forked from ankitgoyalstl/Masters-Thesis
-
Notifications
You must be signed in to change notification settings - Fork 0
/
Bibliography.bib
464 lines (408 loc) · 16.5 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
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
@article{hilbert2011world,
title = {{The World's Technological Capacity to Store, Communicate, and Compute Information}},
author = {Hilbert, Martin and L{\'o}pez, Priscila},
journal = {Science},
volume = {332},
number = {6025},
pages = {60--65},
year = {2011},
doi = {10.1126/science.1200970},
publisher = {American Association for the Advancement of Science}
}
@article{stephens2015big,
title={{Big Data: Astronomical or Genomical?}},
author={Stephens, Zachary D and Lee, Skylar Y and Faghri, Faraz and Campbell, Roy H and Zhai, Chengxiang and Efron, Miles J and Iyer, Ravishankar and Schatz, Michael C and Sinha, Saurabh and Robinson, Gene E},
journal={PLoS Biology},
volume={13},
number={7},
pages={1-11},
year={2015},
publisher={Public Library of Science}
}
@article{hindorff2011catalog,
title={{A Catalog of published Genome-wide Association Studies}},
author={Hindorff, Lucia A and Junkins, Heather A and Hall, PN and Mehta, JP and Manolio, TA},
year={2011}
}
@article{welter2014nhgri,
title={{The NHGRI GWAS Catalog, a curated resource of SNP-trait associations}},
author={Welter, Danielle and MacArthur, Jacqueline and Morales, Joannella and Burdett, Tony and Hall, Peggy and Junkins, Heather and Klemm, Alan and Flicek, Paul and Manolio, Teri and Hindorff, Lucia and others},
journal={Nucleic Acids Research},
volume={42},
number={D1},
pages={D1001--D1006},
year={2014},
publisher={Oxford Univ Press}
}
@article{harris1954distributional,
title={{Distributional Structure}},
author={Harris, Zellig S},
journal={Word},
volume={10},
number={2-3},
pages={146--162},
year={1954},
publisher={Taylor \& Francis}
}
@article{min2012towards,
title={Towards large-scale unsupervised relation extraction from the web},
author={Min, Bonan and Shi, Shuming and Grishman, Ralph and Lin, Chin-Yew},
journal={International Journal on Semantic Web and Information Systems (IJSWIS)},
volume={8},
number={3},
pages={1--23},
year={2012},
publisher={IGI Global}
}
@phdthesis{min2013relation,
title={{Relation Extraction with Weak Supervision and Distributional Semantics}},
author={Min, Bonan},
year={2013},
school={New York University}
}
@inproceedings{zeng2014relation,
title={{Relation Classification via Convolutional Deep Neural Network.}},
author={Zeng, Daojian and Liu, Kang and Lai, Siwei and Zhou, Guangyou and Zhao, Jun and others},
booktitle={COLING},
pages={2335--2344},
year={2014}
}
@article{jain2016weakly,
title={Weakly supervised learning of biomedical information extraction from curated data},
author={Jain, Suvir and Kashyap, R and Kuo, Tsung-Ting and Bhargava, Shitij and Lin, Gordon and Hsu, Chun-Nan},
journal={BMC Bioinformatics},
volume={17},
number={1},
pages={1},
year={2016},
publisher={BioMed Central}
}
@inproceedings{hong2005relation,
title={Relation extraction using support vector machine},
author={Hong, Gumwon},
booktitle={International Conference on Natural Language Processing},
pages={366--377},
year={2005},
organization={Springer}
}
@inproceedings{yao2010multi,
title={{Multi-class Relationship Extraction from Biomedical Literature Using Maximum Entropy}},
author={Yao, Lin and Sun, Chengjie and Wang, Xiaolong and Wang, Xuan},
booktitle={Intelligent Information Hiding and Multimedia Signal Processing (IIH-MSP), 2010 Sixth International Conference on},
pages={551--554},
year={2010},
organization={IEEE}
}
@techreport{riesbeck1976comprehension,
title={{Comprehension by Computer: Expectation-Based Analysis of Sentences in Context.}},
author={Riesbeck, Christopher K and Schank, Roger C},
year={1976},
institution={DTIC Document}
}
@inproceedings{andersen1992automatic,
title={Automatic extraction of facts from press releases to generate news stories},
author={Andersen, Peggy M and Hayes, Philip J and Huettner, Alison K and Schmandt, Linda M and Nirenburg, Irene B and Weinstein, Steven P},
booktitle={Proceedings of the third conference on Applied Natural Language Processing},
pages={170--177},
year={1992},
organization={Association for Computational Linguistics}
}
@inproceedings{grishman1996message,
title={{Message Understanding Conference-6: A Brief History.}},
author={Grishman, Ralph and Sundheim, Beth},
booktitle={COLING},
volume={96},
pages={466--471},
year={1996}
}
@inproceedings{guodong2005exploring,
title={Exploring various knowledge in relation extraction},
author={GuoDong, Zhou and Jian, Su and Jie, Zhang and Min, Zhang},
booktitle={Proceedings of the 43rd annual meeting on Association for Computational Linguistics},
pages={427--434},
year={2005},
organization={Association for Computational Linguistics}
}
@inproceedings{nguyen2014employing,
title={{Employing Word Representations and Regularization for Domain Adaptation of Relation Extraction.}},
author={Nguyen, Thien Huu and Grishman, Ralph},
booktitle={Association for Computational Linguistics},
pages={68--74},
year={2014}
}
@inproceedings{nguyen2015relation,
title={{Relation Extraction: Perspective from Convolutional Neural Networks}},
author={Nguyen, Thien Huu and Grishman, Ralph},
booktitle={Proceedings of NAACL-HLT},
pages={39--48},
year={2015}
}
@inproceedings{qian2008exploiting,
title={Exploiting constituent dependencies for tree kernel-based semantic relation extraction},
author={Qian, Longhua and Zhou, Guodong and Kong, Fang and Zhu, Qiaoming and Qian, Peide},
booktitle={Proceedings of the 22nd International Conference on Computational Linguistics-Volume 1},
pages={697--704},
year={2008},
organization={Association for Computational Linguistics}
}
@inproceedings{culotta2004dependency,
title={Dependency tree kernels for relation extraction},
author={Culotta, Aron and Sorensen, Jeffrey},
booktitle={Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics},
pages={423},
year={2004},
organization={Association for Computational Linguistics}
}
@inproceedings{hasegawa2004discovering,
title={Discovering relations among named entities from large corpora},
author={Hasegawa, Takaaki and Sekine, Satoshi and Grishman, Ralph},
booktitle={Proceedings of the 42nd Annual Meeting on Association for Computational Linguistics},
pages={415},
year={2004},
organization={Association for Computational Linguistics}
}
@inproceedings{chen2005unsupervised,
title={Unsupervised feature selection for relation extraction},
author={Chen, Jinxiu and Ji, Donghong and Tan, Chew Lim and Niu, Zhengyu},
booktitle={Proceedings of IJCNLP},
year={2005}
}
@inproceedings{mintz2009distant,
title={Distant supervision for relation extraction without labeled data},
author={Mintz, Mike and Bills, Steven and Snow, Rion and Jurafsky, Dan},
booktitle={Proceedings of the Joint Conference of the 47th Annual Meeting of the ACL and the 4th International Joint Conference on Natural Language Processing of the AFNLP: Volume 2-Volume 2},
pages={1003--1011},
year={2009},
organization={Association for Computational Linguistics}
}
@inproceedings{hoffmann2011knowledge,
title={Knowledge-based weak supervision for information extraction of overlapping relations},
author={Hoffmann, Raphael and Zhang, Congle and Ling, Xiao and Zettlemoyer, Luke and Weld, Daniel S},
booktitle={Proceedings of the 49th Annual Meeting of the Association for Computational Linguistics: Human Language Technologies-Volume 1},
pages={541--550},
year={2011},
organization={Association for Computational Linguistics}
}
@article{Goyal2016712,
title = {{Natural Language Processing Using Kepler Workflow System: First Steps}},
journal = {Procedia Computer Science},
volume = {80},
pages = {712 - 721},
year = {2016},
note = {International Conference on Computational Science 2016, \{ICCS\} 2016, 6-8 June 2016, San Diego, California, \{USA\}},
issn = {[1877-0509]},
author = {Ankit Goyal and Alok Singh and Shitij Bhargava and Daniel Crawl and Ilkay Altintas and Chun-Nan Hsu},
}
@article{hindorff2014catalog,
title={{Comprehensive curation and visualization of ethnicity information from published genome-wide association studies (GWAS): an improved GWAS catalog.}},
author={Lucia A. Hindorff and Jacqueline A. L. MacArthur and Joannella Morales and Emily H. Bowler and Peggy Hall and Kent Klemm and Heather A. Junkins and Tony Burdett and Danielle Welter and Teri A. Manolio, and Helen Parkinson},
year={2014}
}
@article{hubel1959receptive,
title={Receptive fields of single neurones in the cat's striate cortex},
author={Hubel, David H and Wiesel, Torsten N},
journal={The Journal of physiology},
volume={148},
number={3},
pages={574--591},
year={1959},
publisher={Wiley Online Library}
}
@article{grefenstette2014deep,
title={A deep architecture for semantic parsing},
author={Grefenstette, Edward and Blunsom, Phil and de Freitas, Nando and Hermann, Karl Moritz},
journal={arXiv preprint arXiv:1404.7296},
year={2014}
}
@article{kalchbrenner2014convolutional,
title={A convolutional neural network for modelling sentences},
author={Kalchbrenner, Nal and Grefenstette, Edward and Blunsom, Phil},
journal={arXiv preprint arXiv:1404.2188},
year={2014}
}
@article{kim2014convolutional,
title={Convolutional neural networks for sentence classification},
author={Kim, Yoon},
journal={arXiv preprint arXiv:1408.5882},
year={2014}
}
@inproceedings{son2012continuous,
title={Continuous space translation models with neural networks},
author={Son, Le Hai and Allauzen, Alexandre and Yvon, Fran{\c{c}}ois},
booktitle={Proceedings of the 2012 conference of the north American chapter of the Association for Computational Linguistics: Human language technologies},
pages={39--48},
year={2012},
organization={Association for Computational Linguistics}
}
@inproceedings{zeng2015distant,
title={Distant supervision for relation extraction via piecewise convolutional neural networks},
author={Zeng, Daojian and Liu, Kang and Chen, Yubo and Zhao, Jun},
booktitle={Proceedings of the 2015 Conference on Empirical Methods in Natural Language Processing (EMNLP), Lisbon, Portugal},
pages={17--21},
year={2015}
}
@inproceedings{mikolov2013distributed,
title={Distributed representations of words and phrases and their compositionality},
author={Mikolov, Tomas and Sutskever, Ilya and Chen, Kai and Corrado, Greg S and Dean, Jeff},
booktitle={Advances in neural information processing systems},
pages={3111--3119},
year={2013}
}
@article{johnson2014effective,
title={Effective use of word order for text categorization with convolutional neural networks},
author={Johnson, Rie and Zhang, Tong},
journal={arXiv preprint arXiv:1412.1058},
year={2014}
}
@inproceedings{pennington2014glove,
title={{Glove: Global Vectors for Word Representation.}},
author={Pennington, Jeffrey and Socher, Richard and Manning, Christopher D},
booktitle={EMNLP},
volume={14},
pages={1532--43},
year={2014}
}
@article{zeiler2012adadelta,
title={{ADADELTA: an adaptive learning rate method}},
author={Zeiler, Matthew D},
journal={arXiv preprint arXiv:1212.5701},
year={2012}
}
@article{collobert2011natural,
title={Natural language processing (almost) from scratch},
author={Collobert, Ronan and Weston, Jason and Bottou, L{\'e}on and Karlen, Michael and Kavukcuoglu, Koray and Kuksa, Pavel},
journal={Journal of Machine Learning Research},
volume={12},
number={Aug},
pages={2493--2537},
year={2011}
}
@inproceedings{craven1999constructing,
title={Constructing biological knowledge bases by extracting information from text sources.},
author={Craven, Mark and Kumlien, Johan and others},
booktitle={ISMB},
volume={1999},
pages={77--86},
year={1999}
}
@inproceedings{bunescu2007learning,
title={Learning to extract relations from the web using minimal supervision},
author={Bunescu, Razvan C and Mooney, Raymond},
booktitle={Annual meeting - Association for Computational Linguistics},
volume={45},
pages={576},
year={2007}
}
@inproceedings{riedel2010modeling,
title={Modeling relations and their mentions without labeled text},
author={Riedel, Sebastian and Yao, Limin and McCallum, Andrew},
booktitle={Joint European Conference on Machine Learning and Knowledge Discovery in Databases},
pages={148--163},
year={2010},
organization={Springer}
}
@inproceedings{surdeanu2012multi,
title={Multi-instance multi-label learning for relation extraction},
author={Surdeanu, Mihai and Tibshirani, Julie and Nallapati, Ramesh and Manning, Christopher D},
booktitle={Proceedings of the 2012 Joint Conference on Empirical Methods in Natural Language Processing and Computational Natural Language Learning},
pages={455--465},
year={2012},
organization={Association for Computational Linguistics}
}
@inproceedings{takamatsu2012reducing,
title={Reducing wrong labels in distant supervision for relation extraction},
author={Takamatsu, Shingo and Sato, Issei and Nakagawa, Hiroshi},
booktitle={Proceedings of the 50th Annual Meeting of the Association for Computational Linguistics: Long Papers-Volume 1},
pages={721--729},
year={2012},
organization={Association for Computational Linguistics}
}
@inproceedings{wang2011relation,
title={Relation extraction with relation topics},
author={Wang, Chang and Fan, James and Kalyanpur, Aditya and Gondek, David},
booktitle={Proceedings of the Conference on Empirical Methods in Natural Language Processing},
pages={1426--1436},
year={2011},
organization={Association for Computational Linguistics}
}
@inproceedings{wu2007autonomously,
title={Autonomously semantifying wikipedia},
author={Wu, Fei and Weld, Daniel S},
booktitle={Proceedings of the sixteenth ACM conference on Conference on information and knowledge management},
pages={41--50},
year={2007},
organization={ACM}
}
@inproceedings{yao2011structured,
title={Structured relation discovery using generative models},
author={Yao, Limin and Haghighi, Aria and Riedel, Sebastian and McCallum, Andrew},
booktitle={Proceedings of the Conference on Empirical Methods in Natural Language Processing},
pages={1456--1466},
year={2011},
organization={Association for Computational Linguistics}
}
@inproceedings{kok2008extracting,
title={Extracting semantic networks from text via relational clustering},
author={Kok, Stanley and Domingos, Pedro},
booktitle={Joint European Conference on Machine Learning and Knowledge Discovery in Databases},
pages={624--639},
year={2008},
organization={Springer}
}
@article{grishman2005nyu,
title={{NYU's English ACE 2005 system description}},
author={Grishman, Ralph and Westbrook, David and Meyers, Adam},
journal={ACE},
volume={5},
year={2005}
}
@article{zelenko2003kernel,
title={Kernel methods for relation extraction},
author={Zelenko, Dmitry and Aone, Chinatsu and Richardella, Anthony},
journal={Journal of machine learning research},
volume={3},
number={Feb},
pages={1083--1106},
year={2003}
}
@article{pyysalo2013distributional,
title={Distributional semantics resources for biomedical text processing},
author={Pyysalo, Sampo and Ginter, Filip and Moen, Hans and Salakoski, Tapio and Ananiadou, Sophia},
journal={Proceedings of Languages in Biology and Medicine},
year={2013}
}
@mastersthesis{kashyapthesis,
author = {Kashyap R. Tumkur},
title = {{Learning from the Catalog of GWAS to Extract Population Characteristics}},
school = {University of California, San Diego},
year = {2015},
}
@mastersthesis{malcomthesis,
author = {Malcom W. Greaves},
title = {{Relation Extraction using Distant Supervision, SVMs and Probabilistic First Order Logic}},
school = {Carnegie Mellon University},
year = {2014},
}
@mastersthesis{shitijthesis,
author = {Shitij Bhargava},
title = {{Learning from the Catalog of GWAS to Extract Population Characteristics}},
school = {University of California, San Diego},
year = {2015},
}
@inproceedings{jiang2007systematic,
title={{A Systematic Exploration of the Feature Space for Relation Extraction.}},
author={Jiang, Jing and Zhai, ChengXiang},
booktitle={HLT-NAACL},
pages={113--120},
year={2007}
}
@article{krallinger2008evaluation,
title={{Evaluation of text-mining systems for biology: overview of the Second BioCreative community challenge}},
author={Krallinger, Martin and Morgan, Alexander and Smith, Larry and Leitner, Florian and Tanabe, Lorraine and Wilbur, John and Hirschman, Lynette and Valencia, Alfonso},
journal={Genome biology},
volume={9},
number={2},
pages={1},
year={2008},
publisher={BioMed Central}
}