Inverse Covariance Estimation for a Million Variables}}
}
@article{computo,
title = {Computo: reproducible computational/algorithmic contributions in statistics and machine learning},
author = {{Computo Team}},
year = {2021},
journal = {computo}
}
@Manual{R-base,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2020},
url = {https://www.R-project.org/},
}
@Manual{R-reticulate,
title = {reticulate: Interface to Python},
author = {Kevin Ushey and JJ Allaire and Yuan Tang},
year = {2020},
note = {R package version 1.18},
url = {https://github.com/rstudio/reticulate},
}
@article{perez2011python,
title = {Python: an ecosystem for scientific computing},
author = {Perez, Fernando and Granger, Brian E and Hunter, John D},
journal = {Computing in Science \\& Engineering},
volume = {13},
number = {2},
pages = {13--21},
year = {2011},
publisher = {AIP Publishing}
}