Wet lab → Web lab
Anisha Keshavan
University of Washington
eScience Institute & Institute for Neuroengineering
Child Mind Institute
The Brain.
Development
Mental Health
Pathology
Aging
We need a lot of data.
Because we are all so unique
Computers can store our data
source: flickr
We have algorithms
A markov chain (wikimedia)
Neuroinformatics: A new discipline?
PhD student
Neuroinformatics reality:
A set of existing (distinct) disciplines?
Maybe neuroinformatics should be a web of disciplines?
create a web, not another mountain
The web, quite literally
me, a UWIN postdoc
Pediatric Mental Health
- Most mental health disorder are diagnosed at childhood and adolescence
-
How do brain tissue volumes change during development?
- are individual differences in development meaningful?
Healthy Brain Network
10,000 MRI scans
SO MUCH (statistical) POWER
a biobank from the Child Mind Institute
An MRI scan takes 5 min
Some kids can't stay still
Bad quality data
Bad inferences
Data needs visual inspection
10,000 MRI scans
Why not algorithms?
45 MPH
STOP!
we need some expertise
We should work together
Algorithms
- fast
- sometimes stupid
- needs lots of data to learn
Humans
- slow
- sometimes smart
- learns from sparse data
Braindr
Brain Data Review
Keshavan, Anisha, Jason Yeatman, and Ariel Rokem. "Combining citizen science and deep learning to amplify expertise in neuroimaging." bioRxiv (2018): 363382. (under review)
Instructions
Swipe Left
Swipe Right
Win Prizes
Many Ratings
But often, no agreement
Fail
Pass
Need to "down-weight" some raters
| image id | rater 0 | rater 1 |
|---|---|---|
| 1 | 0 | 1 |
| 2 | 1 | - |
| Expert |
|---|
| 1 |
| 0 |
each rater is a feature
each image
is a sample
missing data
Rater importance vs # ratings
Corrected Ratings
Predict image quality
> 100,000 ratings
> 400 users
0.99 AUC = near perfect
Swipes for Science
Thanks eLife Innovation!
oceanography/marine bio
How do brain tissue volumes change during development?
back to our question:
TL;DR
too long, didn't read in internet-speak
lets work together
to study the brain with Big Data
the web can break down barriers
between disciplines
Thanks to my Web Lab!
Ariel Rokem
Jason Yeatman
Satra Ghosh
Dylan Nielson
Sharabesh Ramesh
Dave Kennedy
JB Poline
Neel Somani
Sharabesh Ramesh
Katie Bottenhorn
Arno Klein
Amanda Easson
Adam Richie-Halford
Josh Smith
Greg Kiar
Sook-Lei Liew
Chris Madan
Chris Markiewicz
Elizabeth Dupre
Kesshi Jordan
Rob Fatland
Shima Abadi
Naomi Penfold
Andreea Hrincu
Adam Thomas
NVIDIA
AWS
Microsoft Azure
eLife Innovation
UW Institute for Neuroengineering
eScience Institute
All braindr raters
Questions?
Copy of wet to web, UWIN
By Anisha Keshavan
