-
Notifications
You must be signed in to change notification settings - Fork 1
/
bibliography.bib
449 lines (407 loc) · 15.3 KB
/
bibliography.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
@article{li2016first,
title={The first step for neuroimaging data analysis: {DICOM} to {NIfTI} conversion},
author={Li, Xiangrui and Morgan, Paul S and Ashburner, John and Smith, Jolinda and Rorden, Christopher},
journal={Journal of neuroscience methods},
volume={264},
pages={47--56},
year={2016},
publisher={Elsevier}
}
@url{conp,
year = {Accessed: 23 Jul, 2021},
title = {Canadian Open Neuroscience Platform},
howpublished = {http://portal.conp.ca}
}
@article{wilkinson2016fair,
title={The {FAIR} Guiding Principles for scientific data management and stewardship},
author={Wilkinson, Mark D and Dumontier, Michel and Aalbersberg, IJsbrand Jan and Appleton, Gabrielle and Axton, Myles and Baak, Arie and Blomberg, Niklas and Boiten, Jan-Willem and da Silva Santos, Luiz Bonino and Bourne, Philip E and others},
journal={Scientific data},
volume={3},
number={1},
pages={1--9},
year={2016},
publisher={Nature Publishing Group}
}
@article{gardner2008neuroscience,
title={The neuroscience information framework: a data and knowledge environment for neuroscience},
author={Gardner, Daniel and Akil, Huda and Ascoli, Giorgio A and Bowden, Douglas M and Bug, William and Donohue, Duncan E and Goldberg, David H and Grafstein, Bernice and Grethe, Jeffrey S and Gupta, Amarnath and others},
journal={Neuroinformatics},
volume={6},
number={3},
pages={149--160},
year={2008},
publisher={Springer}
}
@article{kennedy2016nitrc,
title={The {NITRC} image repository},
author={Kennedy, David N and Haselgrove, Christian and Riehl, Jon and Preuss, Nina and Buccigrossi, Robert},
journal={NeuroImage},
volume={124},
pages={1069--1073},
year={2016},
publisher={Elsevier}
}
@article{markiewicz2021openneuro,
title={{OpenNeuro}: An open resource for sharing of neuroimaging data},
author={Markiewicz, Christopher J and Gorgolewski, Krzysztof Jacek and Feingold, Franklin and Blair, Ross and Halchenko, Yaroslav O and Miller, Eric and Hardcastle, Nell and Wexler, Joe and Esteban, Oscar and Goncalves, Mathias and others},
journal={bioRxiv},
year={2021},
publisher={Cold Spring Harbor Laboratory}
}
@misc{oracle,
title = {Oracle Machine Learning for {P}ython User's Guide, Release 1.0},
Author = {David McDermid},
Contributors = {Mark Hornick, Mandeep Kaur, Sherry Lamonica, Feng Li, Boriana Milenova, Venkatanathan Varadarajan , Andi Wang, Qin Wang, Yu Xiang},
howpublished = {\url{https://docs.oracle.com/en/database/oracle/machine-learning/oml4py/1/mlpug/algoritm-selection.html#GUID-C7A22403-6F4F-4C94-B193-220D0DCC2722}},
}
@article{bids,
title={The brain imaging data structure, a format for organizing and describing outputs of neuroimaging experiments},
author={Gorgolewski, Krzysztof J and Auer, Tibor and Calhoun, Vince D and Craddock, R Cameron and Das, Samir and Duff, Eugene P and Flandin, Guillaume and Ghosh, Satrajit S and Glatard, Tristan and Halchenko, Yaroslav O and others},
journal={Scientific data},
volume={3},
number={1},
pages={1--9},
year={2016},
publisher={Nature Publishing Group}
}
@inproceedings{missier2013w3c,
title={The W3C PROV family of specifications for modelling provenance metadata},
author={Missier, Paolo and Belhajjame, Khalid and Cheney, James},
booktitle={Proceedings of the 16th International Conference on Extending Database Technology},
pages={773--776},
year={2013}
}
@misc{https://doi.org/10.25495/7gxk-rd71,
doi = {10.25495/7GXK-RD71},
howpublished = {https://www.zenodo.org/},
author = {{European Organization For Nuclear Research} and {OpenAIRE}},
keywords = {FOS: Physical sciences, Publication, Dataset},
language = {en},
title = {Zenodo},
publisher = {CERN},
year = {2013}
}
@article{maumet2016sharing,
title={Sharing brain mapping statistical results with the neuroimaging data model},
author={Maumet, Camille and Auer, Tibor and Bowring, Alexander and Chen, Gang and Das, Samir and Flandin, Guillaume and Ghosh, Satrajit and Glatard, Tristan and Gorgolewski, Krzysztof J and Helmer, Karl G and others},
journal={Scientific data},
volume={3},
number={1},
pages={1--15},
year={2016},
publisher={Nature Publishing Group}
}
@misc{gitannex,
author = {Joey Hess},
title = { git-annex },
Operating_systems = {Linux,FreeBSD,Android,OS X, Windows},
year = {Accessed 23 Jul, 2021},
Size = {44.2 MB},
Type = {File synchronization},
License ={GPL3+, AGPL3+},
howpublished = {https://git-annex.branchable.com/}
}
@misc{datalad2021,
year = {2021},
title = {DataLad version 0.14.6},
howpublished = {https://doi.org/10.5281/zenodo.5034875}
}
@misc{UnitedNationsGeneralAssembly,
author = {United Nations General Assembly},
year = {2015},
title = {Sustainable Development Goals},
url = {\url{https://sustainabledevelopment.un.org/}}
}
@article{NeuroimagingDataModel,
title={Sharing brain mapping statistical results with the neuroimaging data model},
author={Maumet, Camille and Auer, Tibor and Bowring, Alexander and Chen, Gang and Das, Samir and Flandin, Guillaume and Ghosh, Satrajit and Glatard, Tristan and Gorgolewski, Krzysztof J and Helmer, Karl G and others},
journal={Scientific data},
volume={3},
number={1},
pages={1--15},
year={2016},
publisher={Nature Publishing Group}
}
@misc{DATSDocumentation,
author = { Philippe Rocca-Serra and Alejandra Gonzalez-Beltran. },
year = {2016},
title = {{bioCADDIE DATS}'s documentation},
howpublished = {https://datatagsuite.github.io/docs/html}
}
@misc{NIMHDataArchive,
author = {National Institute of Mental Health },
title = {NIMH Data Archive},
url = {\url{https://nda.nih.gov/}}
}
@article{sansone2017dats,
title={{DATS}, the data tag suite to enable discoverability of datasets},
author={Sansone, Susanna-Assunta and Gonzalez-Beltran, Alejandra and Rocca-Serra, Philippe and Alter, George and Grethe, Jeffrey S and Xu, Hua and Fore, Ian M and Lyle, Jared and Gururaj, Anupama E and Chen, Xiaoling and others},
journal={Scientific data},
volume={4},
number={1},
pages={1--8},
year={2017},
publisher={Nature Publishing Group}
}
@article{botvinik2020variability,
title={Variability in the analysis of a single neuroimaging dataset by many teams},
author={Botvinik-Nezer, Rotem and Holzmeister, Felix and Camerer, Colin F and Dreber, Anna and Huber, Juergen and Johannesson, Magnus and Kirchler, Michael and Iwanir, Roni and Mumford, Jeanette A and Adcock, R Alison and others},
journal={Nature},
pages={1--7},
year={2020},
publisher={Nature Publishing Group}
}
@book{rajaraman2011mining,
title={Mining of massive datasets},
author={Rajaraman, Anand and Ullman, Jeffrey David},
year={2011},
publisher={Cambridge University Press}
}
@article{koren2009matrix,
title={Matrix factorization techniques for recommender systems},
author={Koren, Yehuda and Bell, Robert and Volinsky, Chris},
journal={Computer},
volume={42},
number={8},
pages={30--37},
year={2009},
publisher={IEEE}
}
@inproceedings{hu2008collaborative,
title={Collaborative filtering for implicit feedback datasets},
author={Hu, Yifan and Koren, Yehuda and Volinsky, Chris},
booktitle={2008 Eighth IEEE International Conference on Data Mining},
pages={263--272},
year={2008},
organization={Ieee}
}
@article{gorgolewski2017openneuro,
title={OpenNeuro—a free online platform for sharing and analysis of neuroimaging data},
author={Gorgolewski, Krzysztof and Esteban, Oscar and Schaefer, Gunnar and Wandell, Brian and Poldrack, Russell},
journal={Organization for human brain mapping. Vancouver, Canada},
volume={1677},
number={2},
year={2017}
}
@article{kiar2019serverless,
title={A serverless tool for platform agnostic computational experiment management},
author={Kiar, Gregory and Brown, Shawn T and Glatard, Tristan and Evans, Alan C},
journal={Frontiers in neuroinformatics},
volume={13},
pages={12},
year={2019},
publisher={Frontiers}
}
@article{glatard2018boutiques,
title={Boutiques: a flexible framework to integrate command-line applications in computing platforms},
author={Glatard, Tristan and Kiar, Gregory and Aumentado-Armstrong, Tristan and Beck, Natacha and Bellec, Pierre and Bernard, R{\'e}mi and Bonnet, Axel and Brown, Shawn T and Camarasu-Pop, Sorina and Cervenansky, Fr{\'e}d{\'e}ric and others},
journal={GigaScience},
volume={7},
number={5},
pages={giy016},
year={2018},
publisher={Oxford University Press}
}
@article{bokde2015matrix,
title={Matrix factorization model in collaborative filtering algorithms: A survey},
author={Bokde, Dheeraj and Girase, Sheetal and Mukhopadhyay, Debajyoti},
journal={Procedia Computer Science},
volume={49},
pages={136--146},
year={2015},
publisher={Elsevier}
}
@inproceedings{bell2007improved,
title={Improved neighborhood-based collaborative filtering},
author={Bell, Robert M and Koren, Yehuda},
booktitle={KDD cup and workshop at the 13th ACM SIGKDD international conference on knowledge discovery and data mining},
pages={7--14},
year={2007},
organization={Citeseer}
}
@article{rossi2016syntactic,
title={A SYNTACTIC AND SEMANTIC VIEW OF BIG DATA},
author={Rossi, Rog{\'e}rio and Hirama, Kechi},
year={2016}
}
@article{vincent2016minc,
title={MINC 2.0: a flexible format for multi-modal images},
author={Vincent, Robert D and Neelin, Peter and Khalili-Mahani, Najmeh and Janke, Andrew L and Fonov, Vladimir S and Robbins, Steven M and Baghdadi, Leila and Lerch, Jason and Sled, John G and Adalat, Reza and others},
journal={Frontiers in neuroinformatics},
volume={10},
pages={35},
year={2016},
publisher={Frontiers}
}
@article{larobina2014medical,
title={Medical image file formats},
author={Larobina, Michele and Murino, Loredana},
journal={Journal of digital imaging},
volume={27},
number={2},
pages={200--206},
year={2014},
publisher={Springer}
}
@article{smith2002fast,
title={Fast robust automated brain extraction},
author={Smith, Stephen M},
journal={Human brain mapping},
volume={17},
number={3},
pages={143--155},
year={2002},
publisher={Wiley Online Library}
}
@article{la2021evaluating,
title={Evaluating recommender systems for {AI}-driven biomedical informatics},
author={La Cava, William and Williams, Heather and Fu, Weixuan and Vitale, Steve and Srivatsan, Durga and Moore, Jason H},
journal={Bioinformatics},
volume={37},
number={2},
pages={250--256},
year={2021},
publisher={Oxford University Press}
}
@article{fecher2014open,
title={Open science: one term, five schools of thought},
author={Fecher, Benedikt and Friesike, Sascha},
journal={Opening science},
pages={17--47},
year={2014},
publisher={Springer, Cham}
}
@incollection{pazzani2007content,
title={Content-based recommendation systems},
author={Pazzani, Michael J and Billsus, Daniel},
booktitle={The adaptive web},
pages={325--341},
year={2007},
publisher={Springer}
}
@article{dinov2014perfect,
title={The perfect neuroimaging-genetics-computation storm: collision of petabytes of data, millions of hardware devices and thousands of software tools},
author={Dinov, Ivo D and Petrosyan, Petros and Liu, Zhizhong and Eggert, Paul and Zamanyan, Alen and Torri, Federica and Macciardi, Fabio and Hobel, Sam and Moon, Seok Woo and Sung, Young Hee and others},
journal={Brain imaging and behavior},
volume={8},
number={2},
pages={311--322},
year={2014},
publisher={Springer}
}
@article{koren2015advances,
title={Advances in collaborative filtering},
author={Koren, Yehuda and Bell, Robert},
journal={Recommender systems handbook},
pages={77--118},
year={2015},
publisher={Springer}
}
@article{berrar2019cross,
title={Cross-validation},
author={Berrar, Daniel},
journal={Encyclopedia of bioinformatics and computational biology},
volume={1},
pages={542--545},
year={2019},
publisher={Academic}
}
@article{powers2007evaluation,
title={Evaluation: From precision, recall and F-factor to ROC, informedness, markedness \& correlation (Tech. Rep.)},
author={Powers, DM},
journal={Adelaide, Australia},
year={2007}
}
@inproceedings{lamprecht2010synthesis,
title={Synthesis-based loose programming},
author={Lamprecht, Anna-Lena and Naujokat, Stefan and Margaria, Tiziana and Steffen, Bernhard},
booktitle={2010 Seventh International Conference on the Quality of Information and Communications Technology},
pages={262--267},
year={2010},
organization={IEEE}
}
@inproceedings{naujokat2012loose,
title={Loose programming with PROPHETS},
author={Naujokat, Stefan and Lamprecht, Anna-Lena and Steffen, Bernhard},
booktitle={International Conference on Fundamental Approaches to Software Engineering},
pages={94--98},
year={2012},
organization={Springer}
}
@article{lamprecht2013user,
title={User-level workflow design},
author={Lamprecht, Anna-Lena},
journal={Lecture Notes in Computer Science},
volume={8311},
year={2013},
publisher={Springer}
}
@article{ison2013edam,
title={EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats},
author={Ison, Jon and Kala{\v{s}}, Mat{\'u}{\v{s}} and Jonassen, Inge and Bolser, Dan and Uludag, Mahmut and McWilliam, Hamish and Malone, James and Lopez, Rodrigo and Pettifer, Steve and Rice, Peter},
journal={Bioinformatics},
volume={29},
number={10},
pages={1325--1332},
year={2013},
publisher={Oxford University Press}
}
@article{palmblad2019automated,
title={Automated workflow composition in mass spectrometry-based proteomics},
author={Palmblad, Magnus and Lamprecht, Anna-Lena and Ison, Jon and Schw{\"a}mmle, Veit},
journal={Bioinformatics},
volume={35},
number={4},
pages={656--664},
year={2019},
publisher={Oxford University Press}
}
@article{gil2010wings,
title={Wings: Intelligent workflow-based design of computational experiments},
author={Gil, Yolanda and Ratnakar, Varun and Kim, Jihie and Gonzalez-Calero, Pedro and Groth, Paul and Moody, Joshua and Deelman, Ewa},
journal={IEEE Intelligent Systems},
volume={26},
number={1},
pages={62--72},
year={2010},
publisher={IEEE}
}
@article{kumar2021tool,
title={Tool recommender system in {G}alaxy using deep learning},
author={Kumar, Anup and Rasche, Helena and Gr{\"u}ning, Bj{\"o}rn and Backofen, Rolf},
journal={GigaScience},
volume={10},
number={1},
pages={giaa152},
year={2021},
publisher={Oxford University Press}
}
@inproceedings{tornede2019algorithm,
title={Algorithm selection as recommendation: From collaborative filtering to dyad ranking},
author={Tornede, Alexander and Wever, Marcel and H{\"u}llermeier, Eyke},
booktitle={CI Workshop, Dortmund},
year={2019}
}
@article{vartak2017meta,
title={A meta-learning perspective on cold-start recommendations for items},
author={Vartak, Manasi and Thiagarajan, Arvind and Miranda, Conrado and Bratman, Jeshua and Larochelle, Hugo},
year={2017}
}
@inproceedings{tornede2020extreme,
title={Extreme algorithm selection with dyadic feature representation},
author={Tornede, Alexander and Wever, Marcel and H{\"u}llermeier, Eyke},
booktitle={International Conference on Discovery Science},
pages={309--324},
year={2020},
organization={Springer}
}
@article{schafer2018dyad,
title={Dyad ranking using Plackett--Luce models based on joint feature representations},
author={Sch{\"a}fer, Dirk and H{\"u}llermeier, Eyke},
journal={Machine Learning},
volume={107},
number={5},
pages={903--941},
year={2018},
publisher={Springer}
}