Ciyuan Peng

Ciyuan Peng, Feng Xia, Mehdi Naseriparsa et al.

With the explosive growth of artificial intelligence (AI) and big data, it has become vitally important to organize and represent the enormous volume of knowledge appropriately. As graph data, knowledge graphs accumulate and convey knowledge of the real world. It has been well-recognized that knowledge graphs effectively represent complex information; hence, they rapidly gain the attention of academia and industry in recent years. Thus to develop a deeper understanding of knowledge graphs, this paper presents a systematic overview of this field. Specifically, we focus on the opportunities and challenges of knowledge graphs. We first review the opportunities of knowledge graphs in terms of two aspects: (1) AI systems built upon knowledge graphs; (2) potential application fields of knowledge graphs. Then, we thoroughly discuss severe technical challenges in this field, such as knowledge graph embeddings, knowledge acquisition, knowledge graph completion, knowledge fusion, and knowledge reasoning. We expect that this survey will shed new light on future research and the development of knowledge graphs.

Ahsan Shehzad, Feng Xia, Shagufta Abid et al.

Graph transformers are a recent advancement in machine learning, offering a new class of neural network models for graph-structured data. The synergy between transformers and graph learning demonstrates strong performance and versatility across various graph-related tasks. This survey provides an in-depth review of recent progress and challenges in graph transformer research. We begin with foundational concepts of graphs and transformers. We then explore design perspectives of graph transformers, focusing on how they integrate graph inductive biases and graph attention mechanisms into the transformer architecture. Furthermore, we propose a taxonomy classifying graph transformers based on depth, scalability, and pre-training strategies, summarizing key principles for effective development of graph transformer models. Beyond technical analysis, we discuss the applications of graph transformer models for node-level, edge-level, and graph-level tasks, exploring their potential in other application scenarios as well. Finally, we identify remaining challenges in the field, such as scalability and efficiency, generalization and robustness, interpretability and explainability, dynamic and complex graphs, as well as data quality and diversity, charting future directions for graph transformer research.

Shuo Yu, Ciyuan Peng, Yingbo Wang et al.

Quantum theory has shown its superiority in enhancing machine learning. However, facilitating quantum theory to enhance graph learning is in its infancy. This survey investigates the current advances in quantum graph learning (QGL) from three perspectives, i.e., underlying theories, methods, and prospects. We first look at QGL and discuss the mutualism of quantum theory and graph learning, the specificity of graph-structured data, and the bottleneck of graph learning, respectively. A new taxonomy of QGL is presented, i.e., quantum computing on graphs, quantum graph representation, and quantum circuits for graph neural networks. Pitfall traps are then highlighted and explained. This survey aims to provide a brief but insightful introduction to this emerging field, along with a detailed discussion of frontiers and outlook yet to be investigated.

Dexuan Ding, Ciyuan Peng, Endrowednes Kuantama et al.

High-dimensional structural MRI (sMRI) images are widely used for Alzheimer's Disease (AD) diagnosis. Most existing methods for sMRI representation learning rely on 3D architectures (e.g., 3D CNNs), slice-wise feature extraction with late aggregation, or apply training-free feature extractions using 2D foundation models (e.g., DINO). However, these three paradigms suffer from high computational cost, loss of cross-slice relations, and limited ability to extract discriminative features, respectively. To address these challenges, we propose Multimodal Visual Surrogate Compression (MVSC). It learns to compress and adapt large 3D sMRI volumes into compact 2D features, termed as visual surrogates, which are better aligned with frozen 2D foundation models to extract powerful representations for final AD classification. MVSC has two key components: a Volume Context Encoder that captures global cross-slice context under textual guidance, and an Adaptive Slice Fusion module that aggregates slice-level information in a text-enhanced, patch-wise manner. Extensive experiments on three large-scale Alzheimer's disease benchmarks demonstrate our MVSC performs favourably on both binary and multi-class classification tasks compared against state-of-the-art methods.

Ciyuan Peng, Jiayuan He, Feng Xia

Multimodal data pervades various domains, including healthcare, social media, and transportation, where multimodal graphs play a pivotal role. Machine learning on multimodal graphs, referred to as multimodal graph learning (MGL), is essential for successful artificial intelligence (AI) applications. The burgeoning research in this field encompasses diverse graph data types and modalities, learning techniques, and application scenarios. This survey paper conducts a comparative analysis of existing works in multimodal graph learning, elucidating how multimodal learning is achieved across different graph types and exploring the characteristics of prevalent learning techniques. Additionally, we delineate significant applications of multimodal graph learning and offer insights into future directions in this domain. Consequently, this paper serves as a foundational resource for researchers seeking to comprehend existing MGL techniques and their applicability across diverse scenarios.

Ciyuan Peng, Yuelong Huang, Qichao Dong et al.

State-of-the-art brain graph analysis methods fail to fully encode the small-world architecture of brain graphs (accompanied by the presence of hubs and functional modules), and therefore lack biological plausibility to some extent. This limitation hinders their ability to accurately represent the brain's structural and functional properties, thereby restricting the effectiveness of machine learning models in tasks such as brain disorder detection. In this work, we propose a novel Biologically Plausible Brain Graph Transformer (BioBGT) that encodes the small-world architecture inherent in brain graphs. Specifically, we present a network entanglement-based node importance encoding technique that captures the structural importance of nodes in global information propagation during brain graph communication, highlighting the biological properties of the brain structure. Furthermore, we introduce a functional module-aware self-attention to preserve the functional segregation and integration characteristics of brain graphs in the learned representations. Experimental results on three benchmark datasets demonstrate that BioBGT outperforms state-of-the-art models, enhancing biologically plausible brain graph representations for various brain graph analytical tasks

Nguyen Linh Dan Le, Jing Ren, Ciyuan Peng et al.

Recent years have seen a surge in research focused on leveraging graph learning techniques to detect neurodegenerative diseases. However, existing graph-based approaches typically lack the ability to localize and extract the specific brain regions driving neurodegenerative pathology within the full connectome. Additionally, recent works on multimodal brain graph models often suffer from high computational complexity, limiting their practical use in resource-constrained devices. In this study, we present BrainMAP, a novel multimodal graph learning framework designed for precise and computationally efficient identification of brain regions affected by neurodegenerative diseases. First, BrainMAP utilizes an atlas-driven filtering approach guided by the AAL atlas to pinpoint and extract critical brain subgraphs. Unlike recent state-of-the-art methods, which model the entire brain network, BrainMAP achieves more than 50% reduction in computational overhead by concentrating on disease-relevant subgraphs. Second, we employ an advanced multimodal fusion process comprising cross-node attention to align functional magnetic resonance imaging (fMRI) and diffusion tensor imaging (DTI) data, coupled with an adaptive gating mechanism to blend and integrate these modalities dynamically. Experimental results demonstrate that BrainMAP outperforms state-of-the-art methods in computational efficiency, without compromising predictive accuracy.

Saba Fathi Rabooki, Bowen Li, Falih Gozi Febrinanto et al.

Cyber-physical-social systems (CPSSs) have emerged in many applications over recent decades, requiring increased attention to security concerns. The rise of sophisticated threats like Advanced Persistent Threats (APTs) makes ensuring security in CPSSs particularly challenging. Provenance graph analysis has proven effective for tracing and detecting anomalies within systems, but the sheer size and complexity of these graphs hinder the efficiency of existing methods, especially those relying on graph neural networks (GNNs). To address these challenges, we present GraphDART, a modular framework designed to distill provenance graphs into compact yet informative representations, enabling scalable and effective anomaly detection. GraphDART can take advantage of diverse graph distillation techniques, including classic and modern graph distillation methods, to condense large provenance graphs while preserving essential structural and contextual information. This approach significantly reduces computational overhead, allowing GNNs to learn from distilled graphs efficiently and enhance detection performance. Extensive evaluations on benchmark datasets demonstrate the robustness of GraphDART in detecting malicious activities across cyber-physical-social systems. By optimizing computational efficiency, GraphDART provides a scalable and practical solution to safeguard interconnected environments against APTs.

Tianqi Guo, Liping Chen, Ciyuan Peng et al.

Understanding the evolution of brain functional networks over time is of great significance for the analysis of cognitive mechanisms and the diagnosis of neurological diseases. Existing methods often have difficulty in capturing the temporal evolution characteristics of connections between specific functional communities. To this end, this paper proposes a new path-level trajectory modeling framework (NeuroPathNet) to characterize the dynamic behavior of connection pathways between brain functional partitions. Based on medically supported static partitioning schemes (such as Yeo and Smith ICA), we extract the time series of connection strengths between each pair of functional partitions and model them using a temporal neural network. We validate the model performance on three public functional Magnetic Resonance Imaging (fMRI) datasets, and the results show that it outperforms existing mainstream methods in multiple indicators. This study can promote the development of dynamic graph learning methods for brain network analysis, and provide possible clinical applications for the diagnosis of neurological diseases.

Ciyuan Peng, Nguyen Linh Dan Le, Shan Jin et al.

Brain graph learning has demonstrated significant achievements in the fields of neuroscience and artificial intelligence. However, existing methods struggle to selectively learn disease-related knowledge, leading to heavy parameters and computational costs. This challenge diminishes their efficiency, as well as limits their practicality for real-world clinical applications. To this end, we propose a lightweight Brain PathoGraph Learning (BrainPoG) model that enables efficient brain graph learning by pathological pattern filtering and pathological feature distillation. Specifically, BrainPoG first contains a filter to extract the pathological pattern formulated by highly disease-relevant subgraphs, achieving graph pruning and lesion localization. A PathoGraph is therefore constructed by dropping less disease-relevant subgraphs from the whole brain graph. Afterwards, a pathological feature distillation module is designed to reduce disease-irrelevant noise features and enhance pathological features of each node in the PathoGraph. BrainPoG can exclusively learn informative disease-related knowledge while avoiding less relevant information, achieving efficient brain graph learning. Extensive experiments on four benchmark datasets demonstrate that BrainPoG exhibits superiority in both model performance and computational efficiency across various brain disease detection tasks.

Feng Xia, Ciyuan Peng, Jing Ren et al.

Graph learning has rapidly evolved into a critical subfield of machine learning and artificial intelligence (AI). Its development began with early graph-theoretic methods, gaining significant momentum with the advent of graph neural networks (GNNs). Over the past decade, progress in scalable architectures, dynamic graph modeling, multimodal learning, generative AI, explainable AI (XAI), and responsible AI has broadened the applicability of graph learning to various challenging environments. Graph learning is significant due to its ability to model complex, non-Euclidean relationships that traditional machine learning struggles to capture, thus better supporting real-world applications ranging from drug discovery and fraud detection to recommender systems and scientific reasoning. However, challenges like scalability, generalization, heterogeneity, interpretability, and trustworthiness must be addressed to unlock its full potential. This survey provides a comprehensive introduction to graph learning, focusing on key dimensions including scalable, temporal, multimodal, generative, explainable, and responsible graph learning. We review state-of-the-art techniques for efficiently handling large-scale graphs, capturing dynamic temporal dependencies, integrating heterogeneous data modalities, generating novel graph samples, and enhancing interpretability to foster trust and transparency. We also explore ethical considerations, such as privacy and fairness, to ensure responsible deployment of graph learning models. Additionally, we identify and discuss emerging topics, highlighting recent integration of graph learning and other AI paradigms and offering insights into future directions. This survey serves as a valuable resource for researchers and practitioners seeking to navigate the rapidly evolving landscape of graph learning.

Ciyuan Peng, Feng Xia, Vidya Saikrishna et al.

An expeditious development of graph learning in recent years has found innumerable applications in several diversified fields. Of the main associated challenges are the volume and complexity of graph data. The graph learning models suffer from the inability to efficiently learn graph information. In order to indemnify this inefficacy, physics-informed graph learning (PIGL) is emerging. PIGL incorporates physics rules while performing graph learning, which has enormous benefits. This paper presents a systematic review of PIGL methods. We begin with introducing a unified framework of graph learning models followed by examining existing PIGL methods in relation to the unified framework. We also discuss several future challenges for PIGL. This survey paper is expected to stimulate innovative research and development activities pertaining to PIGL.