Forecasting Brain Activity Based on Models of Spatio-Temporal Brain Dynamics: A Comparison of Graph Neural Network Architectures

Comprehending the interplay between spatial and temporal characteristics of neural dynamics can contribute to our understanding of information processing in the human brain. Graph neural networks (GNNs) provide a new possibility to interpret graph structured signals like those observed in complex brain networks. In our study we compare different spatio-temporal GNN architectures and study their ability to model neural activity distributions obtained in functional MRI (fMRI) studies. We evaluate the performance of the GNN models on a variety of scenarios in MRI studies and also compare it to a VAR model, which is currently often used for directed functional connectivity analysis. We show that by learning localized functional interactions on the anatomical substrate, GNN based approaches are able to robustly scale to large network studies, even when available data are scarce. By including anatomical connectivity as the physical substrate for information propagation, such GNNs also provide a multi-modal perspective on directed connectivity analysis, offering a novel possibility to investigate the spatio-temporal dynamics in brain networks

Forecasting brain activity based on models of spatiotemporal brain dynamics: A comparison of graph neural network architectures

Comprehending the interplay between spatial and temporal characteristics of neural dynamics can contribute to our understanding of information processing in the human brain. Graph neural networks (GNNs) provide a new possibility to interpret graph-structured signals like those observed in complex brain networks. In our study we compare different spatiotemporal GNN architectures and study their ability to model neural activity distributions obtained in functional MRI (fMRI) studies. We evaluate the performance of the GNN models on a variety of scenarios in MRI studies and also compare it to a VAR model, which is currently often used for directed functional connectivity analysis. We show that by learning localized functional interactions on the anatomical substrate, GNN-based approaches are able to robustly scale to large network studies, even when available data are scarce. By including anatomical connectivity as the physical substrate for information propagation, such GNNs also provide a multimodal perspective on directed connectivity analysis, offering a novel possibility to investigate the spatiotemporal dynamics in brain networks

Doctor of Philosophy

dissertationThe human brain is the seat of cognition and behavior. Understanding the brain mechanistically is essential for appreciating its linkages with cognitive processes and behavioral outcomes in humans. Mechanisms of brain function categorically represent rich and widely under-investigated biological substrates for neural-driven studies of psychiatry and mental health. Research examining intrinsic connectivity patterns across whole brain systems utilizes functional magnetic resonance imaging (fMRI) to trace spontaneous fluctuations in blood oxygen-level dependent (BOLD) signals. In the first study presented, we reveal patterns of dynamic attractors in resting state functional connectivity data corresponding to well-documented biological networks. We introduce a novel simulation for whole brain dynamics that can be adapted to either group-level analysis or single-subject level models. We describe stability of intrinsic functional architecture in terms of transient and global steady states resembling biological networks. In the second study, we demonstrate plasticity in functional connectivity following a minimum six-week intervention to train cognitive performance in a speed reading task. Long-term modulation of connectivity with language regions indicate functional connectivity as a candidate biomarker for tracking and measuring functional changes in neural systems as outcomes of cognitive training. The third study demonstrates utility of functional biomarkers in predicting individual differences in behavioral and cognitive features. We successfully predict three major domains of personality psychologyintelligence, agreeableness, and conscientiousnessin individual subjects using a large (N=475) open source data sample compiled by the National Institutes of Healths Human Connectome Project

Computational modelling: moonlighting on the neuroscience and medicine

Computational modelling has emerged as a powerful tool to study the behaviour of complex systems. Computer simulation may lead to a better understanding of the function of biological systems and the pathophysiological mechanisms underlying various diseases. In neuroscience, modelling techniques have provided knowledge about the electrical properties of neurons, activity of ion channels, synaptic function, information processing, and signalling pathways. Using simulations and analysis in network models has resulted in greater understanding of the behaviour of neural networks and dynamics of synaptic connectivity. Moreover, the correlation between the neurobiological mechanisms and a cluster of physiological, cognitive, and behavioural phenomena may be explored by the computational modelling of the neuronal systems. In this context, a significant progress has been made in understanding of the neural network architectures including those with a high degree of connectivity between the units, information processing, performance of complex cognitive tasks, integration of brain signals, as well as the dynamic mechanisms and computations implemented in the brain for making goal-directed choices. Computational models are able to explore the interactions between the brain areas which are involved in predictive processes and high-level skills. In this review, the significance of computational modelling in the study of neural networks, decision-making procedure, nerve growth factor signalling, and endocannabinoid system along with its medical applications have been highlighted.Biomedical Reviews 2013; 24: 25-31

Graph theoretical analysis of complex networks in the brain

Since the discovery of small-world and scale-free networks the study of complex systems from a network perspective has taken an enormous flight. In recent years many important properties of complex networks have been delineated. In particular, significant progress has been made in understanding the relationship between the structural properties of networks and the nature of dynamics taking place on these networks. For instance, the 'synchronizability' of complex networks of coupled oscillators can be determined by graph spectral analysis. These developments in the theory of complex networks have inspired new applications in the field of neuroscience. Graph analysis has been used in the study of models of neural networks, anatomical connectivity, and functional connectivity based upon fMRI, EEG and MEG. These studies suggest that the human brain can be modelled as a complex network, and may have a small-world structure both at the level of anatomical as well as functional connectivity. This small-world structure is hypothesized to reflect an optimal situation associated with rapid synchronization and information transfer, minimal wiring costs, as well as a balance between local processing and global integration. The topological structure of functional networks is probably restrained by genetic and anatomical factors, but can be modified during tasks. There is also increasing evidence that various types of brain disease such as Alzheimer's disease, schizophrenia, brain tumours and epilepsy may be associated with deviations of the functional network topology from the optimal small-world pattern

MULTIVARIATE MODELING OF COGNITIVE PERFORMANCE AND CATEGORICAL PERCEPTION FROM NEUROIMAGING DATA

State-of-the-art cognitive-neuroscience mainly uses hypothesis-driven statistical testing to characterize and model neural disorders and diseases. While such techniques have proven to be powerful in understanding diseases and disorders, they are inadequate in explaining causal relationships as well as individuality and variations. In this study, we proposed multivariate data-driven approaches for predictive modeling of cognitive events and disorders. We developed network descriptions of both structural and functional connectivities that are critical in multivariate modeling of cognitive performance (i.e., fluency, attention, and working memory) and categorical perceptions (i.e., emotion, speech perception). We also performed dynamic network analysis on brain connectivity measures to determine the role of different functional areas in relation to categorical perceptions and cognitive events. Our empirical studies of structural connectivity were performed using Diffusion Tensor Imaging (DTI). The main objective was to discover the role of structural connectivity in selecting clinically interpretable features that are consistent over a large range of model parameters in classifying cognitive performances in relation to Acute Lymphoblastic Leukemia (ALL). The proposed approach substantially improved accuracy (13% - 26%) over existing models and also selected a relevant, small subset of features that were verified by domain experts. In summary, the proposed approach produced interpretable models with better generalization.Functional connectivity is related to similar patterns of activation in different brain regions regardless of the apparent physical connectedness of the regions. The proposed data-driven approach to the source localized electroencephalogram (EEG) data includes an array of tools such as graph mining, feature selection, and multivariate analysis to determine the functional connectivity in categorical perceptions. We used the network description to correctly classify listeners behavioral responses with an accuracy over 92% on 35 participants. State-of-the-art network description of human brain assumes static connectivities. However, brain networks in relation to perception and cognition are complex and dynamic. Analysis of transient functional networks with spatiotemporal variations to understand cognitive functions remains challenging. One of the critical missing links is the lack of sophisticated methodologies in understanding dynamics neural activity patterns. We proposed a clustering-based complex dynamic network analysis on source localized EEG data to understand the commonality and differences in gender-specific emotion processing. Besides, we also adopted Bayesian nonparametric framework for segmentation neural activity with a finite number of microstates. This approach enabled us to find the default network and transient pattern of the underlying neural mechanism in relation to categorical perception. In summary, multivariate and dynamic network analysis methods developed in this dissertation to analyze structural and functional connectivities will have a far-reaching impact on computational neuroscience to identify meaningful changes in spatiotemporal brain activities

Markov models for fMRI correlation structure: is brain functional connectivity small world, or decomposable into networks?

Correlations in the signal observed via functional Magnetic Resonance Imaging (fMRI), are expected to reveal the interactions in the underlying neural populations through hemodynamic response. In particular, they highlight distributed set of mutually correlated regions that correspond to brain networks related to different cognitive functions. Yet graph-theoretical studies of neural connections give a different picture: that of a highly integrated system with small-world properties: local clustering but with short pathways across the complete structure. We examine the conditional independence properties of the fMRI signal, i.e. its Markov structure, to find realistic assumptions on the connectivity structure that are required to explain the observed functional connectivity. In particular we seek a decomposition of the Markov structure into segregated functional networks using decomposable graphs: a set of strongly-connected and partially overlapping cliques. We introduce a new method to efficiently extract such cliques on a large, strongly-connected graph. We compare methods learning different graph structures from functional connectivity by testing the goodness of fit of the model they learn on new data. We find that summarizing the structure as strongly-connected networks can give a good description only for very large and overlapping networks. These results highlight that Markov models are good tools to identify the structure of brain connectivity from fMRI signals, but for this purpose they must reflect the small-world properties of the underlying neural systems