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

braindr.us

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

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

Copy of wet to web, UWIN

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