-
Notifications
You must be signed in to change notification settings - Fork 8
/
kavli19.html
472 lines (304 loc) · 9.97 KB
/
kavli19.html
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
<!DOCTYPE html>
<html>
<head>
<title>Kavli</title>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8"/>
<link rel="stylesheet" href="fonts/quadon/quadon.css">
<link rel="stylesheet" href="fonts/gentona/gentona.css">
<link rel="stylesheet" href="slides_style.css">
<script type="text/javascript" src="assets/plotly/plotly-latest.min.js"></script>
</head>
<body>
<textarea id="source">
name:opening
# NeuroData (Science)
Joshua T. Vogelstein
<img src="images/neurodata_purple.png" style="height:150px;float:right;"/>
<br><br><br><br><br><br><br><br><br><br>
<img src="images/funding/jhu_bme_blue.png" STYLE="HEIGHT:95px;"/>
<img src="images/funding/KNDI.png" STYLE="HEIGHT:95px;"/>
.foot[[jovo@jhu.edu](mailto:[email protected]) | <http://neurodata.io/talks/> | [@neuro_data](https://twitter.com/neuro_data)]
---
### What is Neural Data Science?
A field that develops and applies statistical models, algorithms, and (database / machine learning) systems to
- manage
- visualize
- wrangle
- summarize
- generalize
- control
neural data.
---
### Why is it hard?
1. volume: terabytes
2. variety: multi-modal (images, atlases, annotations, networks)
4. veracity: noisy
Subject matter expertise is required to mitigate these challenges, including
- computer science
- statistical machine learning
- brain science
---
### NeuroData Approach
1. build computational tools for manage & visualize
2. build statistical tools wrangle, summarize, and control
3. apply them to answer hard & important questions!
---
### Manage
Data management systems enable users to create, read, edit, and delete "records"
<!-- NeuroData management has the following requirements: -->
- stores multiple modalities (e.g., images & annotations)
- scales to terabytes
- atlases
- annotations
- networks
---
#### Example: NeuroData Cloud
<img src="images/bossDB.png" STYLE="width:100%;"/>
- 200+ teravoxels
- 100+ public & private datasets
- 30+ collaborators
- All 3D+ data & annotations (no ephys, etc.)
- Largest public open neuroscience data repository in the world!
.footnote[https://neurodata.io/ndcloud/]
---
### Visualize
Data visualization systems generate maps, charts, and tables to highlight/illustrate insightful perspectives on the data.
- pan
- zoom
- overlay multiple channels
- overlay annotations
- manually annotate
---
#### Example: NeuroGlancer
<img src="images/AT_rorb.png" style="position:absolute; left:0px; top:0px; width: 100%;"/>
.footnote[https://github.com/neurodata/neuroglancer]
---
### Wrangle
Data wrangling consists of any operation one applies to the data that maintains its representation, such as outlier detection, missing value imputation, and deconvolution
- bias field correction
- motion correction
- nonlinear multi-modal registration
---
#### Example: COBALT
<img src="images/ndreg.png" style="width: 100%;"/>
- Large deformation diffeomorphic metric mapping (LDDMM)
- Fully automatic (no landmarks)
- Modalities: iDisco, CLARITY, MRI, histology, etc.,
- Species: human, rat, mouse, zebrafish...
.footnote[https://neurodata.io/ndreg/]
---
### Summarize
Data summaries include point estimates, confidence intervals, clusters, principle components analysis, etc.
- network estimation from MRI
- spike detection from calcium imaging
- synapse detection
- cell body detection from CLARITY images
---
#### Example: COBALT
<img src="images/clarity_cells.png" style="position:absolute; left:0px; top:0px; height: 100%;"/>
.footnote[https://neurodata.io/ndreg]
---
### Generalize
Infer properties of a "population" (typically very high-dimensional)
- hypothesis testing
- modeling
- simulation
---
<!-- ### Example: 20 nonlinear simulations -->
<img src="images/FigSimVisual.svg" style="width: 100%;"/>
---
<!-- #### Example: MGC -->
<img src="images/FigHDPower.png" style="width: 100%;"/>
.footnote[https://neurodata.io/mgc]
---
### Predict
Prediction the something about a future sample given a data corpus
- classify: X is of type A
- regress: given X, Y is expected to be 6
- forecast: X is expected to be 6 tomorrow
---
### Example: RerF
<img src="images/error_histogram_benchmarks.png" style="width: 100%;"/>
- generalization of random forests
- significantly improve over best machine learning algs on >100 benchmark problems
.footnote[https://neurodata.io/rerf/]
---
class: middle
## .center[Applications in Connectomics]
---
### Human Connectome Heritability
<img src="images/human_connectome_heritability.png" style="width: 100%;"/>
.footnote[https://neurodata.io/graspy]
---
### Modeling Drosophila Mushroom Body
<img src="images/drosophila_model.png" style="width: 100%;"/>
.footnote[https://neurodata.io/graspy]
---
class: inverse
### Batch Effects in Connectomics
<img src="images/batch.png" style="width: 100%;"/>
- 20 datasets, >3000 scans
.footnote[https://neurodata.io/ndmg]
---
class: inverse
### Batch Effects in Connectomics
<img src="images/batch_sex.png" style="width: 100%;"/>
- 20 datasets, >3000 scans
- sex effect is smaller than site effect
.footnote[https://neurodata.io/ndmg]
---
### Papers
1. Vogelstein et al. *Nature Methods* (2018) [[manage & viz]](https://rdcu.be/banSS)
2. Kutten et al. *MICCAI* (2018) [[wrangle]](https://link.springer.com/chapter/10.1007%2F978-3-319-66182-7_32)
3. Vogelstein et al. *eLife* (2019) [[generalize]](https://elifesciences.org/articles/41690)
4. Tomita et al. *arXiv* (2015) [[predict]](https://arxiv.org/abs/1506.03410)
5. Athreya et al. *JMLR* (2018) [[graphs]](http://jmlr.org/papers/v18/17-448.html)
6. Kiar et al. *bioRxiv* (2018) [[MRI]](https://www.biorxiv.org/content/10.1101/188706v6)
.pull-left[
##### Tools
- [ndcloud](https://neurodata.io/ndcloud)
- [COBALT](https://neurodata.io/ndreg)
- [MGC](https://neurodata.io/mgc)
- [RerF](https://neurodata.io/rerf)
- [GrasPy](https://neurodata.io/graspy)
- [ndmg](https://neurodata.io/ndmg)
]
.pull-right[
##### Collaborations
- JHU Neuro, CS, AMS,
- JHSPH Biostats
- Stanford (dlab)
- Child Mind Institute
- Allen Institute
- Janelia Research Campus
- Applied Physics Lab
- Google
]
---
### Acknowledgements
<div class="small-container">
<img src="faces/cep.png"/>
<div class="centered">Carey Priebe</div>
</div>
<div class="small-container">
<img src="faces/randal.jpg"/>
<div class="centered">Randal Burns</div>
</div>
<div class="small-container">
<img src="faces/mim.jpg"/>
<div class="centered">Michael Miller</div>
</div>
<div class="small-container">
<img src="faces/dtward.jpg"/>
<div class="centered">Daniel Tward</div>
</div>
<div class="small-container">
<img src="faces/ebridge.jpg"/>
<div class="centered">Eric Bridgeford</div>
</div>
<div class="small-container">
<img src="faces/vikram.jpg"/>
<div class="centered">Vikram Chandrashekhar</div>
</div>
<div class="small-container">
<img src="faces/drishti.jpg"/>
<div class="centered">Drishti Mannan</div>
</div>
<div class="small-container">
<img src="faces/jesse.jpg"/>
<div class="centered">Jesse Patsolic</div>
</div>
<div class="small-container">
<img src="faces/falk_ben.jpg"/>
<div class="centered">Benjamin Falk</div>
</div>
<div class="small-container">
<img src="faces/kwame.jpg"/>
<div class="centered">Kwame Kutten</div>
</div>
<div class="small-container">
<img src="faces/perlman.jpg"/>
<div class="centered">Eric Perlman</div>
</div>
<div class="small-container">
<img src="faces/loftus.jpg"/>
<div class="centered">Alex Loftus</div>
</div>
<div class="small-container">
<img src="faces/bcaffo.jpg"/>
<div class="centered">Brian Caffo</div>
</div>
<div class="small-container">
<img src="faces/minh.jpg"/>
<div class="centered">Minh Tang</div>
</div>
<div class="small-container">
<img src="faces/avanti.jpg"/>
<div class="centered">Avanti Athreya</div>
</div>
<div class="small-container">
<img src="faces/vince.jpg"/>
<div class="centered">Vince Lyzinski</div>
</div>
<div class="small-container">
<img src="faces/dpmcsuss.jpg"/>
<div class="centered">Daniel Sussman</div>
</div>
<div class="small-container">
<img src="faces/youngser.jpg"/>
<div class="centered">Youngser Park</div>
</div>
<div class="small-container">
<img src="faces/cshen.jpg"/>
<div class="centered">Cencheng Shen</div>
</div>
<div class="small-container">
<img src="faces/shangsi.jpg"/>
<div class="centered">Shangsi Wang</div>
</div>
<div class="small-container">
<img src="faces/tyler.jpg"/>
<div class="centered">Tyler Tomita</div>
</div>
<div class="small-container">
<img src="faces/james.jpg"/>
<div class="centered">James Brown</div>
</div>
<div class="small-container">
<img src="faces/disa.jpg"/>
<div class="centered">Disa Mhembere</div>
</div>
<div class="small-container">
<img src="faces/pedigo.jpg"/>
<div class="centered">Ben Pedigo</div>
</div>
<div class="small-container">
<img src="faces/jaewon.jpg"/>
<div class="centered">Jaewon Chung</div>
</div>
<div class="small-container">
<img src="faces/gkiar.jpg"/>
<div class="centered">Greg Kiar</div>
</div>
<div class="small-container">
<img src="faces/jeremias.png"/>
<div class="centered">Jeremias Sulam</div>
</div><span style="font-size:200%; color:red;">♥, 🦁, 👪, 🌎, 🌌</span>
<img src="images/funding/nsf_fpo.png" STYLE="HEIGHT:95px;"/>
<img src="images/funding/nih_fpo.png" STYLE="HEIGHT:95px;"/>
<img src="images/funding/darpa_fpo.png" STYLE=" HEIGHT:95px;"/>
<img src="images/funding/iarpa_fpo.jpg" STYLE="HEIGHT:95px;"/>
<img src="images/funding/KAVLI.jpg" STYLE="HEIGHT:95px;"/>
<img src="images/funding/schmidt.jpg" STYLE="HEIGHT:95px;"/>
---
class:center
<img src="images/lion_l2m.JPG" style="position:absolute; top:0px; left:0px; height:100%;"/>
</textarea>
<!-- <script src="https://gnab.github.io/remark/downloads/remark-latest.min.js"></script> -->
<script src="remark-latest.min.js"></script>
<script type="text/javascript">
var options = {};
var slideshow = remark.create(options)
</script>
</body>
</html>