In recent years, functional magnetic resonance imaging has emerged as a powerful tool for investigating the human brain's functional connectivity networks. Related studies demonstrate that functional connectivity networks in the human brain can help to improve the efficiency of diagnosing neurological disorders. However, there still exist two challenges that limit the progress of functional neuroimaging. Firstly, there exists an abundance of noise and redundant information in functional connectivity data, resulting in poor performance. Secondly, existing brain network models have tended to prioritize either classification performance or the interpretation of neuroscience findings behind the learned models. To deal with these challenges, this paper proposes a novel brain graph learning framework called Template-induced Brain Graph Learning (TiBGL), which has both discriminative and interpretable abilities. Motivated by the related medical findings on functional connectivites, TiBGL proposes template-induced brain graph learning to extract template brain graphs for all groups. The template graph can be regarded as an augmentation process on brain networks that removes noise information and highlights important connectivity patterns. To simultaneously support the tasks of discrimination and interpretation, TiBGL further develops template-induced convolutional neural network and template-induced brain interpretation analysis. Especially, the former fuses rich information from brain graphs and template brain graphs for brain disorder tasks, and the latter can provide insightful connectivity patterns related to brain disorders based on template brain graphs. Experimental results on three real-world datasets show that the proposed TiBGL can achieve superior performance compared with nine state-of-the-art methods and keep coherent with neuroscience findings in recent literatures.
A rising trend in theoretical deep learning is to understand why deep learning works through Neural Tangent Kernel (NTK) [jgh18], a kernel method that is equivalent to using gradient descent to train a multi-layer infinitely-wide neural network. NTK is a major step forward in the theoretical deep learning because it allows researchers to use traditional mathematical tools to analyze properties of deep neural networks and to explain various neural network techniques from a theoretical view. A natural extension of NTK on graph learning is \textit{Graph Neural Tangent Kernel (GNTK)}, and researchers have already provide GNTK formulation for graph-level regression and show empirically that this kernel method can achieve similar accuracy as GNNs on various bioinformatics datasets [dhs+19]. The remaining question now is whether solving GNTK regression is equivalent to training an infinite-wide multi-layer GNN using gradient descent. In this paper, we provide three new theoretical results. First, we formally prove this equivalence for graph-level regression. Second, we present the first GNTK formulation for node-level regression. Finally, we prove the equivalence for node-level regression.
Humans are constantly exposed to sequences of events in the environment. Those sequences frequently evince statistical regularities, such as the probabilities with which one event transitions to another. Collectively, inter-event transition probabilities can be modeled as a graph or network. Many real-world networks are organized hierarchically and understanding how humans learn these networks is an ongoing aim of current investigations. While much is known about how humans learn basic transition graph topology, whether and to what degree humans can learn hierarchical structures in such graphs remains unknown. We investigate how humans learn hierarchical graphs of the Sierpi\'nski family using computer simulations and behavioral laboratory experiments. We probe the mental estimates of transition probabilities via the surprisal effect: a phenomenon in which humans react more slowly to less expected transitions, such as those between communities or modules in the network. Using mean-field predictions and numerical simulations, we show that surprisal effects are stronger for finer-level than coarser-level hierarchical transitions. Surprisal effects at coarser levels of the hierarchy are difficult to detect for limited learning times or in small samples. Using a serial response experiment with human participants (n=$100$), we replicate our predictions by detecting a surprisal effect at the finer-level of the hierarchy but not at the coarser-level of the hierarchy. To further explain our findings, we evaluate the presence of a trade-off in learning, whereby humans who learned the finer-level of the hierarchy better tended to learn the coarser-level worse, and vice versa. Our study elucidates the processes by which humans learn hierarchical sequential events. Our work charts a road map for future investigation of the neural underpinnings and behavioral manifestations of graph learning.
Along with the proliferation of electric vehicles (EVs), optimizing the use of EV charging space can significantly alleviate the growing load on intelligent transportation systems. As the foundation to achieve such an optimization, a spatiotemporal method for EV charging demand prediction in urban areas is required. Although several solutions have been proposed by using data-driven deep learning methods, it can be found that these performance-oriented methods may suffer from misinterpretations to correctly handle the reverse relationship between charging demands and prices. To tackle the emerging challenges of training an accurate and interpretable prediction model, this paper proposes a novel approach that enables the integration of graph and temporal attention mechanisms for feature extraction and the usage of physic-informed meta-learning in the model pre-training step for knowledge transfer. Evaluation results on a dataset of 18,013 EV charging piles in Shenzhen, China, show that the proposed approach, named PAG, can achieve state-of-the-art forecasting performance and the ability in understanding the adaptive changes in charging demands caused by price fluctuations.
Designing versatile graph learning approaches is important, considering the diverse graphs and tasks existing in real-world applications. Existing methods have attempted to achieve this target through automated machine learning techniques, pre-training and fine-tuning strategies, and large language models. However, these methods are not versatile enough for graph learning, as they work on either limited types of graphs or a single task. In this paper, we propose to explore versatile graph learning approaches with LLM-based agents, and the key insight is customizing the graph learning procedures for diverse graphs and tasks. To achieve this, we develop several LLM-based agents, equipped with diverse profiles, tools, functions and human experience. They collaborate to configure each procedure with task and data-specific settings step by step towards versatile solutions, and the proposed method is dubbed GL-Agent. By evaluating on diverse tasks and graphs, the correct results of the agent and its comparable performance showcase the versatility of the proposed method, especially in complex scenarios.The low resource cost and the potential to use open-source LLMs highlight the efficiency of GL-Agent.
Irregular data in real-world are usually organized as heterogeneous graphs (HGs) consisting of multiple types of nodes and edges. To explore useful knowledge from real-world data, both the large-scale encyclopedic HG datasets and corresponding effective learning methods are crucial, but haven't been well investigated. In this paper, we construct a large-scale HG benchmark dataset named UniKG from Wikidata to facilitate knowledge mining and heterogeneous graph representation learning. Overall, UniKG contains more than 77 million multi-attribute entities and 2000 diverse association types, which significantly surpasses the scale of existing HG datasets. To perform effective learning on the large-scale UniKG, two key measures are taken, including (i) the semantic alignment strategy for multi-attribute entities, which projects the feature description of multi-attribute nodes into a common embedding space to facilitate node aggregation in a large receptive field; (ii) proposing a novel plug-and-play anisotropy propagation module (APM) to learn effective multi-hop anisotropy propagation kernels, which extends methods of large-scale homogeneous graphs to heterogeneous graphs. These two strategies enable efficient information propagation among a tremendous number of multi-attribute entities and meantimes adaptively mine multi-attribute association through the multi-hop aggregation in large-scale HGs. We set up a node classification task on our UniKG dataset, and evaluate multiple baseline methods which are constructed by embedding our APM into large-scale homogenous graph learning methods. Our UniKG dataset and the baseline codes have been released at https://github.com/Yide-Qiu/UniKG.
Patients undergoing chest X-rays (CXR) often endure multiple lung diseases. When evaluating a patient's condition, due to the complex pathologies, subtle texture changes of different lung lesions in images, and patient condition differences, radiologists may make uncertain even when they have experienced long-term clinical training and professional guidance, which makes much noise in extracting disease labels based on CXR reports. In this paper, we re-extract disease labels from CXR reports to make them more realistic by considering disease severity and uncertainty in classification. Our contributions are as follows: 1. We re-extracted the disease labels with severity and uncertainty by a rule-based approach with keywords discussed with clinical experts. 2. To further improve the explainability of chest X-ray diagnosis, we designed a multi-relationship graph learning method with an expert uncertainty-aware loss function. 3. Our multi-relationship graph learning method can also interpret the disease classification results. Our experimental results show that models considering disease severity and uncertainty outperform previous state-of-the-art methods.
Diabetic Retinopathy (DR) is a significant cause of blindness globally, highlighting the urgent need for early detection and effective treatment. Recent advancements in Machine Learning (ML) techniques have shown promise in DR detection, but the availability of labeled data often limits their performance. This research proposes a novel Semi-Supervised Graph Learning SSGL algorithm tailored for DR detection, which capitalizes on the relationships between labelled and unlabeled data to enhance accuracy. The work begins by investigating data augmentation and preprocessing techniques to address the challenges of image quality and feature variations. Techniques such as image cropping, resizing, contrast adjustment, normalization, and data augmentation are explored to optimize feature extraction and improve the overall quality of retinal images. Moreover, apart from detection and diagnosis, this work delves into applying ML algorithms for predicting the risk of developing DR or the likelihood of disease progression. Personalized risk scores for individual patients are generated using comprehensive patient data encompassing demographic information, medical history, and retinal images. The proposed Semi-Supervised Graph learning algorithm is rigorously evaluated on two publicly available datasets and is benchmarked against existing methods. Results indicate significant improvements in classification accuracy, specificity, and sensitivity while demonstrating robustness against noise and outlie rs.Notably, the proposed algorithm addresses the challenge of imbalanced datasets, common in medical image analysis, further enhancing its practical applicability.
Accurate segmentation of surgical instrument tip is an important task for enabling downstream applications in robotic surgery, such as surgical skill assessment, tool-tissue interaction and deformation modeling, as well as surgical autonomy. However, this task is very challenging due to the small sizes of surgical instrument tips, and significant variance of surgical scenes across different procedures. Although much effort has been made on visual-based methods, existing segmentation models still suffer from low robustness thus not usable in practice. Fortunately, kinematics data from the robotic system can provide reliable prior for instrument location, which is consistent regardless of different surgery types. To make use of such multi-modal information, we propose a novel visual-kinematics graph learning framework to accurately segment the instrument tip given various surgical procedures. Specifically, a graph learning framework is proposed to encode relational features of instrument parts from both image and kinematics. Next, a cross-modal contrastive loss is designed to incorporate robust geometric prior from kinematics to image for tip segmentation. We have conducted experiments on a private paired visual-kinematics dataset including multiple procedures, i.e., prostatectomy, total mesorectal excision, fundoplication and distal gastrectomy on cadaver, and distal gastrectomy on porcine. The leave-one-procedure-out cross validation demonstrated that our proposed multi-modal segmentation method significantly outperformed current image-based state-of-the-art approaches, exceeding averagely 11.2% on Dice.
The recent Long-Range Graph Benchmark (LRGB, Dwivedi et al. 2022) introduced a set of graph learning tasks strongly dependent on long-range interaction between vertices. Empirical evidence suggests that on these tasks Graph Transformers significantly outperform Message Passing GNNs (MPGNNs). In this paper, we carefully reevaluate multiple MPGNN baselines as well as the Graph Transformer GPS (Ramp\'a\v{s}ek et al. 2022) on LRGB. Through a rigorous empirical analysis, we demonstrate that the reported performance gap is overestimated due to suboptimal hyperparameter choices. It is noteworthy that across multiple datasets the performance gap completely vanishes after basic hyperparameter optimization. In addition, we discuss the impact of lacking feature normalization for LRGB's vision datasets and highlight a spurious implementation of LRGB's link prediction metric. The principal aim of our paper is to establish a higher standard of empirical rigor within the graph machine learning community.
Anchor-based multi-view graph clustering (AMVGC) has received abundant attention owing to its high efficiency and the capability to capture complementary structural information across multiple views. Intuitively, a high-quality anchor graph plays an essential role in the success of AMVGC. However, the existing AMVGC methods only consider single-structure information, i.e., local or global structure, which provides insufficient information for the learning task. To be specific, the over-scattered global structure leads to learned anchors failing to depict the cluster partition well. In contrast, the local structure with an improper similarity measure results in potentially inaccurate anchor assignment, ultimately leading to sub-optimal clustering performance. To tackle the issue, we propose a novel anchor-based multi-view graph clustering framework termed Efficient Multi-View Graph Clustering with Local and Global Structure Preservation (EMVGC-LG). Specifically, a unified framework with a theoretical guarantee is designed to capture local and global information. Besides, EMVGC-LG jointly optimizes anchor construction and graph learning to enhance the clustering quality. In addition, EMVGC-LG inherits the linear complexity of existing AMVGC methods respecting the sample number, which is time-economical and scales well with the data size. Extensive experiments demonstrate the effectiveness and efficiency of our proposed method.
The success of existing multi-view clustering (MVC) relies on the assumption that all views are complete. However, samples are usually partially available due to data corruption or sensor malfunction, which raises the research of incomplete multi-view clustering (IMVC). Although several anchor-based IMVC methods have been proposed to process the large-scale incomplete data, they still suffer from the following drawbacks: i) Most existing approaches neglect the inter-view discrepancy and enforce cross-view representation to be consistent, which would corrupt the representation capability of the model; ii) Due to the samples disparity between different views, the learned anchor might be misaligned, which we referred as the Anchor-Unaligned Problem for Incomplete data (AUP-ID). Such the AUP-ID would cause inaccurate graph fusion and degrades clustering performance. To tackle these issues, we propose a novel incomplete anchor graph learning framework termed Scalable Incomplete Multi-View Clustering with Structure Alignment (SIMVC-SA). Specially, we construct the view-specific anchor graph to capture the complementary information from different views. In order to solve the AUP-ID, we propose a novel structure alignment module to refine the cross-view anchor correspondence. Meanwhile, the anchor graph construction and alignment are jointly optimized in our unified framework to enhance clustering quality. Through anchor graph construction instead of full graphs, the time and space complexity of the proposed SIMVC-SA is proven to be linearly correlated with the number of samples. Extensive experiments on seven incomplete benchmark datasets demonstrate the effectiveness and efficiency of our proposed method. Our code is publicly available at https://github.com/wy1019/SIMVC-SA.
The electronic design automation of analog circuits has been a longstanding challenge in the integrated circuit field due to the huge design space and complex design trade-offs among circuit specifications. In the past decades, intensive research efforts have mostly been paid to automate the transistor sizing with a given circuit topology. By recognizing the graph nature of circuits, this paper presents a Circuit Graph Neural Network (CktGNN) that simultaneously automates the circuit topology generation and device sizing based on the encoder-dependent optimization subroutines. Particularly, CktGNN encodes circuit graphs using a two-level GNN framework (of nested GNN) where circuits are represented as combinations of subgraphs in a known subgraph basis. In this way, it significantly improves design efficiency by reducing the number of subgraphs to perform message passing. Nonetheless, another critical roadblock to advancing learning-assisted circuit design automation is a lack of public benchmarks to perform canonical assessment and reproducible research. To tackle the challenge, we introduce Open Circuit Benchmark (OCB), an open-sourced dataset that contains $10$K distinct operational amplifiers with carefully-extracted circuit specifications. OCB is also equipped with communicative circuit generation and evaluation capabilities such that it can help to generalize CktGNN to design various analog circuits by producing corresponding datasets. Experiments on OCB show the extraordinary advantages of CktGNN through representation-based optimization frameworks over other recent powerful GNN baselines and human experts' manual designs. Our work paves the way toward a learning-based open-sourced design automation for analog circuits. Our source code is available at \url{https://github.com/zehao-dong/CktGNN}.
In this paper, a dynamic dual-graph fusion convolutional network is proposed to improve Alzheimer's disease (AD) diagnosis performance. The following are the paper's main contributions: (a) propose a novel dynamic GCN architecture, which is an end-to-end pipeline for diagnosis of the AD task; (b) the proposed architecture can dynamically adjust the graph structure for GCN to produce better diagnosis outcomes by learning the optimal underlying latent graph; (c) incorporate feature graph learning and dynamic graph learning, giving those useful features of subjects more weight while decreasing the weights of other noise features. Experiments indicate that our model provides flexibility and stability while achieving excellent classification results in AD diagnosis.
Infectious disease forecasting has been a key focus and proved to be crucial in controlling epidemic. A recent trend is to develop forecast-ing models based on graph neural networks (GNNs). However, existing GNN-based methods suffer from two key limitations: (1) Current models broaden receptive fields by scaling the depth of GNNs, which is insuffi-cient to preserve the semantics of long-range connectivity between distant but epidemic related areas. (2) Previous approaches model epidemics within single spatial scale, while ignoring the multi-scale epidemic pat-terns derived from different scales. To address these deficiencies, we devise the Multi-scale Spatio-temporal Graph Neural Network (MSGNN) based on an innovative multi-scale view. To be specific, in the proposed MSGNN model, we first devise a novel graph learning module, which directly captures long-range connectivity from trans-regional epidemic signals and integrates them into a multi-scale graph. Based on the learned multi-scale graph, we utilize a newly designed graph convolution module to exploit multi-scale epidemic patterns. This module allows us to facilitate multi-scale epidemic modeling by mining both scale-shared and scale-specific pat-terns. Experimental results on forecasting new cases of COVID-19 in United State demonstrate the superiority of our method over state-of-arts. Further analyses and visualization also show that MSGNN offers not only accurate, but also robust and interpretable forecasting result.
Graph homomorphism counts, first explored by Lov\'asz in 1967, have recently garnered interest as a powerful tool in graph-based machine learning. Grohe (PODS 2020) proposed the theoretical foundations for using homomorphism counts in machine learning on graph level as well as node level tasks. By their very nature, these capture local structural information, which enables the creation of robust structural embeddings. While a first approach for graph level tasks has been made by Nguyen and Maehara (ICML 2020), we experimentally show the effectiveness of homomorphism count based node embeddings. Enriched with node labels, node weights, and edge weights, these offer an interpretable representation of graph data, allowing for enhanced explainability of machine learning models. We propose a theoretical framework for isomorphism-invariant homomorphism count based embeddings which lend themselves to a wide variety of downstream tasks. Our approach capitalises on the efficient computability of graph homomorphism counts for bounded treewidth graph classes, rendering it a practical solution for real-world applications. We demonstrate their expressivity through experiments on benchmark datasets. Although our results do not match the accuracy of state-of-the-art neural architectures, they are comparable to other advanced graph learning models. Remarkably, our approach demarcates itself by ensuring explainability for each individual feature. By integrating interpretable machine learning algorithms like SVMs or Random Forests, we establish a seamless, end-to-end explainable pipeline. Our study contributes to the advancement of graph-based techniques that offer both performance and interpretability.
We address catastrophic forgetting issues in graph learning as incoming data transits from one to another graph distribution. Whereas prior studies primarily tackle one setting of graph continual learning such as incremental node classification, we focus on a universal approach wherein each data point in a task can be a node or a graph, and the task varies from node to graph classification. We propose a novel method that enables graph neural networks to excel in this universal setting. Our approach perseveres knowledge about past tasks through a rehearsal mechanism that maintains local and global structure consistency across the graphs. We benchmark our method against various continual learning baselines in real-world graph datasets and achieve significant improvement in average performance and forgetting across tasks.
Graphs represent interconnected structures prevalent in a myriad of real-world scenarios. Effective graph analytics, such as graph learning methods, enables users to gain profound insights from graph data, underpinning various tasks including node classification and link prediction. However, these methods often suffer from data imbalance, a common issue in graph data where certain segments possess abundant data while others are scarce, thereby leading to biased learning outcomes. This necessitates the emerging field of imbalanced learning on graphs, which aims to correct these data distribution skews for more accurate and representative learning outcomes. In this survey, we embark on a comprehensive review of the literature on imbalanced learning on graphs. We begin by providing a definitive understanding of the concept and related terminologies, establishing a strong foundational understanding for readers. Following this, we propose two comprehensive taxonomies: (1) the problem taxonomy, which describes the forms of imbalance we consider, the associated tasks, and potential solutions; (2) the technique taxonomy, which details key strategies for addressing these imbalances, and aids readers in their method selection process. Finally, we suggest prospective future directions for both problems and techniques within the sphere of imbalanced learning on graphs, fostering further innovation in this critical area.
Class imbalance is prevalent in real-world node classification tasks and poses great challenges for graph learning models. Most existing studies are rooted in a class-rebalancing (CR) perspective and address class imbalance with class-wise reweighting or resampling. In this work, we approach the root cause of class-imbalance bias from an topological paradigm. Specifically, we theoretically reveal two fundamental phenomena in the graph topology that greatly exacerbate the predictive bias stemming from class imbalance. On this basis, we devise a lightweight topological augmentation framework BAT to mitigate the class-imbalance bias without class rebalancing. Being orthogonal to CR, BAT can function as an efficient plug-and-play module that can be seamlessly combined with and significantly boost existing CR techniques. Systematic experiments on real-world imbalanced graph learning tasks show that BAT can deliver up to 46.27% performance gain and up to 72.74% bias reduction over existing techniques. Code, examples, and documentations are available at https://github.com/ZhiningLiu1998/BAT.
Graph Neural Networks (GNNs) have demonstrated superior performance on various graph learning tasks, including recommendation, where they leverage user-item collaborative filtering signals in graphs. However, theoretical formulations of their capability are scarce, despite their empirical effectiveness in state-of-the-art recommender models. Recently, research has explored the expressiveness of GNNs in general, demonstrating that message passing GNNs are at most as powerful as the Weisfeiler-Lehman test, and that GNNs combined with random node initialization are universal. Nevertheless, the concept of "expressiveness" for GNNs remains vaguely defined. Most existing works adopt the graph isomorphism test as the metric of expressiveness, but this graph-level task may not effectively assess a model's ability in recommendation, where the objective is to distinguish nodes of different closeness. In this paper, we provide a comprehensive theoretical analysis of the expressiveness of GNNs in recommendation, considering three levels of expressiveness metrics: graph isomorphism (graph-level), node automorphism (node-level), and topological closeness (link-level). We propose the topological closeness metric to evaluate GNNs' ability to capture the structural distance between nodes, which aligns closely with the objective of recommendation. To validate the effectiveness of this new metric in evaluating recommendation performance, we introduce a learning-less GNN algorithm that is optimal on the new metric and can be optimal on the node-level metric with suitable modification. We conduct extensive experiments comparing the proposed algorithm against various types of state-of-the-art GNN models to explore the explainability of the new metric in the recommendation task. For reproducibility, implementation codes are available at https://github.com/HKUDS/GTE.