arXiv subjects

Guoren Wang

Publications and source records attributed to Guoren Wang.

At least 73 records · Page 4Linked to original sources

arXiv2025

Handling Label Noise via Instance-Level Difficulty Modeling and Dynamic Optimization

Recent studies indicate that deep neural networks degrade in generalization performance under noisy supervision. Existing methods focus on isolating clean subsets or correcting noisy labels, facing limitations such as high computational costs, heavy hyperparameter tuning process, and coarse-grained optimization. To address these challenges, we propose a novel two-stage noisy learning framework that enables instance-level optimization through a dynamically weighted loss function, avoiding hyperparameter tuning. To obtain stable and accurate information about noise modeling, we introduce a simple yet effective metric, termed wrong event, which dynamically models the cleanliness and difficulty of individual samples while maintaining computational costs. Our framework first collects wrong event information and builds a strong base model. Then we perform noise-robust training on the base model, using a probabilistic model to handle the wrong event information of samples. Experiments on five synthetic and real-world LNL benchmarks demonstrate our method surpasses state-of-the-art methods in performance, achieves a nearly 75% reduction in computational time and improves model scalability.

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arXiv2025

Unveiling the Vulnerability of Graph-LLMs: An Interpretable Multi-Dimensional Adversarial Attack on TAGs

Graph Neural Networks (GNNs) have become a pivotal framework for modeling graph-structured data, enabling a wide range of applications from social network analysis to molecular chemistry. By integrating large language models (LLMs), text-attributed graphs (TAGs) enhance node representations with rich textual semantics, significantly boosting the expressive power of graph-based learning. However, this sophisticated synergy introduces critical vulnerabilities, as Graph-LLMs are susceptible to adversarial attacks on both their structural topology and textual attributes. Although specialized attack methods have been designed for each of these aspects, no work has yet unified them into a comprehensive approach. In this work, we propose the Interpretable Multi-Dimensional Graph Attack (IMDGA), a novel human-centric adversarial attack framework designed to orchestrate multi-level perturbations across both graph structure and textual features. IMDGA utilizes three tightly integrated modules to craft attacks that balance interpretability and impact, enabling a deeper understanding of Graph-LLM vulnerabilities. Through rigorous theoretical analysis and comprehensive empirical evaluations on diverse datasets and architectures, IMDGA demonstrates superior interpretability, attack effectiveness, stealthiness, and robustness compared to existing methods. By exposing critical weaknesses in TAG representation learning, this work uncovers a previously underexplored semantic dimension of vulnerability in Graph-LLMs, offering valuable insights for improving their resilience. Our code and resources are publicly available at https://anonymous.4open.science/r/IMDGA-7289.

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arXiv2025

MagicDock: Toward Docking-oriented De Novo Ligand Design via Gradient Inversion

De novo ligand design is a fundamental task that seeks to generate protein or molecule candidates that can effectively dock with protein receptors and achieve strong binding affinity entirely from scratch. It holds paramount significance for a wide spectrum of biomedical applications. However, most existing studies are constrained by the \textbf{Pseudo De Novo}, \textbf{Limited Docking Modeling}, and \textbf{Inflexible Ligand Type}. To address these issues, we propose MagicDock, a forward-looking framework grounded in the progressive pipeline and differentiable surface modeling. (1) We adopt a well-designed gradient inversion framework. To begin with, general docking knowledge of receptors and ligands is incorporated into the backbone model. Subsequently, the docking knowledge is instantiated as reverse gradient flows by binding prediction, which iteratively guide the de novo generation of ligands. (2) We emphasize differentiable surface modeling in the docking process, leveraging learnable 3D point-cloud representations to precisely capture binding details, thereby ensuring that the generated ligands preserve docking validity through direct and interpretable spatial fingerprints. (3) We introduce customized designs for different ligand types and integrate them into a unified gradient inversion framework with flexible triggers, thereby ensuring broad applicability. Moreover, we provide rigorous theoretical guarantees for each component of MagicDock. Extensive experiments across 9 scenarios demonstrate that MagicDock achieves average improvements of 27.1\% and 11.7\% over SOTA baselines specialized for protein or molecule ligand design, respectively.

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arXiv2025

FedBook: A Unified Federated Graph Foundation Codebook with Intra-domain and Inter-domain Knowledge Modeling

Foundation models have shown remarkable cross-domain generalization in language and vision, inspiring the development of graph foundation models (GFMs). However, existing GFMs typically assume centralized access to multi-domain graphs, which is often infeasible due to privacy and institutional constraints. Federated Graph Foundation Models (FedGFMs) address this limitation, but their effectiveness fundamentally hinges on constructing a robust global codebook that achieves intra-domain coherence by consolidating mutually reinforcing semantics within each domain, while also maintaining inter-domain diversity by retaining heterogeneous knowledge across domains. To this end, we propose FedBook, a unified federated graph foundation codebook that systematically aggregates clients' local codebooks during server-side federated pre-training. FedBook follows a two-phase process: (1) Intra-domain Collaboration, where low-frequency tokens are refined by referencing more semantically reliable high-frequency tokens across clients to enhance domain-specific coherence; and (2) Inter-domain Integration, where client contributions are weighted by the semantic distinctiveness of their codebooks during the aggregation of the global GFM, thereby preserving cross-domain diversity. Extensive experiments on 8 benchmarks across multiple domains and tasks demonstrate that FedBook consistently outperforms 21 baselines, including isolated supervised learning, FL/FGL, federated adaptations of centralized GFMs, and FedGFM techniques.

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arXiv2025

DiRW: Path-Aware Digraph Learning for Heterophily

Recently, graph neural network (GNN) has emerged as a powerful representation learning tool for graph-structured data. However, most approaches are tailored for undirected graphs, neglecting the abundant information in the edges of directed graphs (digraphs). In fact, digraphs are widely applied in the real world and confirmed to address heterophily challenges. Despite recent advancements, existing spatial- and spectral-based DiGNNs have limitations due to their complex learning mechanisms and reliance on high-quality topology, resulting in low efficiency and unstable performance. To address these issues, we propose Directed Random Walk (DiRW), a plug-and-play strategy for most spatial-based DiGNNs and also an innovative model which offers a new digraph learning paradigm. Specifically, it utilizes a direction-aware path sampler optimized from the perspectives of walk probability, length, and number in a weight-free manner by considering node profiles and topologies. Building upon this, DiRW incorporates a node-wise learnable path aggregator for generalized node representations. Extensive experiments on 9 datasets demonstrate that DiRW: (1) enhances most spatial-based methods as a plug-and-play strategy; (2) achieves SOTA performance as a new digraph learning paradigm. The source code and data are available at https://github.com/dhsiuu/DiRW.

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arXiv2025

Two Facets of the Same Optimization Coin: Model Degradation and Representation Collapse in Graph Foundation Models

Inspired by the success of LLMs, GFMs are designed to learn the optimal embedding functions from multi-domain text-attributed graphs for the downstream cross-task generalization capability. Among the diverse architectures, graph VQ-MAE stands out among the increasingly diverse landscape of GFM. This is attributed to its ability to jointly encode topology and textual attributes from multiple domains into discrete embedding spaces with clear semantic boundaries. Despite its potential, domain generalization conflicts cause imperceptible pitfalls. In this paper, we instantiate two of them, and they are just like two sides of the same GFM optimization coin - Side 1 Model Degradation: The encoder and codebook fail to capture the diversity of inputs; Side 2 Representation Collapse: The hidden embedding and codebook vector fail to preserve semantic separability due to constraints from narrow representation subspaces. These two pitfalls (sides) collectively impair the decoder and generate the low-quality reconstructed supervision, causing the GFM optimization dilemma during pre-training (coin). Through empirical investigation, we attribute the above challenges to Information Bottleneck and Regularization Deficit. To address them, we propose MoT - (1) Information Tinker for Two Pitfalls, which utilizes an edge-wise semantic fusion strategy and a mixture-of-codebooks with domain-aware routing to improve information capacity. (2) Regularization Tinker for Optimization Coin, which utilizes two additional regularizations to further improve gradient supervision in our proposed Information Tinker. Notably, as a flexible architecture, MoT adheres to the scaling laws of GFM, offering a controllable model scale. Compared to SOTA baselines, experiments on 22 datasets across 6 domains demonstrate that MoT achieves significant improvements in supervised, few-shot, and zero-shot scenarios.

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arXiv2025

State Space Models over Directed Graphs

Directed graphs are ubiquitous across numerous domains, where the directionality of edges encodes critical causal dependencies. However, existing GNNs and graph Transformers tailored for directed graphs face two major challenges: (1) effectively capturing long-range causal dependencies derived from directed edges; (2) balancing accuracy and training efficiency when processing large-scale graph datasets. In recent years, state space models (SSMs) have achieved substantial progress in causal sequence tasks, and their variants designed for graphs have demonstrated state-of-the-art accuracy while maintaining high efficiency across various graph learning benchmarks. However, existing graph state space models are exclusively designed for undirected graphs, which limits their performance in directed graph learning. To this end, we propose an innovative approach DirEgo2Token which sequentializes directed graphs via k-hop ego graphs. This marks the first systematic extension of state space models to the field of directed graph learning. Building upon this, we develop DirGraphSSM, a novel directed graph neural network architecture that implements state space models on directed graphs via the message-passing mechanism. Experimental results demonstrate that DirGraphSSM achieves state-of-the-art performance on three representative directed graph learning tasks while attaining competitive performance on two additional tasks with 1.5$\times $ to 2$\times $ training speed improvements compared to existing state-of-the-art models.

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arXiv2025

Efficient Exact Resistance Distance Computation on Small-Treewidth Graphs: a Labelling Approach

Resistance distance computation is a fundamental problem in graph analysis, yet existing random walk-based methods are limited to approximate solutions and suffer from poor efficiency on small-treewidth graphs (e.g., road networks). In contrast, shortest-path distance computation achieves remarkable efficiency on such graphs by leveraging cut properties and tree decompositions. Motivated by this disparity, we first analyze the cut property of resistance distance. While a direct generalization proves impractical due to costly matrix operations, we overcome this limitation by integrating tree decompositions, revealing that the resistance distance $r(s,t)$ depends only on labels along the paths from $s$ and $t$ to the root of the decomposition. This insight enables compact labelling structures. Based on this, we propose \treeindex, a novel index method that constructs a resistance distance labelling of size $O(n \cdot h_{\mathcal{G}})$ in $O(n \cdot h_{\mathcal{G}}^2 \cdot d_{\max})$ time, where $h_{\mathcal{G}}$ (tree height) and $d_{\max}$ (maximum degree) behave as small constants in many real-world small-treewidth graphs (e.g., road networks). Our labelling supports exact single-pair queries in $O(h_{\mathcal{G}})$ time and single-source queries in $O(n \cdot h_{\mathcal{G}})$ time. Extensive experiments show that TreeIndex substantially outperforms state-of-the-art approaches. For instance, on the full USA road network, it constructs a $405$ GB labelling in $7$ hours (single-threaded) and answers exact single-pair queries in $10^{-3}$ seconds and single-source queries in $190$ seconds--the first exact method scalable to such large graphs.

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arXiv2025

Graph-Based Feature Augmentation for Predictive Tasks on Relational Datasets

Data has become a foundational asset driving innovation across domains such as finance, healthcare, and e-commerce. In these areas, predictive modeling over relational tables is commonly employed, with increasing emphasis on reducing manual effort through automated machine learning (AutoML) techniques. This raises an interesting question: can feature augmentation itself be automated and identify and utilize task-related relational signals? To address this challenge, we propose an end-to-end automated feature augmentation framework, ReCoGNN, which enhances initial datasets using features extracted from multiple relational tables to support predictive tasks. ReCoGNN first captures semantic dependencies within each table by modeling intra-table attribute relationships, enabling it to partition tables into structured, semantically coherent segments. It then constructs a heterogeneous weighted graph that represents inter-row relationships across all segments. Finally, ReCoGNN leverages message-passing graph neural networks to propagate information through the graph, guiding feature selection and augmenting the original dataset. Extensive experiments conducted on ten real-life and synthetic datasets demonstrate that ReCoGNN consistently outperforms existing methods on both classification and regression tasks.

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arXiv2025

Optimal $(α,β)$-Dense Subgraph Search in Bipartite Graphs

Dense subgraph search in bipartite graphs is a fundamental problem in graph analysis, with wide-ranging applications in fraud detection, recommendation systems, and social network analysis. The recently proposed $(α, β)$-dense subgraph model has demonstrated superior capability in capturing the intrinsic density structure of bipartite graphs compared to existing alternatives. However, despite its modeling advantages, the $(α, β)$-dense subgraph model lacks efficient support for query processing and dynamic updates, limiting its practical utility in large-scale applications. To address these limitations, we propose BD-Index, a novel index that answers $(α, β)$-dense subgraph queries in optimal time while using only linear space $O(|E|)$, making it well-suited for real-world applications requiring both fast query processing and low memory consumption. We further develop two complementary maintenance strategies for dynamic bipartite graphs to support efficient updates to the BD-Index. The space-efficient strategy updates the index in time complexity of $O(p \cdot |E|^{1.5})$ per edge insertion or deletion, while maintaining a low space cost of $O(|E|)$ (the same as the index itself), where $p$ is typically a small constant in real-world graphs. In contrast, the time-efficient strategy significantly reduces the update time to $O(p \cdot |E|)$ per edge update by maintaining auxiliary orientation structures, at the cost of increased memory usage up to $O(p \cdot |E|)$. These two strategies provide flexible trade-offs between maintenance efficiency and memory usage, enabling BD-Index to adapt to diverse application requirements. Extensive experiments on 10 large-scale real-world datasets demonstrate high efficiency and scalability of our proposed solutions.

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arXiv2025

Rethinking Client-oriented Federated Graph Learning

As a new distributed graph learning paradigm, Federated Graph Learning (FGL) facilitates collaborative model training across local systems while preserving data privacy. We review existing FGL approaches and categorize their optimization mechanisms into: (1) Server-Client (S-C), where clients upload local model parameters for server-side aggregation and global updates; (2) Client-Client (C-C), which allows direct exchange of information between clients and customizing their local training process. We reveal that C-C shows superior potential due to its refined communication structure. However, existing C-C methods broadcast redundant node representations, incurring high communication costs and privacy risks at the node level. To this end, we propose FedC4, which combines graph Condensation with C-C Collaboration optimization. Specifically, FedC4 employs graph condensation technique to refine the knowledge of each client's graph into a few synthetic embeddings instead of transmitting node-level knowledge. Moreover, FedC4 introduces three novel modules that allow the source client to send distinct node representations tailored to the target client's graph properties. Experiments on eight public real-world datasets show that FedC4 outperforms state-of-the-art baselines in both task performance and communication cost. Our code is now available on https://github.com/Ereshkigal1/FedC4.

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arXiv2025

DeepFaith: A Domain-Free and Model-Agnostic Unified Framework for Highly Faithful Explanations

Explainable AI (XAI) builds trust in complex systems through model attribution methods that reveal the decision rationale. However, due to the absence of a unified optimal explanation, existing XAI methods lack a ground truth for objective evaluation and optimization. To address this issue, we propose Deep architecture-based Faith explainer (DeepFaith), a domain-free and model-agnostic unified explanation framework under the lens of faithfulness. By establishing a unified formulation for multiple widely used and well-validated faithfulness metrics, we derive an optimal explanation objective whose solution simultaneously achieves optimal faithfulness across these metrics, thereby providing a ground truth from a theoretical perspective. We design an explainer learning framework that leverages multiple existing explanation methods, applies deduplicating and filtering to construct high-quality supervised explanation signals, and optimizes both pattern consistency loss and local correlation to train a faithful explainer. Once trained, DeepFaith can generate highly faithful explanations through a single forward pass without accessing the model being explained. On 12 diverse explanation tasks spanning 6 models and 6 datasets, DeepFaith achieves the highest overall faithfulness across 10 metrics compared to all baseline methods, highlighting its effectiveness and cross-domain generalizability.

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arXiv2025

Federated Graph Unlearning

The demand for data privacy has led to the development of frameworks like Federated Graph Learning (FGL), which facilitate decentralized model training. However, a significant operational challenge in such systems is adhering to the right to be forgotten. This principle necessitates robust mechanisms for two distinct types of data removal: the selective erasure of specific entities and their associated knowledge from local subgraphs and the wholesale removal of a user's entire dataset and influence. Existing methods often struggle to fully address both unlearning requirements, frequently resulting in incomplete data removal or the persistence of residual knowledge within the system. This work introduces a unified framework, conceived to provide a comprehensive solution to these challenges. The proposed framework employs a bifurcated strategy tailored to the specific unlearning request. For fine-grained Meta Unlearning, it uses prototype gradients to direct the initial local forgetting process, which is then refined by generating adversarial graphs to eliminate any remaining data traces among affected clients. In the case of complete client unlearning, the framework utilizes adversarial graph generation exclusively to purge the departed client's contributions from the remaining network. Extensive experiments on multiple benchmark datasets validate the proposed approach. The framework achieves substantial improvements in model prediction accuracy across both client and meta-unlearning scenarios when compared to existing methods. Furthermore, additional studies confirm its utility as a plug-in module, where it materially enhances the predictive capabilities and unlearning effectiveness of other established methods.

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arXiv2025

LAVA: Language Driven Scalable and Versatile Traffic Video Analytics

In modern urban environments, camera networks generate massive amounts of operational footage -- reaching petabytes each day -- making scalable video analytics essential for efficient processing. Many existing approaches adopt an SQL-based paradigm for querying such large-scale video databases; however, this constrains queries to rigid patterns with predefined semantic categories, significantly limiting analytical flexibility. In this work, we explore a language-driven video analytics paradigm aimed at enabling flexible and efficient querying of high-volume video data driven by natural language. Particularly, we build \textsc{Lava}, a system that accepts natural language queries and retrieves traffic targets across multiple levels of granularity and arbitrary categories. \textsc{Lava} comprises three main components: 1) a multi-armed bandit-based efficient sampling method for video segment-level localization; 2) a video-specific open-world detection module for object-level retrieval; and 3) a long-term object trajectory extraction scheme for temporal object association, yielding complete trajectories for object-of-interests. To support comprehensive evaluation, we further develop a novel benchmark by providing diverse, semantically rich natural language predicates and fine-grained annotations for multiple videos. Experiments on this benchmark demonstrate that \textsc{Lava} improves $F_1$-scores for selection queries by $\mathbf{14\%}$, reduces MPAE for aggregation queries by $\mathbf{0.39}$, and achieves top-$k$ precision of $\mathbf{86\%}$, while processing videos $ \mathbf{9.6\times} $ faster than the most accurate baseline. Our code and dataset are available at https://github.com/yuyanrui/LAVA.

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arXiv2025

HIAL: A New Paradigm for Hypergraph Active Learning via Influence Maximization

In recent years, Hypergraph Neural Networks (HNNs) have demonstrated immense potential in handling complex systems with high-order interactions. However, acquiring large-scale, high-quality labeled data for these models is costly, making Active Learning (AL) a critical technique. Existing Graph Active Learning (GAL) methods, when applied to hypergraphs, often rely on techniques like "clique expansion," which destroys the high-order structural information crucial to a hypergraph's success, thereby leading to suboptimal performance. To address this challenge, we introduce HIAL (Hypergraph Active Learning), a native active learning framework designed specifically for hypergraphs. We innovatively reformulate the Hypergraph Active Learning (HAL) problem as an Influence Maximization task. The core of HIAL is a dual-perspective influence function that, based on our novel "High-Order Interaction-Aware (HOI-Aware)" propagation mechanism, synergistically evaluates a node's feature-space coverage (via Magnitude of Influence, MoI) and its topological influence (via Expected Diffusion Value, EDV). We prove that this objective function is monotone and submodular, thus enabling the use of an efficient greedy algorithm with a formal (1-1/e) approximation guarantee. Extensive experiments on seven public datasets demonstrate that HIAL significantly outperforms state-of-the-art baselines in terms of performance, efficiency, generality, and robustness, establishing an efficient and powerful new paradigm for active learning on hypergraphs.

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arXiv2025

A Comprehensive Data-centric Overview of Federated Graph Learning

In the era of big data applications, Federated Graph Learning (FGL) has emerged as a prominent solution that reconcile the tradeoff between optimizing the collective intelligence between decentralized datasets holders and preserving sensitive information to maximum. Existing FGL surveys have contributed meaningfully but largely focus on integrating Federated Learning (FL) and Graph Machine Learning (GML), resulting in early stage taxonomies that emphasis on methodology and simulated scenarios. Notably, a data centric perspective, which systematically examines FGL methods through the lens of data properties and usage, remains unadapted to reorganize FGL research, yet it is critical to assess how FGL studies manage to tackle data centric constraints to enhance model performances. This survey propose a two-level data centric taxonomy: Data Characteristics, which categorizes studies based on the structural and distributional properties of datasets used in FGL, and Data Utilization, which analyzes the training procedures and techniques employed to overcome key data centric challenges. Each taxonomy level is defined by three orthogonal criteria, each representing a distinct data centric configuration. Beyond taxonomy, this survey examines FGL integration with Pretrained Large Models, showcases realistic applications, and highlights future direction aligned with emerging trends in GML.

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arXiv2025

QUEST: Query Optimization in Unstructured Document Analysis

Most recently, researchers have started building large language models (LLMs) powered data systems that allow users to analyze unstructured text documents like working with a database because LLMs are very effective in extracting attributes from documents. In such systems, LLM-based extraction operations constitute the performance bottleneck of query execution due to the high monetary cost and slow LLM inference. Existing systems typically borrow the query optimization principles popular in relational databases to produce query execution plans, which unfortunately are ineffective in minimizing LLM cost. To fill this gap, we propose QUEST, which features a bunch of novel optimization strategies for unstructured document analysis. First, we introduce an index-based strategy to minimize the cost of each extraction operation. With this index, QUEST quickly retrieves the text segments relevant to the target attributes and only feeds them to LLMs. Furthermore, we design an evidence-augmented retrieval strategy to reduce the possibility of missing relevant segments. Moreover, we develop an instance-optimized query execution strategy: because the attribute extraction cost could vary significantly document by document, QUEST produces different plans for different documents. For each document, QUEST produces a plan to minimize the frequency of attribute extraction. The innovations include LLM cost-aware operator ordering strategies and an optimized join execution approach that transforms joins into filters. Extensive experiments on 3 real-world datasets demonstrate the superiority of QUEST, achieving 30%-6x cost savings while improving the F1 score by 10% -27% compared with state-of-the-art baselines.

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arXiv2025

Improved Algorithms for Effective Resistance Computation on Graphs

Effective Resistance (ER) is a fundamental tool in various graph learning tasks. In this paper, we address the problem of efficiently approximating ER on a graph $\mathcal{G}=(\mathcal{V},\mathcal{E})$ with $n$ vertices and $m$ edges. First, we focus on local online-computation algorithms for ER approximation, aiming to improve the dependency on the approximation error parameter $ε$. Specifically, for a given vertex pair $(s,t)$, we propose a local algorithm with a time complexity of $\tilde{O}(\sqrt{d}/ε)$ to compute an $ε$-approximation of the $s,t$-ER value for expander graphs, where $d=\min \{d_s,d_t\}$. This improves upon the previous state-of-the-art, including an $\tilde{O}(1/ε^2)$ time algorithm based on random walk sampling by Andoni et al. (ITCS'19) and Peng et al. (KDD'21). Our method achieves this improvement by combining deterministic search with random walk sampling to reduce variance. Second, we establish a lower bound for ER approximation on expander graphs. We prove that for any $ε\in (0,1)$, there exist an expander graph and a vertex pair $(s,t)$ such that any local algorithm requires at least $Ω(1/ε)$ time to compute the $ε$-approximation of the $s,t$-ER value. Finally, we extend our techniques to index-based algorithms for ER computation. We propose an algorithm with $\tilde{O}(\min \{m+n/ε^{1.5},\sqrt{nm}/ε\})$ processing time, $\tilde{O}(n/ε)$ space complexity and $O(1)$ query complexity, which returns an $ε$-approximation of the $s,t$-ER value for any $s,t\in \mathcal{V}$ for expander graphs. Our approach improves upon the state-of-the-art $\tilde{O}(m/ε)$ processing time by Dwaraknath et al. (NeurIPS'24) and the $\tilde{O}(m+n/ε^2)$ processing time by Li and Sachdeva (SODA'23).

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