Ariel Rokem, University of Washington eScience Institute

Follow along at: https://arokem.github.io/2018-05-24-uw-pbio

The era of brain observatories

Allen Institute for Brain Science

n=1200

n=500,000

Opportunities

New data sets will enable important new discoveries

New methods

Data-driven discovery

Challenges

Methods that work in standard use may not apply to large datasets

=> Train machine learning algorithms to replace expert decision making

Tools are needed for data exploration and transparent sharing of results

=> Build browser-based applications for exploratory data analysis and data sharing

Algorithms are needed to extract information from complex high-dimensional data

=> Translate statistical techniques into practice in neuroscience

Sociotechnical structures are strained: collaboration, publication, training

=> Open source software collaborations and science-focused hack weeks

Challenge: Methods that work in standard datasets may fail in Big Data

Some methods require expert examination

Time consuming, tedious

=> Do not scale well!

The solution

Expert => results

Expert => training data => machine learning => results

Learning to replace experts

Aaron Lee

Sa Xiao

Parmita
Mehta

Magda
Balazinska

The UW OCT/EMR data-base

Artificial neural networks

A family of machine learning algorithms

Biologically inspired

Artificial neural networks

Artificial neural networks

A family of machine learning algorithms

Biologically inspired

Implement a cascade of linear/non-linear operations

Convolutional networks

Capitalize on spatial correlations in images

Inspired by the mammalian visual system

Deep learning accurately classifies age-related macular degeneration (AMD)

Solving multi-class multi-label problems

Binary classification doesn't model clinical decision making

Patients can have any of a several diseases

Or more than one disease

=> Train several networks and integrate across them

Augmenting the neural network with additional patient information

Detecting clinical features: intraretinal fluid segmentation

Detecting clinical features: intraretinal fluid segmentation

Detecting clinical features: intraretinal fluid segmentation

Detecting clinical features: intraretinal fluid segmentation

Segmenting experimental data:

oxygen induced retinopathy

Segmenting experimental data:

oxygen induced retinopathy

Segmenting experimental data:

oxygen induced retinopathy

The solution

Expert => results

Expert => training data => machine learning => results

But: for many tasks, not enough training data

=> Amplify labeled data-sets with citizen science

Expert => citizen science => training data => machine learning => results

Scaling expertise with citizen science

Anisha Keshavan

Jason Yeatman

Example

Quality control of T1-weighted images

https://braindr.us

Braindr

Multiple ratings per image

But often, no agreement

Aggregating across raters

Aggregating across raters

Aggregating across raters

Aggregating across raters

How do we scale this up?

Scaling expertise using citizen scientist ratings

Scaling expertise using citizen scientist ratings

Summary

When there is enough training data: deep learning

When we need to scale up: citizen scientists

Model of expertise (random forest) for aggregation

Model of perception (neural network) for automation and scaling

Future applications

Other tasks

Tumor segmentation in MRI

Other types of data and other procedures

Challenges

Methods that work in standard use may not apply to large datasets

=> Train machine learning algorithms to replace expert decision making

Tools are needed for data exploration and transparent sharing of results

=> Build browser-based applications for exploratory data analysis and data sharing

Challenge: tools for exploration of complex data

Results from large datasets are hard to understand

Hard to communicate

Hard to reproduce

Data sharing is not incentivized and is not easy enough

Normal behavior is supported by brain connectivity

Not just passive cables

Brain connections develop and mature with age

Individual differences account for differences in behaviour

Adapt and change with learning

Diffusion MRI

Diffusion MRI

Diffusion MRI

Diffusion statistics

Mean diffusivity

Fractional anisotropy

Principal diffusion direction

Amyotrophic Lateral Sclerosis (ALS)

Classify patients based on the tissue properties in this part of the brain

Random Forest algorithm => 80% accuracy

How could we improve on this?

Challenge: improved data exploration and data sharing

Jason Yeatman

Adam
Richie-Halford

Josh Smith

Anisha
Keshavan

The solution

A web-based application

Builds a web-site for a diffusion MRI dataset

Automatically uploads the website to Github

https://yeatmanlab.github.io/Sarica_2017

Exploratory data analysis

Enhances published results

Linked visualizations facilitate easy exploration

Enables new discoveries in old datasets

Automatic data sharing

Further exploration

Summary

Exploratory data analysis

Automated data sharing

Dimensionality reduced data in tidy table format

Future applications

Other analysis pipelines

Dimensionality reduction in multi-channel neural recordings

Challenges

Methods that work in standard use may not apply to large datasets

=> Train machine learning algorithms to replace expert decision making

Tools are needed for data exploration and transparent sharing of results

=> Build browser-based applications for exploratory data analysis and data sharing

Algorithms are needed to extract information from complex high-dimensional data

=> Translate statistical techniques into practice in neuroscience

Opportunity: data-driven discovery

Adam Richie-Halford

Noah Simon

Jason Yeatman

Diffusion MRI data has group structure

Logistic regression

But in our case p (number of variables) >> n (number of subjects)

The Lasso

Enforces sparsity

But ignores group structure in the data

Accuracy: ~71% (AUC: ~71%)

Does not discover the right features

Top 10 features include some CST, but also other parts of the brain

The Group Lasso

Where l are groups of variables

p(l) is the number of variables in group l

In our case: all the measurements of a tissue propetry within a tract

Enforces selection of groups

But does not enforce L1 sparsity within included groups

Sparse Group Lasso

Enforces sparsity both at the group level and the within-group level

Subsumes the Lasso (λ₁ = 0)

And the Group Lasso (λ₂ = 0)

But more meta-parameters

Fitting meta-parameters

Nested cross-validation

Fitting meta-parameters

Nested cross-validation

Fitting meta-parameters

Nested cross-validation

Accurate classification and feature detection

Classification accuracy of ~84% (AUC of 0.9)

Top 10 features selected include CST

Summary

Sparse Group Lasso accurately discovers structure in dMRI data

Classification of disease states

In a regression setting, prediction of continuous measures
(e.g, "brain age", IQ, reading skills)

Future applications

Multi-region, multi-neuron recordings

Multi-neuron recordings also have group structure

Challenges

Methods that work in standard use may not apply to large datasets

=> Train machine learning algorithms to replace expert decision making

Tools are needed for data exploration and transparent sharing of results

=> Build browser-based applications for exploratory data analysis and data sharing

Algorithms are needed to extract information from complex high-dimensional data

=> Translate statistical techniques into practice in neuroscience

Sociotechnical structures are strained: collaboration, publication, training

=> Open source software collaborations and science-focused hack weeks

Open source software is a necessary complement to brain observatories

Required for reproducibility

Enables building on previous work

Open source diffusion MRI

Open to users

Open to contributors

Distributed collaboration

Challenge: training

Methods in data science are rapidly changing

Learning often require substantial hands-on experience

=> Hack weeks

Week-long events

Combination of learning and project work

Participant driven

Astrohackweek

Neurohackweek

Geohackweek

A fine balance of pedagogy and hacking

Neurohackademy

Thanks!

"All across our campus, the process of discovery will increasingly rely on researchers’ ability to extract knowledge from vast amounts of data... In order to remain at the forefront, UW must be a leader in advancing these techniques and technologies, and in making [them] accessible to researchers in the broadest imaginable range of fields"