-
Notifications
You must be signed in to change notification settings - Fork 8
/
data19.html
421 lines (247 loc) · 7.99 KB
/
data19.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
<!DOCTYPE html>
<html>
<head>
<title>NeuroDataSets</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
## NeuroDataSets
Joshua T. Vogelstein
<img src="images/neurodata_purple.png" style="height:250px; 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)]
---
## list of projects
- description, goal, next
- people/teams that claim one means that they will work on it and be first author on paper that we write about it this year
- will involve some data munging, some analysis, possibly some novel methods development
- will be the top research priority for people who claim it
- will visit the data generators in next month or so to get more details / make more plans
- goal is to submit nature paper nlt end of calendar year
---
### Satterthwaite Irritation (pitt)
- human dMRI graphs provided
- ~100 subjects
- age, sex, irritation provided
<br>
- goal: find signal subgraph with > chance accuracy
- next: run different signal subgraph codes on data
.footnote[guodong?]
---
### Satterthwaite Multiview biclustering (pitt)
- several hundred humans
- multiple views of each, including structural brain imaging, dMRI, psychiatric evaluation
<br>
- goal: learn an interpretable joint embedding
- next: get data, start writing what to do on whiteboard, consider both RF-based on linear-based methods
---
### kiehl (new mexico)
- human strucual MRI & derived features
- ~500 subjects
- age, sex, {murderer, violent non-murderer, non-violent}
<br>
- goal: classification > 0.55 accuracy
- next: run RerF on data
.footnote[alex?]
---
### tolias (baylor/houston)
- mouse single cell ophys
- $>$6,300 cells
- 40k time steps
- time-varying stimulus
<br>
- goal: estimate time-varying intrinsic dimension and/or amount of information brain data has about stimulus
- next: run URerF on data,
- next: extend RerF to support multivariate regression
.footnote[meghana?]
---
### hillman (columbia)
- mouse wide field ophys
- 512 x 512 times for several thousand time steps
- i don't think we have stimulus
<br>
- goal: estimate time-varying intrinsic dimension and/or amount of information brain data has about stimulus
- next: parallel/distributed implementation of RerF/URerF
.footnote[meghana?]
---
### honey (jhu)
- 2 human fMRI datasets, each with ~200 ROIs and ~200 time-steps
- we could get stimulus
<br>
- goal: estimate time-varying intrinsic dimensions and/or amount of information brain data has about stimulus
- next: run URerF on data
.footnote[meghana?]
---
### c elegans (einstein in nyc)
- 2 sexes, 2 connectomes each
- brain across sexes are partially matched
- cell lineage for each neuron
<br>
- goal: hclust graph in such a way to "matches" lineage
- next: run hclust on data
.footnote[pedigo?]
---
### drosophila model selection (janelia/cambridge)
- 2 mushroom bodies (left and right)
- left and right not perfectly matched
<br>
- goal: model selection
- next: get updated data from michael winding
.footnote[pedigo?]
---
### drosophila bilateral homology (janelia/cambridge)
- left and right mushroom bodies
<br>
- goal: test whether left is equivalent to right
- next: get up to date on me + cep + brandon results
.footnote[pedigo?]
---
### HCP data (milham, nyc)
- ~1000 subjects human dMRI graphs
- mono, di, sib
<br>
- goal: quantify heritability
- next: update draft? formalize our notion of heritability? is it discriminability?
.footnote[jaewon]
---
### sea lion and coyote (berns, atlana / milham, nyc)
- 4 sea lions and 4 coyotes
- dMRI graph and atlas from each
<br>
- goal: compare and contrast
- next: do it
.footnote[nobody?]
---
### brazilian child study (milham, nyc)
- several thousand kids
- PRS for each
- some brain imaging data for each
<br>
- goal: determine which "features" of brain data are associated with which PRS
- next: get data into "shape"
.footnote[nobody?]
---
### human cci (milham, nyc)
- HBN + HCP data including dMRI covariates
- run signal subgraph on one dataset to find signal subgraph for some covariate
- once found for one dataset, run the same exact code on the other dataset, to find approximately same signal subgraph
<br>
goal: find signal subgraph robust to site specific batch effects
next: get data organized
.footnote[nobody?]
---
### human batch effects
- 15-20 differnet dMRI and fMRI datasets
- age and sex covariates for each
- graphs already estimated for all
<br>
goal: characterize the magnitude of the batch effects
next: run graph-mgc to test for differences between batches
.footnote[eric?]
---
### some sebastian data (sebastian, princeton)
- connectome of something, unclear the details
<br>
- goal: help them cluster (not first author)
- next: schedule time to visit
.footnote[nobody?]
---
### some jeff data (jeff, harvard)
- connectome of something, unclear the details
<br>
- goal: help them cluster (not first author)
- next: schedule time to visit
.footnote[nobody?]
---
### developmental c. elegans (samuel, harvard)
- connectome of c. elegans at multiple developmental stages
<br>
- goal: anything (unclear if 1st author)
- next: schedule time to visit
.footnote[nobody?]
---
class: inverse, middle
.center[task switch]
---
### neurodata tools workshop
we host weeklong workshop:
- mon: mgc
- tues: rerf
- wed: graspy
- thurs: cobalt / lddmm
- fri: ndmg
---
each day would be organized something like:
- 8am: breakfast
- 09:00-10:15: math/stats lecture
- 10:15-10:45: snack beak
- 10:45-12:00: demo/tutorial on relevant codebase
<br>
- 12: lunch
<br>
- 1-3: hacking on using code to solve some problem
- 3-3.30: snack
- 3:30-5:30: hack
- 7:30 dinner
- 9 fun stuff
---
who to invite
1. Satterthwaite's team
1. Milham's team
1. Jeff's team
1. Sebastian's team
1. Kent's team
1. Andreas's team
1. Elizabeth's team
1. Marta/Albert's team
1. Liam's team
1. Craddock's team
1. Priebe's team (sussman, vince, yichen, etc)
1. Karl D's team
1. Clay's team
1. JHU peeps (Archana, Chris&Janice, Bcaffo, Martin, Zeger)
1. other's?
---
logistics
- would be at kavli
- i'd get money for food
- people will pay for travel/lodging
- would need committment from
- one person to run each day
- one person to run overall thingy
- would have to start planning asap
- would have to find a week that works for those committed asap
.center[who's in?]
---
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 src="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.5.1/katex.min.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.5.1/contrib/auto-render.min.js"></script>
<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/KaTeX/0.5.1/katex.min.css">
<script type="text/javascript">
var options = {};
var renderMath = function() {
renderMathInElement(document.body);
// or if you want to use $...$ for math,
renderMathInElement(document.body, {delimiters: [ // mind the order of delimiters(!?)
{left: "$$", right: "$$", display: true},
{left: "$", right: "$", display: false},
{left: "\\[", right: "\\]", display: true},
{left: "\\(", right: "\\)", display: false},
]});
}
var slideshow = remark.create(options, renderMath);
</script>
</body>
</html>