Combining Citizen Science and Deep Learning to Amplify Expertise in Neuroimaging

Big Data promises to advance science through data-driven discovery. However, many standard lab protocols rely on manual examination, which is not feasible for large-scale datasets. Meanwhile, automated approaches lack the accuracy of expert examination. We propose to (1) start with expertly labeled data, (2) amplify labels through web applications that engage citizen scientists, and (3) train machine learning on amplified labels, to emulate the experts. Demonstrating this, we developed a system to quality control brain magnetic resonance images. Expert-labeled data were amplified by citizen scientists through a simple web interface. A deep learning algorithm was then trained to predict data quality, based on citizen scientist labels. Deep learning performed as well as specialized algorithms for quality control (AUC = 0.99). Combining citizen science and deep learning can generalize and scale expert decision making; this is particularly important in disciplines where specialized, automated tools do not yet exist

Knowing what you know in brain segmentation using Bayesian deep neural networks

In this paper, we describe a Bayesian deep neural network (DNN) for predicting FreeSurfer segmentations of structural MRI volumes, in minutes rather than hours. The network was trained and evaluated on a large dataset (n = 11,480), obtained by combining data from more than a hundred different sites, and also evaluated on another completely held-out dataset (n = 418). The network was trained using a novel spike-and-slab dropout-based variational inference approach. We show that, on these datasets, the proposed Bayesian DNN outperforms previously proposed methods, in terms of the similarity between the segmentation predictions and the FreeSurfer labels, and the usefulness of the estimate uncertainty of these predictions. In particular, we demonstrated that the prediction uncertainty of this network at each voxel is a good indicator of whether the network has made an error and that the uncertainty across the whole brain can predict the manual quality control ratings of a scan. The proposed Bayesian DNN method should be applicable to any new network architecture for addressing the segmentation problem.Comment: Submitted to Frontiers in Neuroinformatic

Auto-filtering validation in citizen science biodiversity monitoring ::a case study

Data quality is the primary concern for researchers working on citizen science projects. The collected data by citizen science participants are heterogeneous and therefore must be validated. There are several validation approaches depending on the theme and objective of the citizen science project, but the most common approach is the expert review. While expert validation is essential in citizen science projects, considering it as the only validation approach can be very difficult and complicated for the experts. In addition, volunteers can get demotivated to contribute if they do not receive any feedback regarding their submissions. This project aims at introducing an automatic filtering mechanism for a biodiversity citizen science project. The goals of this project are to first use an available historical database of the local species to filter out the unusual ones, and second to use machine learning and image recognition techniques to verify if the observation image corresponds with the right species type. The submissions that does not successfully pass the automatic filtering will be flagged as unusual and goes through expert review. The objective is on the one hand to simplify validation task by the experts, and on the other hand to increase participants’ motivation by giving them real-time feedback on their submissions. Finally, the flagged observations will be classified as valid, valid but uncommon, and invalid, and the observation outliers (rare species) can be identified for each specific region

The ENIGMA Stroke Recovery Working Group: Big data neuroimaging to study brain–behavior relationships after stroke

The goal of the Enhancing Neuroimaging Genetics through Meta‐Analysis (ENIGMA) Stroke Recovery working group is to understand brain and behavior relationships using well‐powered meta‐ and mega‐analytic approaches. ENIGMA Stroke Recovery has data from over 2,100 stroke patients collected across 39 research studies and 10 countries around the world, comprising the largest multisite retrospective stroke data collaboration to date. This article outlines the efforts taken by the ENIGMA Stroke Recovery working group to develop neuroinformatics protocols and methods to manage multisite stroke brain magnetic resonance imaging, behavioral and demographics data. Specifically, the processes for scalable data intake and preprocessing, multisite data harmonization, and large‐scale stroke lesion analysis are described, and challenges unique to this type of big data collaboration in stroke research are discussed. Finally, future directions and limitations, as well as recommendations for improved data harmonization through prospective data collection and data management, are provided

From the Wet Lab to the Web Lab: A Paradigm Shift in Brain Imaging Research

Web technology has transformed our lives, and has led to a paradigm shift in the computational sciences. As the neuroimaging informatics research community amasses large datasets to answer complex neuroscience questions, we find that the web is the best medium to facilitate novel insights by way of improved collaboration and communication. Here, we review the landscape of web technologies used in neuroimaging research, and discuss future applications, areas for improvement, and the limitations of using web technology in research. Fully incorporating web technology in our research lifecycle requires not only technical skill, but a widespread culture change; a shift from the small, focused “wet lab” to a multidisciplinary and largely collaborative “web lab.

An analysis-ready and quality controlled resource for pediatric brain white-matter research

We created a set of resources to enable research based on openly-available diffusion MRI (dMRI) data from the Healthy Brain Network (HBN) study. First, we curated the HBN dMRI data (N = 2747) into the Brain Imaging Data Structure and preprocessed it according to best-practices, including denoising and correcting for motion effects, susceptibility-related distortions, and eddy currents. Preprocessed, analysis-ready data was made openly available. Data quality plays a key role in the analysis of dMRI. To optimize QC and scale it to this large dataset, we trained a neural network through the combination of a small data subset scored by experts and a larger set scored by community scientists. The network performs QC highly concordant with that of experts on a held out set (ROC-AUC = 0.947). A further analysis of the neural network demonstrates that it relies on image features with relevance to QC. Altogether, this work both delivers resources to advance transdiagnostic research in brain connectivity and pediatric mental health, and establishes a novel paradigm for automated QC of large datasets

An analysis-ready and quality controlled resource for pediatric brain white-matter research

We created a set of resources to enable research based on openly-available diffusion MRI (dMRI) data from the Healthy Brain Network (HBN) study. First, we curated the HBN dMRI data (N = 2747) into the Brain Imaging Data Structure and preprocessed it according to best-practices, including denoising and correcting for motion effects, susceptibility-related distortions, and eddy currents. Preprocessed, analysis-ready data was made openly available. Data quality plays a key role in the analysis of dMRI. To optimize QC and scale it to this large dataset, we trained a neural network through the combination of a small data subset scored by experts and a larger set scored by community scientists. The network performs QC highly concordant with that of experts on a held out set (ROC-AUC = 0.947). A further analysis of the neural network demonstrates that it relies on image features with relevance to QC. Altogether, this work both delivers resources to advance transdiagnostic research in brain connectivity and pediatric mental health, and establishes a novel paradigm for automated QC of large datasets

The ENIGMA Stroke Recovery Working Group: Big data neuroimaging to study brain-behavior relationships after stroke

The goal of the Enhancing Neuroimaging Genetics through Meta-Analysis (ENIGMA) Stroke Recovery working group is to understand brain and behavior relationships using well-powered meta- and mega-analytic approaches. ENIGMA Stroke Recovery has data from over 2,100 stroke patients collected across 39 research studies and 10 countries around the world, comprising the largest multisite retrospective stroke data collaboration to date. This article outlines the efforts taken by the ENIGMA Stroke Recovery working group to develop neuroinformatics protocols and methods to manage multisite stroke brain magnetic resonance imaging, behavioral and demographics data. Specifically, the processes for scalable data intake and preprocessing, multisite data harmonization, and large-scale stroke lesion analysis are described, and challenges unique to this type of big data collaboration in stroke research are discussed. Finally, future directions and limitations, as well as recommendations for improved data harmonization through prospective data collection and data management, are provided