Binary code similarity detection is an important problem with applications in areas such as malware analysis, vulnerability research and license violation detection. This paper proposes a novel graph neural network architecture combined with a novel graph data representation called call graphlets. A call graphlet encodes the neighborhood around each function in a binary executable, capturing the local and global context through a series of statistical features. A specialized graph neural network model operates on this graph representation, learning to map it to a feature vector that encodes semantic binary code similarities using deep-metric learning. The proposed approach is evaluated across five distinct datasets covering different architectures, compiler tool chains, and optimization levels. Experimental results show that the combination of call graphlets and the novel graph neural network architecture achieves comparable or state-of-the-art performance compared to baseline techniques across cross-architecture, mono-architecture and zero shot tasks. In addition, our proposed approach also performs well when evaluated against an out-of-domain function inlining task. The work provides a general and effective graph neural network-based solution for conducting binary code similarity detection.
Message-passing graph neural networks (GNNs) excel at capturing local relationships but struggle with long-range dependencies in graphs. In contrast, graph transformers (GTs) enable global information exchange but often oversimplify the graph structure by representing graphs as sets of fixed-length vectors. This work introduces a novel architecture that overcomes the shortcomings of both approaches by combining the long-range information of random walks with local message passing. By treating random walks as sequences, our architecture leverages recent advances in sequence models to effectively capture long-range dependencies within these walks. Based on this concept, we propose a framework that offers (1) more expressive graph representations through random walk sequences, (2) the ability to utilize any sequence model for capturing long-range dependencies, and (3) the flexibility by integrating various GNN and GT architectures. Our experimental evaluations demonstrate that our approach achieves significant performance improvements on 19 graph and node benchmark datasets, notably outperforming existing methods by up to 13\% on the PascalVoc-SP and COCO-SP datasets. The code is available at https://github.com/BorgwardtLab/NeuralWalker.
Predicting genetic mutations from whole slide images is indispensable for cancer diagnosis. However, existing work training multiple binary classification models faces two challenges: (a) Training multiple binary classifiers is inefficient and would inevitably lead to a class imbalance problem. (b) The biological relationships among genes are overlooked, which limits the prediction performance. To tackle these challenges, we innovatively design a Biological-knowledge enhanced PathGenomic multi-label Transformer to improve genetic mutation prediction performances. BPGT first establishes a novel gene encoder that constructs gene priors by two carefully designed modules: (a) A gene graph whose node features are the genes' linguistic descriptions and the cancer phenotype, with edges modeled by genes' pathway associations and mutation consistencies. (b) A knowledge association module that fuses linguistic and biomedical knowledge into gene priors by transformer-based graph representation learning, capturing the intrinsic relationships between different genes' mutations. BPGT then designs a label decoder that finally performs genetic mutation prediction by two tailored modules: (a) A modality fusion module that firstly fuses the gene priors with critical regions in WSIs and obtains gene-wise mutation logits. (b) A comparative multi-label loss that emphasizes the inherent comparisons among mutation status to enhance the discrimination capabilities. Sufficient experiments on The Cancer Genome Atlas benchmark demonstrate that BPGT outperforms the state-of-the-art.
The Transformer architecture has recently gained considerable attention in the field of graph representation learning, as it naturally overcomes several limitations of Graph Neural Networks (GNNs) with customized attention mechanisms or positional and structural encodings. Despite making some progress, existing works tend to overlook external information of graphs, specifically the correlation between graphs. Intuitively, graphs with similar structures should have similar representations. Therefore, we propose Graph External Attention (GEA) -- a novel attention mechanism that leverages multiple external node/edge key-value units to capture inter-graph correlations implicitly. On this basis, we design an effective architecture called Graph External Attention Enhanced Transformer (GEAET), which integrates local structure and global interaction information for more comprehensive graph representations. Extensive experiments on benchmark datasets demonstrate that GEAET achieves state-of-the-art empirical performance. The source code is available for reproducibility at: https://github.com/icm1018/GEAET.
Anomaly detection in continuous-time dynamic graphs is an emerging field yet under-explored in the context of learning algorithms. In this paper, we pioneer structured analyses of link-level anomalies and graph representation learning for identifying categorically anomalous graph links. First, we introduce a fine-grained taxonomy for edge-level anomalies leveraging structural, temporal, and contextual graph properties. Based on these properties, we introduce a method for generating and injecting typed anomalies into graphs. Next, we introduce a novel method to generate continuous-time dynamic graphs featuring consistencies across either or combinations of time, structure, and context. To enable temporal graph learning methods to detect specific types of anomalous links rather than the bare existence of a link, we extend the generic link prediction setting by: (1) conditioning link existence on contextual edge attributes; and (2) refining the training regime to accommodate diverse perturbations in the negative edge sampler. Comprehensive benchmarks on synthetic and real-world datasets -- featuring synthetic and labeled organic anomalies and employing six state-of-the-art link prediction methods -- validate our taxonomy and generation processes for anomalies and benign graphs, as well as our approach to adapting methods for anomaly detection. Our results reveal that different learning methods excel in capturing different aspects of graph normality and detecting different types of anomalies. We conclude with a comprehensive list of findings highlighting opportunities for future research.
Computation graphs are Directed Acyclic Graphs (DAGs) where the nodes correspond to mathematical operations and are used widely as abstractions in optimizations of neural networks. The device placement problem aims to identify optimal allocations of those nodes to a set of (potentially heterogeneous) devices. Existing approaches rely on two types of architectures known as grouper-placer and encoder-placer, respectively. In this work, we bridge the gap between encoder-placer and grouper-placer techniques and propose a novel framework for the task of device placement, relying on smaller computation graphs extracted from the OpenVINO toolkit. The framework consists of five steps, including graph coarsening, node representation learning and policy optimization. It facilitates end-to-end training and takes into account the DAG nature of the computation graphs. We also propose a model variant, inspired by graph parsing networks and complex network analysis, enabling graph representation learning and jointed, personalized graph partitioning, using an unspecified number of groups. To train the entire framework, we use reinforcement learning using the execution time of the placement as a reward. We demonstrate the flexibility and effectiveness of our approach through multiple experiments with three benchmark models, namely Inception-V3, ResNet, and BERT. The robustness of the proposed framework is also highlighted through an ablation study. The suggested placements improve the inference speed for the benchmark models by up to 58.2% over CPU execution and by up to 60.24% compared to other commonly used baselines.
Large-scale graphs are valuable for graph representation learning, yet the abundant data in these graphs hinders the efficiency of the training process. Graph condensation (GC) alleviates this issue by compressing the large graph into a significantly smaller one that still supports effective model training. Although recent research has introduced various approaches to improve the effectiveness of the condensed graph, comprehensive and practical evaluations across different GC methods are neglected. This paper proposes the first large-scale graph condensation benchmark, GCondenser, to holistically evaluate and compare mainstream GC methods. GCondenser includes a standardised GC paradigm, consisting of condensation, validation, and evaluation procedures, as well as enabling extensions to new GC methods and datasets. With GCondenser, a comprehensive performance study is conducted, presenting the effectiveness of existing methods. GCondenser is open-sourced and available at https://github.com/superallen13/GCondenser.
Graph neural networks (GNNs) have achieved state-of-the-art performance in graph representation learning. Message passing neural networks, which learn representations through recursively aggregating information from each node and its neighbors, are among the most commonly-used GNNs. However, a wealth of structural information of individual nodes and full graphs is often ignored in such process, which restricts the expressive power of GNNs. Various graph data augmentation methods that enable the message passing with richer structure knowledge have been introduced as one main way to tackle this issue, but they are often focused on individual structure features and difficult to scale up with more structure features. In this work we propose a novel approach, namely collective structure knowledge-augmented graph neural network (CoS-GNN), in which a new message passing method is introduced to allow GNNs to harness a diverse set of node- and graph-level structure features, together with original node features/attributes, in augmented graphs. In doing so, our approach largely improves the structural knowledge modeling of GNNs in both node and graph levels, resulting in substantially improved graph representations. This is justified by extensive empirical results where CoS-GNN outperforms state-of-the-art models in various graph-level learning tasks, including graph classification, anomaly detection, and out-of-distribution generalization.
Group fairness for Graph Neural Networks (GNNs), which emphasizes algorithmic decisions neither favoring nor harming certain groups defined by sensitive attributes (e.g., race and gender), has gained considerable attention. In particular, the objective of group fairness is to ensure that the decisions made by GNNs are independent of the sensitive attribute. To achieve this objective, most existing approaches involve eliminating sensitive attribute information in node representations or algorithmic decisions. However, such ways may also eliminate task-related information due to its inherent correlation with the sensitive attribute, leading to a sacrifice in utility. In this work, we focus on improving the fairness of GNNs while preserving task-related information and propose a fair GNN framework named FairSAD. Instead of eliminating sensitive attribute information, FairSAD enhances the fairness of GNNs via Sensitive Attribute Disentanglement (SAD), which separates the sensitive attribute-related information into an independent component to mitigate its impact. Additionally, FairSAD utilizes a channel masking mechanism to adaptively identify the sensitive attribute-related component and subsequently decorrelates it. Overall, FairSAD minimizes the impact of the sensitive attribute on GNN outcomes rather than eliminating sensitive attributes, thereby preserving task-related information associated with the sensitive attribute. Furthermore, experiments conducted on several real-world datasets demonstrate that FairSAD outperforms other state-of-the-art methods by a significant margin in terms of both fairness and utility performance. Our source code is available at https://github.com/ZzoomD/FairSAD.
While a number of knowledge graph representation learning (KGRL) methods have been proposed over the past decade, very few theoretical analyses have been conducted on them. In this paper, we present the first PAC-Bayesian generalization bounds for KGRL methods. To analyze a broad class of KGRL models, we propose a generic framework named ReED (Relation-aware Encoder-Decoder), which consists of a relation-aware message passing encoder and a triplet classification decoder. Our ReED framework can express at least 15 different existing KGRL models, including not only graph neural network-based models such as R-GCN and CompGCN but also shallow-architecture models such as RotatE and ANALOGY. Our generalization bounds for the ReED framework provide theoretical grounds for the commonly used tricks in KGRL, e.g., parameter-sharing and weight normalization schemes, and guide desirable design choices for practical KGRL methods. We empirically show that the critical factors in our generalization bounds can explain actual generalization errors on three real-world knowledge graphs.
One main challenge in imbalanced graph classification is to learn expressive representations of the graphs in under-represented (minority) classes. Existing generic imbalanced learning methods, such as oversampling and imbalanced learning loss functions, can be adopted for enabling graph representation learning models to cope with this challenge. However, these methods often directly operate on the graph representations, ignoring rich discriminative information within the graphs and their interactions. To tackle this issue, we introduce a novel multi-scale oversampling graph neural network (MOSGNN) that learns expressive minority graph representations based on intra- and inter-graph semantics resulting from oversampled graphs at multiple scales - subgraph, graph, and pairwise graphs. It achieves this by jointly optimizing subgraph-level, graph-level, and pairwise-graph learning tasks to learn the discriminative information embedded within and between the minority graphs. Extensive experiments on 16 imbalanced graph datasets show that MOSGNN i) significantly outperforms five state-of-the-art models, and ii) offers a generic framework, in which different advanced imbalanced learning loss functions can be easily plugged in and obtain significantly improved classification performance.
Graph Neural Networks (GNNs) are often used for tasks involving the 3D geometry of a given graph, such as molecular dynamics simulation. While incorporating Euclidean distance into Message Passing Neural Networks (referred to as Vanilla DisGNN) is a straightforward way to learn the geometry, it has been demonstrated that Vanilla DisGNN is geometrically incomplete. In this work, we first construct families of novel and symmetric geometric graphs that Vanilla DisGNN cannot distinguish even when considering all-pair distances, which greatly expands the existing counterexample families. Our counterexamples show the inherent limitation of Vanilla DisGNN to capture symmetric geometric structures. We then propose $k$-DisGNNs, which can effectively exploit the rich geometry contained in the distance matrix. We demonstrate the high expressive power of $k$-DisGNNs from three perspectives: 1. They can learn high-order geometric information that cannot be captured by Vanilla DisGNN. 2. They can unify some existing well-designed geometric models. 3. They are universal function approximators from geometric graphs to scalars (when $k\geq 2$) and vectors (when $k\geq 3$). Most importantly, we establish a connection between geometric deep learning (GDL) and traditional graph representation learning (GRL), showing that those highly expressive GNN models originally designed for GRL can also be applied to GDL with impressive performance, and that existing complicated, equivariant models are not the only solution. Experiments verify our theory. Our $k$-DisGNNs achieve many new state-of-the-art results on MD17.
Modern graph representation learning works mostly under the assumption of dealing with regularly sampled temporal graph snapshots, which is far from realistic, e.g., social networks and physical systems are characterized by continuous dynamics and sporadic observations. To address this limitation, we introduce the Temporal Graph Ordinary Differential Equation (TG-ODE) framework, which learns both the temporal and spatial dynamics from graph streams where the intervals between observations are not regularly spaced. We empirically validate the proposed approach on several graph benchmarks, showing that TG-ODE can achieve state-of-the-art performance in irregular graph stream tasks.
Graph Neural Networks (GNNs) have demonstrated state-of-the-art performance in various graph representation learning tasks. Recently, studies revealed their vulnerability to adversarial attacks. In this work, we theoretically define the concept of expected robustness in the context of attributed graphs and relate it to the classical definition of adversarial robustness in the graph representation learning literature. Our definition allows us to derive an upper bound of the expected robustness of Graph Convolutional Networks (GCNs) and Graph Isomorphism Networks subject to node feature attacks. Building on these findings, we connect the expected robustness of GNNs to the orthonormality of their weight matrices and consequently propose an attack-independent, more robust variant of the GCN, called the Graph Convolutional Orthonormal Robust Networks (GCORNs). We further introduce a probabilistic method to estimate the expected robustness, which allows us to evaluate the effectiveness of GCORN on several real-world datasets. Experimental experiments showed that GCORN outperforms available defense methods. Our code is publicly available at: \href{https://github.com/Sennadir/GCORN}{https://github.com/Sennadir/GCORN}.
We introduce the FRactional-Order graph Neural Dynamical network (FROND), a new continuous graph neural network (GNN) framework. Unlike traditional continuous GNNs that rely on integer-order differential equations, FROND employs the Caputo fractional derivative to leverage the non-local properties of fractional calculus. This approach enables the capture of long-term dependencies in feature updates, moving beyond the Markovian update mechanisms in conventional integer-order models and offering enhanced capabilities in graph representation learning. We offer an interpretation of the node feature updating process in FROND from a non-Markovian random walk perspective when the feature updating is particularly governed by a diffusion process. We demonstrate analytically that oversmoothing can be mitigated in this setting. Experimentally, we validate the FROND framework by comparing the fractional adaptations of various established integer-order continuous GNNs, demonstrating their consistently improved performance and underscoring the framework's potential as an effective extension to enhance traditional continuous GNNs. The code is available at \url{https://github.com/zknus/ICLR2024-FROND}.
Graph Transformers (GTs) have made remarkable achievements in graph-level tasks. However, most existing works regard graph structures as a form of guidance or bias for enhancing node representations, which focuses on node-central perspectives and lacks explicit representations of edges and structures. One natural question arises as to whether we can leverage a hypernode to represent some structures. Through experimental analysis, we explore the feasibility of this assumption. Based on our findings, we propose an efficient Loop and Clique Coarsening algorithm with linear complexity for Graph Classification (LCC4GC) on GT architecture. Specifically, we build three unique views, original, coarsening, and conversion, to learn a thorough structural representation. We compress loops and cliques via hierarchical heuristic graph coarsening and restrict them with well-designed constraints, which builds the coarsening view to learn high-level interactions between structures. We also introduce line graphs for edge embeddings and switch to edge-central perspective to alleviate the impact of coarsening reduction. Experiments on eight real-world datasets demonstrate the improvements of LCC4GC over 31 baselines from various architectures.
We propose a graph-based representation learning framework for video summarization. First, we convert an input video to a graph where nodes correspond to each of the video frames. Then, we impose sparsity on the graph by connecting only those pairs of nodes that are within a specified temporal distance. We then formulate the video summarization task as a binary node classification problem, precisely classifying video frames whether they should belong to the output summary video. A graph constructed this way aims to capture long-range interactions among video frames, and the sparsity ensures the model trains without hitting the memory and compute bottleneck. Experiments on two datasets(SumMe and TVSum) demonstrate the effectiveness of the proposed nimble model compared to existing state-of-the-art summarization approaches while being one order of magnitude more efficient in compute time and memory
We explore the adoption of graph representation learning (GRL) algorithms to investigate similarities across services offered by Decentralized Finance (DeFi) protocols. Following existing literature, we use Ethereum transaction data to identify the DeFi building blocks. These are sets of protocol-specific smart contracts that are utilized in combination within single transactions and encapsulate the logic to conduct specific financial services such as swapping or lending cryptoassets. We propose a method to categorize these blocks into clusters based on their smart contract attributes and the graph structure of their smart contract calls. We employ GRL to create embedding vectors from building blocks and agglomerative models for clustering them. To evaluate whether they are effectively grouped in clusters of similar functionalities, we associate them with eight financial functionality categories and use this information as the target label. We find that in the best-case scenario purity reaches .888. We use additional information to associate the building blocks with protocol-specific target labels, obtaining comparable purity (.864) but higher V-Measure (.571); we discuss plausible explanations for this difference. In summary, this method helps categorize existing financial products offered by DeFi protocols, and can effectively automatize the detection of similar DeFi services, especially within protocols.
Graph representation learning has rapidly emerged as a pivotal field of study. Despite its growing popularity, the majority of research has been confined to embedding single-layer graphs, which fall short in representing complex systems with multifaceted relationships. To bridge this gap, we introduce MPXGAT, an innovative attention-based deep learning model tailored to multiplex graph embedding. Leveraging the robustness of Graph Attention Networks (GATs), MPXGAT captures the structure of multiplex networks by harnessing both intra-layer and inter-layer connections. This exploitation facilitates accurate link prediction within and across the network's multiple layers. Our comprehensive experimental evaluation, conducted on various benchmark datasets, confirms that MPXGAT consistently outperforms state-of-the-art competing algorithms.
Graph Neural Networks (GNNs) have emerged as the most powerful weapon for various graph tasks due to the message-passing mechanism's great local information aggregation ability. However, over-smoothing has always hindered GNNs from going deeper and capturing multi-hop neighbors. Unlike GNNs, Transformers can model global information and multi-hop interactions via multi-head self-attention and a proper Transformer structure can show more immunity to the over-smoothing problem. So, can we propose a novel framework to combine GNN and Transformer, integrating both GNN's local information aggregation and Transformer's global information modeling ability to eliminate the over-smoothing problem? To realize this, this paper proposes a collaborative learning scheme for GNN-Transformer and constructs GTC architecture. GTC leverages the GNN and Transformer branch to encode node information from different views respectively, and establishes contrastive learning tasks based on the encoded cross-view information to realize self-supervised heterogeneous graph representation. For the Transformer branch, we propose Metapath-aware Hop2Token and CG-Hetphormer, which can cooperate with GNN to attentively encode neighborhood information from different levels. As far as we know, this is the first attempt in the field of graph representation learning to utilize both GNN and Transformer to collaboratively capture different view information and conduct cross-view contrastive learning. The experiments on real datasets show that GTC exhibits superior performance compared with state-of-the-art methods. Codes can be available at https://github.com/PHD-lanyu/GTC.