BrainNET: Inference of brain network topology using Machine Learning

Objective To develop a new fMRI network inference method, BrainNET, that utilizes an efficient machine learning algorithm to quantify contributions of various regions of interests (ROIs) in the brain to a specific ROI. Methods BrainNET is based on Extremely Randomized Trees (ERT) to estimate network topology from fMRI data and modified to generate an adjacency matrix representing brain network topology, without reliance on arbitrary thresholds. Open source simulated fMRI data of fifty subjects in twenty-eight different simulations under various confounding conditions with known ground truth was used to validate the method. Performance was compared with correlation and partial correlation (PC). The real-world performance was then evaluated in a publicly available Attention-deficit/hyperactivity disorder (ADHD) dataset including 134 Typically Developing Children (mean age: 12.03, males: 83), 75 ADHD Inattentive (mean age: 11.46, males: 56) and 93 ADHD Combined (mean age: 11.86, males: 77) subjects. Network topologies in ADHD were inferred using BrainNET, correlation, and PC. Graph metrics were extracted to determine differences between the ADHD groups. Results BrainNET demonstrated excellent performance across all simulations and varying confounders in identifying true presence of connections. In the ADHD dataset, BrainNET was able to identify significant changes (p< 0.05) in graph metrics between groups. No significant changes in graph metrics between ADHD groups was identified using correlation and PC.