A Review of Graph Neural Networks in Epidemic Modeling

Since the onset of the COVID-19 pandemic, there has been a growing interest in studying epidemiological models. Traditional mechanistic models mathematically describe the transmission mechanisms of infectious diseases. However, they often fall short when confronted with the growing challenges of today. Consequently, Graph Neural Networks (GNNs) have emerged as a progressively popular tool in epidemic research. In this paper, we endeavor to furnish a comprehensive review of GNNs in epidemic tasks and highlight potential future directions. To accomplish this objective, we introduce hierarchical taxonomies for both epidemic tasks and methodologies, offering a trajectory of development within this domain. For epidemic tasks, we establish a taxonomy akin to those typically employed within the epidemic domain. For methodology, we categorize existing work into \textit{Neural Models} and \textit{Hybrid Models}. Following this, we perform an exhaustive and systematic examination of the methodologies, encompassing both the tasks and their technical details. Furthermore, we discuss the limitations of existing methods from diverse perspectives and systematically propose future research directions. This survey aims to bridge literature gaps and promote the progression of this promising field. We hope that it will facilitate synergies between the communities of GNNs and epidemiology, and contribute to their collective progress.

Investigating Out-of-Distribution Generalization of GNNs: An Architecture Perspective

Graph neural networks (GNNs) have exhibited remarkable performance under the assumption that test data comes from the same distribution of training data. However, in real-world scenarios, this assumption may not always be valid. Consequently, there is a growing focus on exploring the Out-of-Distribution (OOD) problem in the context of graphs. Most existing efforts have primarily concentrated on improving graph OOD generalization from two \textbf{model-agnostic} perspectives: data-driven methods and strategy-based learning. However, there has been limited attention dedicated to investigating the impact of well-known \textbf{GNN model architectures} on graph OOD generalization, which is orthogonal to existing research. In this work, we provide the first comprehensive investigation of OOD generalization on graphs from an architecture perspective, by examining the common building blocks of modern GNNs. Through extensive experiments, we reveal that both the graph self-attention mechanism and the decoupled architecture contribute positively to graph OOD generalization. In contrast, we observe that the linear classification layer tends to compromise graph OOD generalization capability. Furthermore, we provide in-depth theoretical insights and discussions to underpin these discoveries. These insights have empowered us to develop a novel GNN backbone model, DGAT, designed to harness the robust properties of both graph self-attention mechanism and the decoupled architecture. Extensive experimental results demonstrate the effectiveness of our model under graph OOD, exhibiting substantial and consistent enhancements across various training strategies.

Enhancing ID and Text Fusion via Alternative Training in Session-based Recommendation

Session-based recommendation has gained increasing attention in recent years, with its aim to offer tailored suggestions based on users' historical behaviors within sessions. To advance this field, a variety of methods have been developed, with ID-based approaches typically demonstrating promising performance. However, these methods often face challenges with long-tail items and overlook other rich forms of information, notably valuable textual semantic information. To integrate text information, various methods have been introduced, mostly following a naive fusion framework. Surprisingly, we observe that fusing these two modalities does not consistently outperform the best single modality by following the naive fusion framework. Further investigation reveals an potential imbalance issue in naive fusion, where the ID dominates and text modality is undertrained. This suggests that the unexpected observation may stem from naive fusion's failure to effectively balance the two modalities, often over-relying on the stronger ID modality. This insight suggests that naive fusion might not be as effective in combining ID and text as previously expected. To address this, we propose a novel alternative training strategy AlterRec. It separates the training of ID and text, thereby avoiding the imbalance issue seen in naive fusion. Additionally, AlterRec designs a novel strategy to facilitate the interaction between the two modalities, enabling them to mutually learn from each other and integrate the text more effectively. Comprehensive experiments demonstrate the effectiveness of AlterRec in session-based recommendation. The implementation is available at https://github.com/Juanhui28/AlterRec.

Navigating Complexity: Toward Lossless Graph Condensation via Expanding Window Matching

Graph condensation aims to reduce the size of a large-scale graph dataset by synthesizing a compact counterpart without sacrificing the performance of Graph Neural Networks (GNNs) trained on it, which has shed light on reducing the computational cost for training GNNs. Nevertheless, existing methods often fall short of accurately replicating the original graph for certain datasets, thereby failing to achieve the objective of lossless condensation. To understand this phenomenon, we investigate the potential reasons and reveal that the previous state-of-the-art trajectory matching method provides biased and restricted supervision signals from the original graph when optimizing the condensed one. This significantly limits both the scale and efficacy of the condensed graph. In this paper, we make the first attempt toward \textit{lossless graph condensation} by bridging the previously neglected supervision signals. Specifically, we employ a curriculum learning strategy to train expert trajectories with more diverse supervision signals from the original graph, and then effectively transfer the information into the condensed graph with expanding window matching. Moreover, we design a loss function to further extract knowledge from the expert trajectories. Theoretical analysis justifies the design of our method and extensive experiments verify its superiority across different datasets. Code is released at https://github.com/NUS-HPC-AI-Lab/GEOM.

A Comprehensive Survey on Graph Reduction: Sparsification, Coarsening, and Condensation

Many real-world datasets can be naturally represented as graphs, spanning a wide range of domains. However, the increasing complexity and size of graph datasets present significant challenges for analysis and computation. In response, graph reduction techniques have gained prominence for simplifying large graphs while preserving essential properties. In this survey, we aim to provide a comprehensive understanding of graph reduction methods, including graph sparsification, graph coarsening, and graph condensation. Specifically, we establish a unified definition for these methods and introduce a hierarchical taxonomy to categorize the challenges they address. Our survey then systematically reviews the technical details of these methods and emphasizes their practical applications across diverse scenarios. Furthermore, we outline critical research directions to ensure the continued effectiveness of graph reduction techniques, as well as provide a comprehensive paper list at https://github.com/ChandlerBang/awesome-graph-reduction. We hope this survey will bridge literature gaps and propel the advancement of this promising field.

A Comprehensive Dynamic Simulation Framework for Coupled Neuromusculoskeletal-Exoskeletal Systems

The modeling and simulation of coupled neuromusculoskeletal-exoskeletal systems play a crucial role in human biomechanical analysis, as well as in the design and control of exoskeletons. However, conventional dynamic simulation frameworks have limitations due to their reliance on experimental data and their inability to capture comprehensive biomechanical signals and dynamic responses. To address these challenges, we introduce an optimization-based dynamic simulation framework that integrates a complete neuromusculoskeletal feedback loop, rigid-body dynamics, human-exoskeleton interaction, and foot-ground contact. Without relying on experimental measurements or empirical data, our framework employs a stepwise optimization process to determine muscle reflex parameters, taking into account multidimensional criteria. This allows the framework to generate a full range of kinematic and biomechanical signals, including muscle activations, muscle forces, joint torques, etc., which are typically challenging to measure experimentally. To validate the effectiveness of the framework, we compare the simulated results with experimental data obtained from a healthy subject wearing an exoskeleton while walking at different speeds (0.9, 1.0, and 1.1 m/s) and terrains (flat and uphill). The results demonstrate that our framework can effectively and accurately capture the qualitative differences in muscle activity associated with different functions, as well as the evolutionary patterns of muscle activity and kinematic signals under varying walking conditions. The simulation framework we propose has the potential to facilitate gait analysis and performance evaluation of coupled human-exoskeleton systems, as well as enable efficient and cost-effective testing of novel exoskeleton designs and control strategies.

Knowledge-Infused Prompting: Assessing and Advancing Clinical Text Data Generation with Large Language Models

Clinical natural language processing requires methods that can address domain-specific challenges, such as complex medical terminology and clinical contexts. Recently, large language models (LLMs) have shown promise in this domain. Yet, their direct deployment can lead to privacy issues and are constrained by resources. To address this challenge, we delve into synthetic clinical text generation using LLMs for clinical NLP tasks. We propose an innovative, resource-efficient approach, ClinGen, which infuses knowledge into the process. Our model involves clinical knowledge extraction and context-informed LLM prompting. Both clinical topics and writing styles are drawn from external domain-specific knowledge graphs and LLMs to guide data generation. Our extensive empirical study across 7 clinical NLP tasks and 16 datasets reveals that ClinGen consistently enhances performance across various tasks, effectively aligning the distribution of real datasets and significantly enriching the diversity of generated training instances. We will publish our code and all the generated data in \url{https://github.com/ritaranx/ClinGen}.

Augment with Care: Enhancing Graph Contrastive Learning with Selective Spectrum Perturbation

In recent years, Graph Contrastive Learning (GCL) has shown remarkable effectiveness in learning representations on graphs. As a component of GCL, good augmentation views are supposed to be invariant to the important information while discarding the unimportant part. Existing augmentation views with perturbed graph structures are usually based on random topology corruption in the spatial domain; however, from perspectives of the spectral domain, this approach may be ineffective as it fails to pose tailored impacts on the information of different frequencies, thus weakening the agreement between the augmentation views. By a preliminary experiment, we show that the impacts caused by spatial random perturbation are approximately evenly distributed among frequency bands, which may harm the invariance of augmentations required by contrastive learning frameworks. To address this issue, we argue that the perturbation should be selectively posed on the information concerning different frequencies. In this paper, we propose GASSER which poses tailored perturbation on the specific frequencies of graph structures in spectral domain, and the edge perturbation is selectively guided by the spectral hints. As shown by extensive experiments and theoretical analysis, the augmentation views are adaptive and controllable, as well as heuristically fitting the homophily ratios and spectrum of graph structures.