Construction of embedded fMRI resting state functional connectivity networks using manifold learning

We construct embedded functional connectivity networks (FCN) from benchmark resting-state functional magnetic resonance imaging (rsfMRI) data acquired from patients with schizophrenia and healthy controls based on linear and nonlinear manifold learning algorithms, namely, Multidimensional Scaling (MDS), Isometric Feature Mapping (ISOMAP) and Diffusion Maps. Furthermore, based on key global graph-theoretical properties of the embedded FCN, we compare their classification potential using machine learning techniques. We also assess the performance of two metrics that are widely used for the construction of FCN from fMRI, namely the Euclidean distance and the lagged cross-correlation metric. We show that the FCN constructed with Diffusion Maps and the lagged cross-correlation metric outperform the other combinations

Topological exploration of artificial neuronal network dynamics

One of the paramount challenges in neuroscience is to understand the dynamics of individual neurons and how they give rise to network dynamics when interconnected. Historically, researchers have resorted to graph theory, statistics, and statistical mechanics to describe the spatiotemporal structure of such network dynamics. Our novel approach employs tools from algebraic topology to characterize the global properties of network structure and dynamics. We propose a method based on persistent homology to automatically classify network dynamics using topological features of spaces built from various spike-train distances. We investigate the efficacy of our method by simulating activity in three small artificial neural networks with different sets of parameters, giving rise to dynamics that can be classified into four regimes. We then compute three measures of spike train similarity and use persistent homology to extract topological features that are fundamentally different from those used in traditional methods. Our results show that a machine learning classifier trained on these features can accurately predict the regime of the network it was trained on and also generalize to other networks that were not presented during training. Moreover, we demonstrate that using features extracted from multiple spike-train distances systematically improves the performance of our method

Phenotyping functional brain dynamics:A deep learning prespective on psychiatry

This thesis explores the potential of deep learning (DL) techniques combined with multi-site functional magnetic resonance imaging (fMRI) to enable automated diagnosis and biomarker discovery for psychiatric disorders. This marks a shift from the convention in the field of applying standard machine learning techniques on hand-crafted features from a single cohort.To enable this, we have focused on three main strategies: utilizing minimally pre-processed data to maintain spatio-temporal dynamics, developing sample-efficient DL models, and applying emerging DL training techniques like self-supervised and transfer learning to leverage large population-based datasets.Our empirical results suggest that DL models can sometimes outperform existing machine learning methods in diagnosing Autism Spectrum Disorder (ASD) and Major Depressive Disorder (MDD) from resting-state fMRI data, despite the smaller datasets and the high data dimensionality. Nonetheless, the generalization performance of these models is currently insufficient for clinical use, raising questions about the feasibility of applying supervised DL for diagnosis or biomarker discovery due to the highly heterogeneous nature of the disorders. Our findings suggest that normative modeling on functional brain dynamics provides a promising alternative to the current paradigm