Graph embeddings play a critical role in graph representation learning, allowing machine learning models to explore and interpret graph-structured data. However, existing methods often rely on opaque, high-dimensional embeddings, limiting interpretability and practical visualization. In this work, we introduce Topological Evolution Rate (TopER), a novel, low-dimensional embedding approach grounded in topological data analysis. TopER simplifies a key topological approach, Persistent Homology, by calculating the evolution rate of graph substructures, resulting in intuitive and interpretable visualizations of graph data. This approach not only enhances the exploration of graph datasets but also delivers competitive performance in graph clustering and classification tasks. Our TopER-based models achieve or surpass state-of-the-art results across molecular, biological, and social network datasets in tasks such as classification, clustering, and visualization.
Graphs are ubiquitous for modeling complex systems involving structured data and relationships. Consequently, graph representation learning, which aims to automatically learn low-dimensional representations of graphs, has drawn a lot of attention in recent years. The overwhelming majority of existing methods handle unsigned graphs. However, signed graphs appear in an increasing number of application domains to model systems involving two types of opposed relationships. Several authors took an interest in signed graphs and proposed methods for providing vertex-level representations, but only one exists for whole-graph representations, and it can handle only fully connected graphs. In this article, we tackle this issue by proposing two approaches to learning whole-graph representations of general signed graphs. The first is a SG2V, a signed generalization of the whole-graph embedding method Graph2vec that relies on a modification of the Weisfeiler--Lehman relabelling procedure. The second one is WSGCN, a whole-graph generalization of the signed vertex embedding method SGCN that relies on the introduction of master nodes into the GCN. We propose several variants of both these approaches. A bottleneck in the development of whole-graph-oriented methods is the lack of data. We constitute a benchmark composed of three collections of signed graphs with corresponding ground truths. We assess our methods on this benchmark, and our results show that the signed whole-graph methods learn better representations for this task. Overall, the baseline obtains an F-measure score of 58.57, when SG2V and WSGCN reach 73.01 and 81.20, respectively. Our source code and benchmark dataset are both publicly available online.
Context-aware Human Activity Recognition (CHAR) is challenging due to the need to recognize the user's current activity from signals that vary significantly with contextual factors such as phone placements and the varied styles with which different users perform the same activity. In this paper, we argue that context-aware activity visit patterns in realistic in-the-wild data can equivocally be considered as a general graph representation learning task. We posit that exploiting underlying graphical patterns in CHAR data can improve CHAR task performance and representation learning. Building on the intuition that certain activities are frequently performed with the phone placed in certain positions, we focus on the context-aware human activity problem of recognizing the <Activity, Phone Placement> tuple. We demonstrate that CHAR data has an underlying graph structure that can be viewed as a heterogenous hypergraph that has multiple types of nodes and hyperedges (an edge connecting more than two nodes). Subsequently, learning <Activity, Phone Placement> representations becomes a graph node representation learning problem. After task transformation, we further propose a novel Heterogeneous HyperGraph Neural Network architecture for Context-aware Human Activity Recognition (HHGNN-CHAR), with three types of heterogeneous nodes (user, phone placement, and activity). Connections between all types of nodes are represented by hyperedges. Rigorous evaluation demonstrated that on an unscripted, in-the-wild CHAR dataset, our proposed framework significantly outperforms state-of-the-art (SOTA) baselines including CHAR models that do not exploit graphs, and GNN variants that do not incorporate heterogeneous nodes or hyperedges with overall improvements 14.04% on Matthews Correlation Coefficient (MCC) and 7.01% on Macro F1 scores.
Although modern imaging technologies allow us to study connectivity between two distinct brain regions in-vivo, an in-depth understanding of how anatomical structure supports brain function and how spontaneous functional fluctuations emerge remarkable cognition is still elusive. Meanwhile, tremendous efforts have been made in the realm of machine learning to establish the nonlinear mapping between neuroimaging data and phenotypic traits. However, the absence of neuroscience insight in the current approaches poses significant challenges in understanding cognitive behavior from transient neural activities. To address this challenge, we put the spotlight on the coupling mechanism of structural connectivity (SC) and functional connectivity (FC) by formulating such network neuroscience question into an expressive graph representation learning problem for high-order topology. Specifically, we introduce the concept of topological detour to characterize how a ubiquitous instance of FC (direct link) is supported by neural pathways (detour) physically wired by SC, which forms a cyclic loop interacted by brain structure and function. In the clich\'e of machine learning, the multi-hop detour pathway underlying SC-FC coupling allows us to devise a novel multi-head self-attention mechanism within Transformer to capture multi-modal feature representation from paired graphs of SC and FC. Taken together, we propose a biological-inspired deep model, coined as NeuroPath, to find putative connectomic feature representations from the unprecedented amount of neuroimages, which can be plugged into various downstream applications such as task recognition and disease diagnosis. We have evaluated NeuroPath on large-scale public datasets including HCP and UK Biobank under supervised and zero-shot learning, where the state-of-the-art performance by our NeuroPath indicates great potential in network neuroscience.
Graph pooling compresses graphs and summarises their topological properties and features in a vectorial representation. It is an essential part of deep graph representation learning and is indispensable in graph-level tasks like classification or regression. Current approaches pool hierarchical structures in graphs by iteratively applying shallow pooling operators up to a fixed depth. However, they disregard the interdependencies between structures at different hierarchical levels and do not adapt to datasets that contain graphs with different sizes that may require pooling with various depths. To address these issues, we propose MDL-Pool, a pooling operator based on the minimum description length (MDL) principle, whose loss formulation explicitly models the interdependencies between different hierarchical levels and facilitates a direct comparison between multiple pooling alternatives with different depths. MDP-Pool builds on the map equation, an information-theoretic objective function for community detection, which naturally implements Occam's razor and balances between model complexity and goodness-of-fit via the MDL. We demonstrate MDL-Pool's competitive performance in an empirical evaluation against various baselines across standard graph classification datasets.
Graph Neural Networks (GNNs) have been widely employed for feature representation learning in molecular graphs. Therefore, it is crucial to enhance the expressiveness of feature representation to ensure the effectiveness of GNNs. However, a significant portion of current research primarily focuses on the structural features within individual molecules, often overlooking the structural similarity between molecules, which is a crucial aspect encapsulating rich information on the relationship between molecular properties and structural characteristics. Thus, these approaches fail to capture the rich semantic information at the molecular structure level. To bridge this gap, we introduce the \textbf{Molecular Structural Similarity Motif GNN (MSSM-GNN)}, a novel molecular graph representation learning method that can capture structural similarity information among molecules from a global perspective. In particular, we propose a specially designed graph that leverages graph kernel algorithms to represent the similarity between molecules quantitatively. Subsequently, we employ GNNs to learn feature representations from molecular graphs, aiming to enhance the accuracy of property prediction by incorporating additional molecular representation information. Finally, through a series of experiments conducted on both small-scale and large-scale molecular datasets, we demonstrate that our model consistently outperforms eleven state-of-the-art baselines. The codes are available at https://github.com/yaoyao-yaoyao-cell/MSSM-GNN.
Ethereum faces growing fraud threats. Current fraud detection methods, whether employing graph neural networks or sequence models, fail to consider the semantic information and similarity patterns within transactions. Moreover, these approaches do not leverage the potential synergistic benefits of combining both types of models. To address these challenges, we propose TLMG4Eth that combines a transaction language model with graph-based methods to capture semantic, similarity, and structural features of transaction data in Ethereum. We first propose a transaction language model that converts numerical transaction data into meaningful transaction sentences, enabling the model to learn explicit transaction semantics. Then, we propose a transaction attribute similarity graph to learn transaction similarity information, enabling us to capture intuitive insights into transaction anomalies. Additionally, we construct an account interaction graph to capture the structural information of the account transaction network. We employ a deep multi-head attention network to fuse transaction semantic and similarity embeddings, and ultimately propose a joint training approach for the multi-head attention network and the account interaction graph to obtain the synergistic benefits of both.
Video question answering (VideoQA) is a task to predict the correct answer to questions posed about a given video. The system must comprehend spatial and temporal relationships among objects extracted from videos to perform causal and temporal reasoning. While prior works have focused on modeling individual object movements using transformer-based methods, they falter when capturing complex scenarios involving multiple objects (e.g., "a boy is throwing a ball in a hoop"). We propose a contrastive language event graph representation learning method called CLanG to address this limitation. Aiming to capture event representations associated with multiple objects, our method employs a multi-layer GNN-cluster module for adversarial graph representation learning, enabling contrastive learning between the question text and its relevant multi-object event graph. Our method outperforms a strong baseline, achieving up to 2.2% higher accuracy on two challenging VideoQA datasets, NExT-QA and TGIF-QA-R. In particular, it is 2.8% better than baselines in handling causal and temporal questions, highlighting its strength in reasoning multiple object-based events.
Graph representation learning has emerged as a powerful tool for preserving graph topology when mapping nodes to vector representations, enabling various downstream tasks such as node classification and community detection. However, most current graph neural network models face the challenge of requiring extensive labeled data, which limits their practical applicability in real-world scenarios where labeled data is scarce. To address this challenge, researchers have explored Graph Contrastive Learning (GCL), which leverages enhanced graph data and contrastive learning techniques. While promising, existing GCL methods often struggle with effectively capturing both local and global graph structures, and balancing the trade-off between nodelevel and graph-level representations. In this work, we propose Graph Representation Embedding Enhanced via Multidimensional Contrastive Learning (GRE2-MDCL). Our model introduces a novel triple network architecture with a multi-head attention GNN as the core. GRE2-MDCL first globally and locally augments the input graph using SVD and LAGNN techniques. It then constructs a multidimensional contrastive loss, incorporating cross-network, cross-view, and neighbor contrast, to optimize the model. Extensive experiments on benchmark datasets Cora, Citeseer, and PubMed demonstrate that GRE2-MDCL achieves state-of-the-art performance, with average accuracies of 82.5%, 72.5%, and 81.6% respectively. Visualizations further show tighter intra-cluster aggregation and clearer inter-cluster boundaries, highlighting the effectiveness of our framework in improving upon baseline GCL models.
Electronic Design Automation (EDA) is essential for IC design and has recently benefited from AI-based techniques to improve efficiency. Logic synthesis, a key EDA stage, transforms high-level hardware descriptions into optimized netlists. Recent research has employed machine learning to predict Quality of Results (QoR) for pairs of And-Inverter Graphs (AIGs) and synthesis recipes. However, the severe scarcity of data due to a very limited number of available AIGs results in overfitting, significantly hindering performance. Additionally, the complexity and large number of nodes in AIGs make plain GNNs less effective for learning expressive graph-level representations. To tackle these challenges, we propose MTLSO - a Multi-Task Learning approach for Logic Synthesis Optimization. On one hand, it maximizes the use of limited data by training the model across different tasks. This includes introducing an auxiliary task of binary multi-label graph classification alongside the primary regression task, allowing the model to benefit from diverse supervision sources. On the other hand, we employ a hierarchical graph representation learning strategy to improve the model's capacity for learning expressive graph-level representations of large AIGs, surpassing traditional plain GNNs. Extensive experiments across multiple datasets and against state-of-the-art baselines demonstrate the superiority of our method, achieving an average performance gain of 8.22\% for delay and 5.95\% for area.
Graph representation learning (GRL) models have succeeded in many scenarios. Real-world graphs have imbalanced distribution, such as node labels and degrees, which leaves a critical challenge to GRL. Imbalanced inputs can lead to imbalanced outputs. However, most existing works ignore it and assume that the distribution of input graphs is balanced, which cannot align with real situations, resulting in worse model performance on tail data. The domination of head data makes tail data underrepresented when training graph neural networks (GNNs). Thus, we propose Graffin, a pluggable tail data augmentation module, to address the above issues. Inspired by recurrent neural networks (RNNs), Graffin flows head features into tail data through graph serialization techniques to alleviate the imbalance of tail representation. The local and global structures are fused to form the node representation under the combined effect of neighborhood and sequence information, which enriches the semantics of tail data. We validate the performance of Graffin on four real-world datasets in node classification tasks. Results show that Graffin can improve the adaptation to tail data without significantly degrading the overall model performance.
Graph representation learning has shown superior performance in numerous real-world applications, such as finance and social networks. Nevertheless, most existing works might make discriminatory predictions due to insufficient attention to fairness in their decision-making processes. This oversight has prompted a growing focus on fair representation learning. Among recent explorations on fair representation learning, prior works based on adversarial learning usually induce unstable or counterproductive performance. To achieve fairness in a stable manner, we present the design and implementation of GRAFair, a new framework based on a variational graph auto-encoder. The crux of GRAFair is the Conditional Fairness Bottleneck, where the objective is to capture the trade-off between the utility of representations and sensitive information of interest. By applying variational approximation, we can make the optimization objective tractable. Particularly, GRAFair can be trained to produce informative representations of tasks while containing little sensitive information without adversarial training. Experiments on various real-world datasets demonstrate the effectiveness of our proposed method in terms of fairness, utility, robustness, and stability.
A second-order-based latent factor (SLF) analysis model demonstrates superior performance in graph representation learning, particularly for high-dimensional and incomplete (HDI) interaction data, by incorporating the curvature information of the loss landscape. However, its objective function is commonly bi-linear and non-convex, causing the SLF model to suffer from a low convergence rate. To address this issue, this paper proposes a PID controller-incorporated SLF (PSLF) model, leveraging two key strategies: a) refining learning error estimation by incorporating the PID controller principles, and b) acquiring second-order information insights through Hessian-vector products. Experimental results on multiple HDI datasets indicate that the proposed PSLF model outperforms four state-of-the-art latent factor models based on advanced optimizers regarding convergence rates and generalization performance.
Unsupervised heterogeneous graph representation learning (UHGRL) has gained increasing attention due to its significance in handling practical graphs without labels. However, heterophily has been largely ignored, despite its ubiquitous presence in real-world heterogeneous graphs. In this paper, we define semantic heterophily and propose an innovative framework called Latent Graphs Guided Unsupervised Representation Learning (LatGRL) to handle this problem. First, we develop a similarity mining method that couples global structures and attributes, enabling the construction of fine-grained homophilic and heterophilic latent graphs to guide the representation learning. Moreover, we propose an adaptive dual-frequency semantic fusion mechanism to address the problem of node-level semantic heterophily. To cope with the massive scale of real-world data, we further design a scalable implementation. Extensive experiments on benchmark datasets validate the effectiveness and efficiency of our proposed framework. The source code and datasets have been made available at https://github.com/zxlearningdeep/LatGRL.
Heterogeneous Graph Neural Networks (HGNNs) have expanded graph representation learning to heterogeneous graph fields. Recent studies have demonstrated their superior performance across various applications, including medical analysis and recommendation systems, often surpassing existing methods. However, GPUs often experience inefficiencies when executing HGNNs due to their unique and complex execution patterns. Compared to traditional Graph Neural Networks, these patterns further exacerbate irregularities in memory access. To tackle these challenges, recent studies have focused on developing domain-specific accelerators for HGNNs. Nonetheless, most of these efforts have concentrated on optimizing the datapath or scheduling data accesses, while largely overlooking the potential benefits that could be gained from leveraging the inherent properties of the semantic graph, such as its topology, layout, and generation. In this work, we focus on leveraging the properties of semantic graphs to enhance HGNN performance. First, we analyze the Semantic Graph Build (SGB) stage and identify significant opportunities for data reuse during semantic graph generation. Next, we uncover the phenomenon of buffer thrashing during the Graph Feature Processing (GFP) stage, revealing potential optimization opportunities in semantic graph layout. Furthermore, we propose a lightweight hardware accelerator frontend for HGNNs, called SiHGNN. This accelerator frontend incorporates a tree-based Semantic Graph Builder for efficient semantic graph generation and features a novel Graph Restructurer for optimizing semantic graph layouts. Experimental results show that SiHGNN enables the state-of-the-art HGNN accelerator to achieve an average performance improvement of 2.95$\times$.
We propose a class of trainable deep learning-based geometries called Neural Spacetimes (NSTs), which can universally represent nodes in weighted directed acyclic graphs (DAGs) as events in a spacetime manifold. While most works in the literature focus on undirected graph representation learning or causality embedding separately, our differentiable geometry can encode both graph edge weights in its spatial dimensions and causality in the form of edge directionality in its temporal dimensions. We use a product manifold that combines a quasi-metric (for space) and a partial order (for time). NSTs are implemented as three neural networks trained in an end-to-end manner: an embedding network, which learns to optimize the location of nodes as events in the spacetime manifold, and two other networks that optimize the space and time geometries in parallel, which we call a neural (quasi-)metric and a neural partial order, respectively. The latter two networks leverage recent ideas at the intersection of fractal geometry and deep learning to shape the geometry of the representation space in a data-driven fashion, unlike other works in the literature that use fixed spacetime manifolds such as Minkowski space or De Sitter space to embed DAGs. Our main theoretical guarantee is a universal embedding theorem, showing that any $k$-point DAG can be embedded into an NST with $1+\mathcal{O}(\log(k))$ distortion while exactly preserving its causal structure. The total number of parameters defining the NST is sub-cubic in $k$ and linear in the width of the DAG. If the DAG has a planar Hasse diagram, this is improved to $\mathcal{O}(\log(k)) + 2)$ spatial and 2 temporal dimensions. We validate our framework computationally with synthetic weighted DAGs and real-world network embeddings; in both cases, the NSTs achieve lower embedding distortions than their counterparts using fixed spacetime geometries.
Recently, generative graph models have shown promising results in learning graph representations through self-supervised methods. However, most existing generative graph representation learning (GRL) approaches rely on random masking across the entire graph, which overlooks the entanglement of learned representations. This oversight results in non-robustness and a lack of explainability. Furthermore, disentangling the learned representations remains a significant challenge and has not been sufficiently explored in GRL research. Based on these insights, this paper introduces DiGGR (Disentangled Generative Graph Representation Learning), a self-supervised learning framework. DiGGR aims to learn latent disentangled factors and utilizes them to guide graph mask modeling, thereby enhancing the disentanglement of learned representations and enabling end-to-end joint learning. Extensive experiments on 11 public datasets for two different graph learning tasks demonstrate that DiGGR consistently outperforms many previous self-supervised methods, verifying the effectiveness of the proposed approach.
Invariant graph representation learning aims to learn the invariance among data from different environments for out-of-distribution generalization on graphs. As the graph environment partitions are usually expensive to obtain, augmenting the environment information has become the de facto approach. However, the usefulness of the augmented environment information has never been verified. In this work, we find that it is fundamentally impossible to learn invariant graph representations via environment augmentation without additional assumptions. Therefore, we develop a set of minimal assumptions, including variation sufficiency and variation consistency, for feasible invariant graph learning. We then propose a new framework Graph invAriant Learning Assistant (GALA). GALA incorporates an assistant model that needs to be sensitive to graph environment changes or distribution shifts. The correctness of the proxy predictions by the assistant model hence can differentiate the variations in spurious subgraphs. We show that extracting the maximally invariant subgraph to the proxy predictions provably identifies the underlying invariant subgraph for successful OOD generalization under the established minimal assumptions. Extensive experiments on datasets including DrugOOD with various graph distribution shifts confirm the effectiveness of GALA.
Graph Neural Networks (GNNs) have become essential tools for graph representation learning in various domains, such as social media and healthcare. However, they often suffer from fairness issues due to inherent biases in node attributes and graph structure, leading to unfair predictions. To address these challenges, we propose a novel GNN framework, DAB-GNN, that Disentangles, Amplifies, and deBiases attribute, structure, and potential biases in the GNN mechanism. DAB-GNN employs a disentanglement and amplification module that isolates and amplifies each type of bias through specialized disentanglers, followed by a debiasing module that minimizes the distance between subgroup distributions. Extensive experiments on five datasets demonstrate that DAB-GNN significantly outperforms ten state-of-the-art competitors in terms of achieving an optimal balance between accuracy and fairness. The codebase of DAB-GNN is available at https://github.com/Bigdasgit/DAB-GNN
Passenger behavior prediction aims to track passenger travel patterns through historical boarding and alighting data, enabling the analysis of urban station passenger flow and timely risk management. This is crucial for smart city development and public transportation planning. Existing research primarily relies on statistical methods and sequential models to learn from individual historical interactions, which ignores the correlations between passengers and stations. To address these issues, this paper proposes DyGPP, which leverages dynamic graphs to capture the intricate evolution of passenger behavior. First, we formalize passengers and stations as heterogeneous vertices in a dynamic graph, with connections between vertices representing interactions between passengers and stations. Then, we sample the historical interaction sequences for passengers and stations separately. We capture the temporal patterns from individual sequences and correlate the temporal behavior between the two sequences. Finally, we use an MLP-based encoder to learn the temporal patterns in the interactions and generate real-time representations of passengers and stations. Experiments on real-world datasets confirmed that DyGPP outperformed current models in the behavior prediction task, demonstrating the superiority of our model.