In this paper, we present the Fast Optimizer Benchmark (FOB), a tool designed for evaluating deep learning optimizers during their development. The benchmark supports tasks from multiple domains such as computer vision, natural language processing, and graph learning. The focus is on convenient usage, featuring human-readable YAML configurations, SLURM integration, and plotting utilities. FOB can be used together with existing hyperparameter optimization (HPO) tools as it handles training and resuming of runs. The modular design enables integration into custom pipelines, using it simply as a collection of tasks. We showcase an optimizer comparison as a usage example of our tool. FOB can be found on GitHub: https://github.com/automl/FOB.
In our recent research, we have developed a framework called GraphSnapShot, which has been proven an useful tool for graph learning acceleration. GraphSnapShot is a framework for fast cache, storage, retrieval and computation for graph learning. It can quickly store and update the local topology of graph structure and allows us to track patterns in the structure of graph networks, just like take snapshots of the graphs. In experiments, GraphSnapShot shows efficiency, it can achieve up to 30% training acceleration and 73% memory reduction for lossless graph ML training compared to current baselines such as dgl.This technique is particular useful for large dynamic graph learning tasks such as social media analysis and recommendation systems to process complex relationships between entities. The code for GraphSnapShot is publicly available at https://github.com/NoakLiu/GraphSnapShot.
In recent years, Graph Neural Networks (GNNs) have become the de facto tool for learning node and graph representations. Most GNNs typically consist of a sequence of neighborhood aggregation (a.k.a., message-passing) layers, within which the representation of each node is updated based on those of its neighbors. The most expressive message-passing GNNs can be obtained through the use of the sum aggregator and of MLPs for feature transformation, thanks to their universal approximation capabilities. However, the limitations of MLPs recently motivated the introduction of another family of universal approximators, called Kolmogorov-Arnold Networks (KANs) which rely on a different representation theorem. In this work, we compare the performance of KANs against that of MLPs on graph learning tasks. We evaluate two different implementations of KANs using two distinct base families of functions, namely B-splines and radial basis functions. We perform extensive experiments on node classification, graph classification and graph regression datasets. Our results indicate that KANs are on-par with or better than MLPs on all studied tasks, making them viable alternatives, at the cost of some computational complexity. Code is available at https: //github.com/RomanBresson/KAGNN.
This paper introduces novel methodologies, the Distance Recomputator and Topology Reconstructor, aimed at enhancing Graph Neural Networks (GNNs). The Distance Recomputator dynamically recalibrates node distances within k-hop neighborhoods using a dynamic encoding scheme, thereby improving the accuracy and adaptability of node representations. Concurrently, the Topology Reconstructor adjusts local graph structures based on computed "similarity distances," optimizing network configurations for improved learning outcomes. These methods address the limitations of static node representations and fixed aggregation schemes in traditional GNNs, offering a more nuanced approach to modeling complex and dynamic graph topologies. Furthermore, our experimental evaluations demonstrate significant performance advantages over existing methods across various benchmark datasets. The proposed Distance Recomputator and Topology Reconstructor not only enhance node relationship modeling accuracy but also optimize information aggregation efficiency through an asynchronous aggregation mechanism. This approach proves particularly effective in scenarios involving dynamic or large-scale graphs, showcasing the methods' robustness and applicability in real-world graph learning tasks.
Message-Passing Neural Networks (MPNNs) are extensively employed in graph learning tasks but suffer from limitations such as the restricted scope of information exchange, by being confined to neighboring nodes during each round of message passing. Various strategies have been proposed to address these limitations, including incorporating virtual nodes to facilitate global information exchange. In this study, we introduce the Hierarchical Support Graph (HSG), an extension of the virtual node concept created through recursive coarsening of the original graph. This approach provides a flexible framework for enhancing information flow in graphs, independent of the specific MPNN layers utilized. We present a theoretical analysis of HSGs, investigate their empirical performance, and demonstrate that HSGs can surpass other methods augmented with virtual nodes, achieving state-of-the-art results across multiple datasets.
Graph deep learning (GDL) has demonstrated impressive performance in predicting population-based brain disorders (BDs) through the integration of both imaging and non-imaging data. However, the effectiveness of GDL based methods heavily depends on the quality of modeling the multi-modal population graphs and tends to degrade as the graph scale increases. Furthermore, these methods often constrain interactions between imaging and non-imaging data to node-edge interactions within the graph, overlooking complex inter-modal correlations, leading to suboptimal outcomes. To overcome these challenges, we propose MM-GTUNets, an end-to-end graph transformer based multi-modal graph deep learning (MMGDL) framework designed for brain disorders prediction at large scale. Specifically, to effectively leverage rich multi-modal information related to diseases, we introduce Modality Reward Representation Learning (MRRL) which adaptively constructs population graphs using a reward system. Additionally, we employ variational autoencoder to reconstruct latent representations of non-imaging features aligned with imaging features. Based on this, we propose Adaptive Cross-Modal Graph Learning (ACMGL), which captures critical modality-specific and modality-shared features through a unified GTUNet encoder taking advantages of Graph UNet and Graph Transformer, and feature fusion module. We validated our method on two public multi-modal datasets ABIDE and ADHD-200, demonstrating its superior performance in diagnosing BDs. Our code is available at https://github.com/NZWANG/MM-GTUNets.
This work studies self-supervised graph learning for text-attributed graphs (TAGs) where nodes are represented by textual attributes. Unlike traditional graph contrastive methods that perturb the numerical feature space and alter the graph's topological structure, we aim to improve view generation through language supervision. This is driven by the prevalence of textual attributes in real applications, which complement graph structures with rich semantic information. However, this presents challenges because of two major reasons. First, text attributes often vary in length and quality, making it difficulty to perturb raw text descriptions without altering their original semantic meanings. Second, although text attributes complement graph structures, they are not inherently well-aligned. To bridge the gap, we introduce GAugLLM, a novel framework for augmenting TAGs. It leverages advanced large language models like Mistral to enhance self-supervised graph learning. Specifically, we introduce a mixture-of-prompt-expert technique to generate augmented node features. This approach adaptively maps multiple prompt experts, each of which modifies raw text attributes using prompt engineering, into numerical feature space. Additionally, we devise a collaborative edge modifier to leverage structural and textual commonalities, enhancing edge augmentation by examining or building connections between nodes. Empirical results across five benchmark datasets spanning various domains underscore our framework's ability to enhance the performance of leading contrastive methods as a plug-in tool. Notably, we observe that the augmented features and graph structure can also enhance the performance of standard generative methods, as well as popular graph neural networks. The open-sourced implementation of our GAugLLM is available at Github.
Dynamic text-attributed graphs (DyTAGs) are prevalent in various real-world scenarios, where each node and edge are associated with text descriptions, and both the graph structure and text descriptions evolve over time. Despite their broad applicability, there is a notable scarcity of benchmark datasets tailored to DyTAGs, which hinders the potential advancement in many research fields. To address this gap, we introduce Dynamic Text-attributed Graph Benchmark (DTGB), a collection of large-scale, time-evolving graphs from diverse domains, with nodes and edges enriched by dynamically changing text attributes and categories. To facilitate the use of DTGB, we design standardized evaluation procedures based on four real-world use cases: future link prediction, destination node retrieval, edge classification, and textual relation generation. These tasks require models to understand both dynamic graph structures and natural language, highlighting the unique challenges posed by DyTAGs. Moreover, we conduct extensive benchmark experiments on DTGB, evaluating 7 popular dynamic graph learning algorithms and their variants of adapting to text attributes with LLM embeddings, along with 6 powerful large language models (LLMs). Our results show the limitations of existing models in handling DyTAGs. Our analysis also demonstrates the utility of DTGB in investigating the incorporation of structural and textual dynamics. The proposed DTGB fosters research on DyTAGs and their broad applications. It offers a comprehensive benchmark for evaluating and advancing models to handle the interplay between dynamic graph structures and natural language. The dataset and source code are available at https://github.com/zjs123/DTGB.
Federated Graph Learning (FGL) has emerged as a promising way to learn high-quality representations from distributed graph data with privacy preservation. Despite considerable efforts have been made for FGL under either cross-device or cross-silo paradigm, how to effectively capture graph knowledge in a more complicated cross-silo cross-device environment remains an under-explored problem. However, this task is challenging because of the inherent hierarchy and heterogeneity of decentralized clients, diversified privacy constraints in different clients, and the cross-client graph integrity requirement. To this end, in this paper, we propose a Hierarchical Federated Graph Learning (HiFGL) framework for cross-silo cross-device FGL. Specifically, we devise a unified hierarchical architecture to safeguard federated GNN training on heterogeneous clients while ensuring graph integrity. Moreover, we propose a Secret Message Passing (SecMP) scheme to shield unauthorized access to subgraph-level and node-level sensitive information simultaneously. Theoretical analysis proves that HiFGL achieves multi-level privacy preservation with complexity guarantees. Extensive experiments on real-world datasets validate the superiority of the proposed framework against several baselines. Furthermore, HiFGL's versatile nature allows for its application in either solely cross-silo or cross-device settings, further broadening its utility in real-world FGL applications.
The field of temporal graph learning aims to learn from evolving network data to forecast future interactions. Given a collection of observed temporal graphs, is it possible to predict the evolution of an unseen network from the same domain? To answer this question, we first present the Temporal Graph Scaling (TGS) dataset, a large collection of temporal graphs consisting of eighty-four ERC20 token transaction networks collected from 2017 to 2023. Next, we evaluate the transferability of Temporal Graph Neural Networks (TGNNs) for the temporal graph property prediction task by pre-training on a collection of up to sixty-four token transaction networks and then evaluating the downstream performance on twenty unseen token networks. We find that the neural scaling law observed in NLP and Computer Vision also applies in temporal graph learning, where pre-training on greater number of networks leads to improved downstream performance. To the best of our knowledge, this is the first empirical demonstration of the transferability of temporal graphs learning. On downstream token networks, the largest pre-trained model outperforms single model TGNNs on thirteen unseen test networks. Therefore, we believe that this is a promising first step towards building foundation models for temporal graphs.
Deep graph learning has gained grand popularity over the past years due to its versatility and success in representing graph data across a wide range of domains. However, the pervasive issue of imbalanced graph data distributions, where certain parts exhibit disproportionally abundant data while others remain sparse, undermines the efficacy of conventional graph learning algorithms, leading to biased outcomes. To address this challenge, Imbalanced Graph Learning (IGL) has garnered substantial attention, enabling more balanced data distributions and better task performance. Despite the proliferation of IGL algorithms, the absence of consistent experimental protocols and fair performance comparisons pose a significant barrier to comprehending advancements in this field. To bridge this gap, we introduce IGL-Bench, a foundational comprehensive benchmark for imbalanced graph learning, embarking on 16 diverse graph datasets and 24 distinct IGL algorithms with uniform data processing and splitting strategies. Specifically, IGL-Bench systematically investigates state-of-the-art IGL algorithms in terms of effectiveness, robustness, and efficiency on node-level and graph-level tasks, with the scope of class-imbalance and topology-imbalance. Extensive experiments demonstrate the potential benefits of IGL algorithms on various imbalanced conditions, offering insights and opportunities in the IGL field. Further, we have developed an open-sourced and unified package to facilitate reproducible evaluation and inspire further innovative research, which is available at https://github.com/RingBDStack/IGL-Bench.
To make accurate predictions, understand mechanisms, and design interventions in systems of many variables, we wish to learn causal graphs from large scale data. Unfortunately the space of all possible causal graphs is enormous so scalably and accurately searching for the best fit to the data is a challenge. In principle we could substantially decrease the search space, or learn the graph entirely, by testing the conditional independence of variables. However, deciding if two variables are adjacent in a causal graph may require an exponential number of tests. Here we build a scalable and flexible method to evaluate if two variables are adjacent in a causal graph, the Differentiable Adjacency Test (DAT). DAT replaces an exponential number of tests with a provably equivalent relaxed problem. It then solves this problem by training two neural networks. We build a graph learning method based on DAT, DAT-Graph, that can also learn from data with interventions. DAT-Graph can learn graphs of 1000 variables with state of the art accuracy. Using the graph learned by DAT-Graph, we also build models that make much more accurate predictions of the effects of interventions on large scale RNA sequencing data.
Link prediction is a fundamental task in graph learning, inherently shaped by the topology of the graph. While traditional heuristics are grounded in graph topology, they encounter challenges in generalizing across diverse graphs. Recent research efforts have aimed to leverage the potential of heuristics, yet a unified formulation accommodating both local and global heuristics remains undiscovered. Drawing insights from the fact that both local and global heuristics can be represented by adjacency matrix multiplications, we propose a unified matrix formulation to accommodate and generalize various heuristics. We further propose the Heuristic Learning Graph Neural Network (HL-GNN) to efficiently implement the formulation. HL-GNN adopts intra-layer propagation and inter-layer connections, allowing it to reach a depth of around 20 layers with lower time complexity than GCN. Extensive experiments on the Planetoid, Amazon, and OGB datasets underscore the effectiveness and efficiency of HL-GNN. It outperforms existing methods by a large margin in prediction performance. Additionally, HL-GNN is several orders of magnitude faster than heuristic-inspired methods while requiring only a few trainable parameters. The case study further demonstrates that the generalized heuristics and learned weights are highly interpretable.
Graph signal processing represents an important advancement in the field of data analysis, extending conventional signal processing methodologies to complex networks and thereby facilitating the exploration of informative patterns and structures across various domains. However, acquiring the underlying graphs for specific applications remains a challenging task. While graph inference based on smooth graph signal representation has become one of the state-of-the-art methods, these approaches usually overlook the unique properties of networks, which are generally derived from domain-specific knowledge. Overlooking this information could make the approaches less interpretable and less effective overall. In this study, we propose a new graph inference method that leverages available domain knowledge. The proposed methodology is evaluated on the task of denoising and imputing missing sensor data, utilizing graph signal reconstruction techniques. The results demonstrate that incorporating domain knowledge into the graph inference process can improve graph signal reconstruction in district heating networks. Our code is available at \href{https://github.com/Keiv4n/IGL}{github.com/Keiv4n/IGL}.
Previous graph-based approaches in Aspect based Sentiment Analysis(ABSA) have demonstrated impressive performance by utilizing graph neural networks and attention mechanisms to learn structures of static dependency trees and dynamic latent trees. However, incorporating both semantic and syntactic information simultaneously within complex global structures can introduce irrelevant contexts and syntactic dependencies during the process of graph structure learning, potentially resulting in inaccurate predictions. In order to address the issues above, we propose S$^2$GSL, incorporating Segment to Syntactic enhanced Graph Structure Learning for ABSA. Specifically,S$^2$GSL is featured with a segment-aware semantic graph learning and a syntax-based latent graph learning enabling the removal of irrelevant contexts and dependencies, respectively. We further propose a self-adaptive aggregation network that facilitates the fusion of two graph learning branches, thereby achieving complementarity across diverse structures. Experimental results on four benchmarks demonstrate the effectiveness of our framework.
In recent years, graph neural networks (GNNs) have become increasingly popular for solving NP-hard combinatorial optimization (CO) problems, such as maximum cut and maximum independent set. The core idea behind these methods is to represent a CO problem as a graph and then use GNNs to learn the node/graph embedding with combinatorial information. Although these methods have achieved promising results, given a specific CO problem, the design of GNN architectures still requires heavy manual work with domain knowledge. Existing automated GNNs are mostly focused on traditional graph learning problems, which is inapplicable to solving NP-hard CO problems. To this end, we present a new class of \textbf{AUTO}mated \textbf{G}NNs for solving \textbf{NP}-hard problems, namely \textbf{AutoGNP}. We represent CO problems by GNNs and focus on two specific problems, i.e., mixed integer linear programming and quadratic unconstrained binary optimization. The idea of AutoGNP is to use graph neural architecture search algorithms to automatically find the best GNNs for a given NP-hard combinatorial optimization problem. Compared with existing graph neural architecture search algorithms, AutoGNP utilizes two-hop operators in the architecture search space. Moreover, AutoGNP utilizes simulated annealing and a strict early stopping policy to avoid local optimal solutions. Empirical results on benchmark combinatorial problems demonstrate the superiority of our proposed model.
In recent years, continual learning (CL) techniques have made significant progress in learning from streaming data while preserving knowledge across sequential tasks, particularly in the realm of euclidean data. To foster fair evaluation and recognize challenges in CL settings, several evaluation frameworks have been proposed, focusing mainly on the single- and multi-label classification task on euclidean data. However, these evaluation frameworks are not trivially applicable when the input data is graph-structured, as they do not consider the topological structure inherent in graphs. Existing continual graph learning (CGL) evaluation frameworks have predominantly focussed on single-label scenarios in the node classification (NC) task. This focus has overlooked the complexities of multi-label scenarios, where nodes may exhibit affiliations with multiple labels, simultaneously participating in multiple tasks. We develop a graph-aware evaluation (\agale) framework that accommodates both single-labeled and multi-labeled nodes, addressing the limitations of previous evaluation frameworks. In particular, we define new incremental settings and devise data partitioning algorithms tailored to CGL datasets. We perform extensive experiments comparing methods from the domains of continual learning, continual graph learning, and dynamic graph learning (DGL). We theoretically analyze \agale and provide new insights about the role of homophily in the performance of compared methods. We release our framework at https://github.com/Tianqi-py/AGALE.
Over the past few years, research on deep graph learning has shifted from static graphs to temporal graphs in response to real-world complex systems that exhibit dynamic behaviors. In practice, temporal graphs are formalized as an ordered sequence of static graph snapshots observed at discrete time points. Sequence models such as RNNs or Transformers have long been the predominant backbone networks for modeling such temporal graphs. Yet, despite the promising results, RNNs struggle with long-range dependencies, while transformers are burdened by quadratic computational complexity. Recently, state space models (SSMs), which are framed as discretized representations of an underlying continuous-time linear dynamical system, have garnered substantial attention and achieved breakthrough advancements in independent sequence modeling. In this work, we undertake a principled investigation that extends SSM theory to temporal graphs by integrating structural information into the online approximation objective via the adoption of a Laplacian regularization term. The emergent continuous-time system introduces novel algorithmic challenges, thereby necessitating our development of GraphSSM, a graph state space model for modeling the dynamics of temporal graphs. Extensive experimental results demonstrate the effectiveness of our GraphSSM framework across various temporal graph benchmarks.
Dynamic graph learning equips the edges with time attributes and allows multiple links between two nodes, which is a crucial technology for understanding evolving data scenarios like traffic prediction and recommendation systems. Existing works obtain the evolving patterns mainly depending on the most recent neighbor sequences. However, we argue that whether two nodes will have interaction with each other in the future is highly correlated with the same interaction that happened in the past. Only considering the recent neighbors overlooks the phenomenon of repeat behavior and fails to accurately capture the temporal evolution of interactions. To fill this gap, this paper presents RepeatMixer, which considers evolving patterns of first and high-order repeat behavior in the neighbor sampling strategy and temporal information learning. Firstly, we define the first-order repeat-aware nodes of the source node as the destination nodes that have interacted historically and extend this concept to high orders as nodes in the destination node's high-order neighbors. Then, we extract neighbors of the source node that interacted before the appearance of repeat-aware nodes with a slide window strategy as its neighbor sequence. Next, we leverage both the first and high-order neighbor sequences of source and destination nodes to learn temporal patterns of interactions via an MLP-based encoder. Furthermore, considering the varying temporal patterns on different orders, we introduce a time-aware aggregation mechanism that adaptively aggregates the temporal representations from different orders based on the significance of their interaction time sequences. Experimental results demonstrate the superiority of RepeatMixer over state-of-the-art models in link prediction tasks, underscoring the effectiveness of the proposed repeat-aware neighbor sampling strategy.
Message Passing Neural Networks (MPNNs) are a staple of graph machine learning. MPNNs iteratively update each node's representation in an input graph by aggregating messages from the node's neighbors, which necessitates a memory complexity of the order of the number of graph edges. This complexity might quickly become prohibitive for large graphs provided they are not very sparse. In this paper, we propose a novel approach to alleviate this problem by approximating the input graph as an intersecting community graph (ICG) -- a combination of intersecting cliques. The key insight is that the number of communities required to approximate a graph does not depend on the graph size. We develop a new constructive version of the Weak Graph Regularity Lemma to efficiently construct an approximating ICG for any input graph. We then devise an efficient graph learning algorithm operating directly on ICG in linear memory and time with respect to the number of nodes (rather than edges). This offers a new and fundamentally different pipeline for learning on very large non-sparse graphs, whose applicability is demonstrated empirically on node classification tasks and spatio-temporal data processing.