A Stage-Aware Mixture of Experts Framework for Neurodegenerative Disease Progression Modelling

The long-term progression of neurodegenerative diseases is commonly conceptualized as a spatiotemporal diffusion process that consists of a graph diffusion process across the structural brain connectome and a localized reaction process within brain regions. However, modeling this progression remains challenging due to 1) the scarcity of longitudinal data obtained through irregular and infrequent subject visits and 2) the complex interplay of pathological mechanisms across brain regions and disease stages, where traditional models assume fixed mechanisms throughout disease progression. To address these limitations, we propose a novel stage-aware Mixture of Experts (MoE) framework that explicitly models how different contributing mechanisms dominate at different disease stages through time-dependent expert weighting.Data-wise, we utilize an iterative dual optimization method to properly estimate the temporal position of individual observations, constructing a co hort-level progression trajectory from irregular snapshots. Model-wise, we enhance the spatial component with an inhomogeneous graph neural diffusion model (IGND) that allows diffusivity to vary based on node states and time, providing more flexible representations of brain networks. We also introduce a localized neural reaction module to capture complex dynamics beyond standard processes.The resulting IGND-MoE model dynamically integrates these components across temporal states, offering a principled way to understand how stage-specific pathological mechanisms contribute to progression. The stage-wise weights yield novel clinical insights that align with literature, suggesting that graph-related processes are more influential at early stages, while other unknown physical processes become dominant later on.

Heterogeneous Graph Structure Learning through the Lens of Data-generating Processes

Inferring the graph structure from observed data is a key task in graph machine learning to capture the intrinsic relationship between data entities. While significant advancements have been made in learning the structure of homogeneous graphs, many real-world graphs exhibit heterogeneous patterns where nodes and edges have multiple types. This paper fills this gap by introducing the first approach for heterogeneous graph structure learning (HGSL). To this end, we first propose a novel statistical model for the data-generating process (DGP) of heterogeneous graph data, namely hidden Markov networks for heterogeneous graphs (H2MN). Then we formalize HGSL as a maximum a-posterior estimation problem parameterized by such DGP and derive an alternating optimization method to obtain a solution together with a theoretical justification of the optimization conditions. Finally, we conduct extensive experiments on both synthetic and real-world datasets to demonstrate that our proposed method excels in learning structure on heterogeneous graphs in terms of edge type identification and edge weight recovery.

Effects of Random Edge-Dropping on Over-Squashing in Graph Neural Networks

Message Passing Neural Networks (MPNNs) are a class of Graph Neural Networks (GNNs) that leverage the graph topology to propagate messages across increasingly larger neighborhoods. The message-passing scheme leads to two distinct challenges: over-smoothing and over-squashing. While several algorithms, e.g. DropEdge and its variants -- DropNode, DropAgg and DropGNN -- have successfully addressed the over-smoothing problem, their impact on over-squashing remains largely unexplored. This represents a critical gap in the literature as failure to mitigate over-squashing would make these methods unsuitable for long-range tasks. In this work, we take the first step towards closing this gap by studying the aforementioned algorithms in the context of over-squashing. We present novel theoretical results that characterize the negative effects of DropEdge on sensitivity between distant nodes, suggesting its unsuitability for long-range tasks. Our findings are easily extended to its variants, allowing us to build a comprehensive understanding of how they affect over-squashing. We evaluate these methods using real-world datasets, demonstrating their detrimental effects. Specifically, we show that while DropEdge-variants improve test-time performance in short range tasks, they deteriorate performance in long-range ones. Our theory explains these results as follows: random edge-dropping lowers the effective receptive field of GNNs, which although beneficial for short-range tasks, misaligns the models on long-range ones. This forces the models to overfit to short-range artefacts in the training set, resulting in poor generalization. Our conclusions highlight the need to re-evaluate various methods designed for training deep GNNs, with a renewed focus on modelling long-range interactions.

Hypergraph Node Classification With Graph Neural Networks

Hypergraphs, with hyperedges connecting more than two nodes, are key for modelling higher-order interactions in real-world data. The success of graph neural networks (GNNs) reveals the capability of neural networks to process data with pairwise interactions. This inspires the usage of neural networks for data with higher-order interactions, thereby leading to the development of hypergraph neural networks (HyperGNNs). GNNs and HyperGNNs are typically considered distinct since they are designed for data on different geometric topologies. However, in this paper, we theoretically demonstrate that, in the context of node classification, most HyperGNNs can be approximated using a GNN with a weighted clique expansion of the hypergraph. This leads to WCE-GNN, a simple and efficient framework comprising a GNN and a weighted clique expansion (WCE), for hypergraph node classification. Experiments on nine real-world hypergraph node classification benchmarks showcase that WCE-GNN demonstrates not only higher classification accuracy compared to state-of-the-art HyperGNNs, but also superior memory and runtime efficiency.