With recent advancements in non-invasive techniques for measuring brain activity, such as magnetic resonance imaging (MRI), the study of structural and functional brain networks through graph signal processing (GSP) has gained notable prominence. GSP stands as a key tool in unraveling the interplay between the brain's function and structure, enabling the analysis of graphs defined by the connections between regions of interest -- referred to as connectomes in this context. Our work represents a further step in this direction by exploring supervised contrastive learning methods within the realm of graph representation learning. The main objective of this approach is to generate subject-level (i.e., graph-level) vector representations that bring together subjects sharing the same label while separating those with different labels. These connectome embeddings are derived from a graph neural network Encoder-Decoder architecture, which jointly considers structural and functional connectivity. By leveraging data augmentation techniques, the proposed framework achieves state-of-the-art performance in a gender classification task using Human Connectome Project data. More broadly, our connectome-centric methodological advances support the promising prospect of using GSP to discover more about brain function, with potential impact to understanding heterogeneity in the neurodegeneration for precision medicine and diagnosis.

Brain age is the estimate of biological age derived from neuroimaging datasets using machine learning algorithms. Increasing \textit{brain age gap} characterized by an elevated brain age relative to the chronological age can reflect increased vulnerability to neurodegeneration and cognitive decline. Hence, brain age gap is a promising biomarker for monitoring brain health. However, black-box machine learning approaches to brain age gap prediction have limited practical utility. Recent studies on coVariance neural networks (VNN) have proposed a relatively transparent deep learning pipeline for neuroimaging data analyses, which possesses two key features: (i) inherent \textit{anatomically interpretablity} of derived biomarkers; and (ii) a methodologically interpretable perspective based on \textit{linkage with eigenvectors of anatomic covariance matrix}. In this paper, we apply the VNN-based approach to study brain age gap using cortical thickness features for various prevalent neurodegenerative conditions. Our results reveal distinct anatomic patterns for brain age gap in Alzheimer's disease, frontotemporal dementia, and atypical Parkinsonian disorders. Furthermore, we demonstrate that the distinct anatomic patterns of brain age gap are linked with the differences in how VNN leverages the eigenspectrum of the anatomic covariance matrix, thus lending explainability to the reported results.

We put forth a principled design of a neural architecture to learn nodal Adjacency Spectral Embeddings (ASE) from graph inputs. By bringing to bear the gradient descent (GD) method and leveraging the principle of algorithm unrolling, we truncate and re-interpret each GD iteration as a layer in a graph neural network (GNN) that is trained to approximate the ASE. Accordingly, we call the resulting embeddings and our parametric model Learned ASE (LASE), which is interpretable, parameter efficient, robust to inputs with unobserved edges, and offers controllable complexity during inference. LASE layers combine Graph Convolutional Network (GCN) and fully-connected Graph Attention Network (GAT) modules, which is intuitively pleasing since GCN-based local aggregations alone are insufficient to express the sought graph eigenvectors. We propose several refinements to the unrolled LASE architecture (such as sparse attention in the GAT module and decoupled layerwise parameters) that offer favorable approximation error versus computation tradeoffs; even outperforming heavily-optimized eigendecomposition routines from scientific computing libraries. Because LASE is a differentiable function with respect to its parameters as well as its graph input, we can seamlessly integrate it as a trainable module within a larger (semi-)supervised graph representation learning pipeline. The resulting end-to-end system effectively learns ``discriminative ASEs'' that exhibit competitive performance in supervised link prediction and node classification tasks, outperforming a GNN even when the latter is endowed with open loop, meaning task-agnostic, precomputed spectral positional encodings.

Large-scale latent variable models require expressive continuous distributions that support efficient sampling and low-variance differentiation, achievable through the reparameterization trick. The Kumaraswamy (KS) distribution is both expressive and supports the reparameterization trick with a simple closed-form inverse CDF. Yet, its adoption remains limited. We identify and resolve numerical instabilities in the inverse CDF and log-pdf, exposing issues in libraries like PyTorch and TensorFlow. We then introduce simple and scalable latent variable models based on the KS, improving exploration-exploitation trade-offs in contextual multi-armed bandits and enhancing uncertainty quantification for link prediction with graph neural networks. Our results support the stabilized KS distribution as a core component in scalable variational models for bounded latent variables.

Graphs serve as generic tools to encode the underlying relational structure of data. Often this graph is not given, and so the task of inferring it from nodal observations becomes important. Traditional approaches formulate a convex inverse problem with a smoothness promoting objective and rely on iterative methods to obtain a solution. In supervised settings where graph labels are available, one can unroll and truncate these iterations into a deep network that is trained end-to-end. Such a network is parameter efficient and inherits inductive bias from the optimization formulation, an appealing aspect for data constrained settings in, e.g., medicine, finance, and the natural sciences. But typically such settings care equally about uncertainty over edge predictions, not just point estimates. Here we introduce novel iterations with independently interpretable parameters, i.e., parameters whose values - independent of other parameters' settings - proportionally influence characteristics of the estimated graph, such as edge sparsity. After unrolling these iterations, prior knowledge over such graph characteristics shape prior distributions over these independently interpretable network parameters to yield a Bayesian neural network (BNN) capable of graph structure learning (GSL) from smooth signal observations. Fast execution and parameter efficiency allow for high-fidelity posterior approximation via Markov Chain Monte Carlo (MCMC) and thus uncertainty quantification on edge predictions. Synthetic and real data experiments corroborate this model's ability to provide well-calibrated estimates of uncertainty, in test cases that include unveiling economic sector modular structure from S$\&$P$500$ data and recovering pairwise digit similarities from MNIST images. Overall, this framework enables GSL in modest-scale applications where uncertainty on the data structure is paramount.

We develop a novel convolutional architecture tailored for learning from data defined over directed acyclic graphs (DAGs). DAGs can be used to model causal relationships among variables, but their nilpotent adjacency matrices pose unique challenges towards developing DAG signal processing and machine learning tools. To address this limitation, we harness recent advances offering alternative definitions of causal shifts and convolutions for signals on DAGs. We develop a novel convolutional graph neural network that integrates learnable DAG filters to account for the partial ordering induced by the graph topology, thus providing valuable inductive bias to learn effective representations of DAG-supported data. We discuss the salient advantages and potential limitations of the proposed DAG convolutional network (DCN) and evaluate its performance on two learning tasks using synthetic data: network diffusion estimation and source identification. DCN compares favorably relative to several baselines, showcasing its promising potential.

Brain age is the estimate of biological age derived from neuroimaging datasets using machine learning algorithms. Increasing brain age with respect to chronological age can reflect increased vulnerability to neurodegeneration and cognitive decline. In this paper, we study NeuroVNN, based on coVariance neural networks, as a paradigm for foundation model for the brain age prediction application. NeuroVNN is pre-trained as a regression model on healthy population to predict chronological age using cortical thickness features and fine-tuned to estimate brain age in different neurological contexts. Importantly, NeuroVNN adds anatomical interpretability to brain age and has a `scale-free' characteristic that allows its transference to datasets curated according to any arbitrary brain atlas. Our results demonstrate that NeuroVNN can extract biologically plausible brain age estimates in different populations, as well as transfer successfully to datasets of dimensionalities distinct from that for the dataset used to train NeuroVNN.

The Random Dot Product Graph (RDPG) is a generative model for relational data, where nodes are represented via latent vectors in low-dimensional Euclidean space. RDPGs crucially postulate that edge formation probabilities are given by the dot product of the corresponding latent positions. Accordingly, the embedding task of estimating these vectors from an observed graph is typically posed as a low-rank matrix factorization problem. The workhorse Adjacency Spectral Embedding (ASE) enjoys solid statistical properties, but it is formally solving a surrogate problem and can be computationally intensive. In this paper, we bring to bear recent advances in non-convex optimization and demonstrate their impact to RDPG inference. We advocate first-order gradient descent methods to better solve the embedding problem, and to organically accommodate broader network embedding applications of practical relevance. Notably, we argue that RDPG embeddings of directed graphs loose interpretability unless the factor matrices are constrained to have orthogonal columns. We thus develop a novel feasible optimization method in the resulting manifold. The effectiveness of the graph representation learning framework is demonstrated on reproducible experiments with both synthetic and real network data. Our open-source algorithm implementations are scalable, and unlike the ASE they are robust to missing edge data and can track slowly-varying latent positions from streaming graphs.

In computational neuroscience, there has been an increased interest in developing machine learning algorithms that leverage brain imaging data to provide estimates of "brain age" for an individual. Importantly, the discordance between brain age and chronological age (referred to as "brain age gap") can capture accelerated aging due to adverse health conditions and therefore, can reflect increased vulnerability towards neurological disease or cognitive impairments. However, widespread adoption of brain age for clinical decision support has been hindered due to lack of transparency and methodological justifications in most existing brain age prediction algorithms. In this paper, we leverage coVariance neural networks (VNN) to propose an explanation-driven and anatomically interpretable framework for brain age prediction using cortical thickness features. Specifically, our brain age prediction framework extends beyond the coarse metric of brain age gap in Alzheimer's disease (AD) and we make two important observations: (i) VNNs can assign anatomical interpretability to elevated brain age gap in AD by identifying contributing brain regions, (ii) the interpretability offered by VNNs is contingent on their ability to exploit specific eigenvectors of the anatomical covariance matrix. Together, these observations facilitate an explainable and anatomically interpretable perspective to the task of brain age prediction.

Graphs are mathematical tools that can be used to represent complex real-world interconnected systems, such as financial markets and social networks. Hence, machine learning (ML) over graphs has attracted significant attention recently. However, it has been demonstrated that ML over graphs amplifies the already existing bias towards certain under-represented groups in various decision-making problems due to the information aggregation over biased graph structures. Faced with this challenge, here we take a fresh look at the problem of bias mitigation in graph-based learning by borrowing insights from graph signal processing. Our idea is to introduce predesigned graph filters within an ML pipeline to reduce a novel unsupervised bias measure, namely the correlation between sensitive attributes and the underlying graph connectivity. We show that the optimal design of said filters can be cast as a convex problem in the graph spectral domain. We also formulate a linear programming (LP) problem informed by a theoretical bias analysis, which attains a closed-form solution and leads to a more efficient fairness-aware graph filter. Finally, for a design whose degrees of freedom are independent of the input graph size, we minimize the bias metric over the family of polynomial graph convolutional filters. Our optimal filter designs offer complementary strengths to explore favorable fairness-utility-complexity tradeoffs. For performance evaluation, we conduct extensive and reproducible node classification experiments over real-world networks. Our results show that the proposed framework leads to better fairness measures together with similar utility compared to state-of-the-art fairness-aware baselines.