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Zhewei Wei

Publications and source records attributed to Zhewei Wei.

At least 55 records · Page 3Linked to original sources

Mixing Time Matters: Accelerating Effective Resistance Estimation via Bidirectional Method

We study the problem of efficiently approximating the \textit{effective resistance} (ER) on undirected graphs, where ER is a widely used node proximity measure with applications in graph spectral sparsification, multi-class graph clustering, network robustness analysis, graph machine learning, and more. Specifically, given any nodes $s$ and $t$ in an undirected graph $G$, we aim to efficiently estimate the ER value $R(s,t)$ between nodes $s$ and $t$, ensuring a small absolute error $ε$. The previous best algorithm for this problem has a worst-case computational complexity of $\tilde{O}\left(\frac{L_{\max}^3}{ε^2 d^2}\right)$, where the value of $L_{\max}$ depends on the mixing time of random walks on $G$, $d = \min\{d(s), d(t)\}$, and $d(s)$, $d(t)$ denote the degrees of nodes $s$ and $t$, respectively. We improve this complexity to $\tilde{O}\left(\min\left\{\frac{L_{\max}^{7/3}}{ε^{2/3}}, \frac{L_{\max}^3}{ε^2d^2}, mL_{\max}\right\}\right)$, achieving a theoretical improvement of $\tilde{O}\left(\max\left\{\frac{L_{\max}^{2/3}}{ε^{4/3} d^2}, 1, \frac{L_{\max}^2}{ε^2 d^2 m}\right\}\right)$ over previous results. Here, $m$ denotes the number of edges. Given that $L_{\max}$ is often very large in real-world networks (e.g., $L_{\max} > 10^4$), our improvement on $L_{\max}$ is significant, especially for real-world networks. We also conduct extensive experiments on real-world and synthetic graph datasets to empirically demonstrate the superiority of our method. The experimental results show that our method achieves a $10\times$ to $1000\times$ speedup in running time while maintaining the same absolute error compared to baseline methods.

cs.SI↗

Exploring the Potential of Large Language Models as Predictors in Dynamic Text-Attributed Graphs

With the rise of large language models (LLMs), there has been growing interest in Graph Foundation Models (GFMs) for graph-based tasks. By leveraging LLMs as predictors, GFMs have demonstrated impressive generalizability across various tasks and datasets. However, existing research on LLMs as predictors has predominantly focused on static graphs, leaving their potential in dynamic graph prediction unexplored. In this work, we pioneer using LLMs for predictive tasks on dynamic graphs. We identify two key challenges: the constraints imposed by context length when processing large-scale historical data and the significant variability in domain characteristics, both of which complicate the development of a unified predictor. To address these challenges, we propose the GraphAgent-Dynamic (GAD) Framework, a multi-agent system that leverages collaborative LLMs. In contrast to using a single LLM as the predictor, GAD incorporates global and local summary agents to generate domain-specific knowledge, enhancing its transferability across domains. Additionally, knowledge reflection agents enable adaptive updates to GAD's knowledge, maintaining a unified and self-consistent architecture. In experiments, GAD demonstrates performance comparable to or even exceeds that of full-supervised graph neural networks without dataset-specific training. Finally, to enhance the task-specific performance of LLM-based predictors, we discuss potential improvements, such as dataset-specific fine-tuning to LLMs. By developing tailored strategies for different tasks, we provide new insights for the future design of LLM-based predictors.

cs.LG↗

A Survey on Large Language Model based Autonomous Agents

Autonomous agents have long been a prominent research focus in both academic and industry communities. Previous research in this field often focuses on training agents with limited knowledge within isolated environments, which diverges significantly from human learning processes, and thus makes the agents hard to achieve human-like decisions. Recently, through the acquisition of vast amounts of web knowledge, large language models (LLMs) have demonstrated remarkable potential in achieving human-level intelligence. This has sparked an upsurge in studies investigating LLM-based autonomous agents. In this paper, we present a comprehensive survey of these studies, delivering a systematic review of the field of LLM-based autonomous agents from a holistic perspective. More specifically, we first discuss the construction of LLM-based autonomous agents, for which we propose a unified framework that encompasses a majority of the previous work. Then, we present a comprehensive overview of the diverse applications of LLM-based autonomous agents in the fields of social science, natural science, and engineering. Finally, we delve into the evaluation strategies commonly used for LLM-based autonomous agents. Based on the previous studies, we also present several challenges and future directions in this field. To keep track of this field and continuously update our survey, we maintain a repository of relevant references at https://github.com/Paitesanshi/LLM-Agent-Survey.

cs.AI↗

Scalable and Certifiable Graph Unlearning: Overcoming the Approximation Error Barrier

Graph unlearning has emerged as a pivotal research area for ensuring privacy protection, given the widespread adoption of Graph Neural Networks (GNNs) in applications involving sensitive user data. Among existing studies, certified graph unlearning is distinguished by providing robust privacy guarantees. However, current certified graph unlearning methods are impractical for large-scale graphs because they necessitate the costly re-computation of graph propagation for each unlearning request. Although numerous scalable techniques have been developed to accelerate graph propagation for GNNs, their integration into certified graph unlearning remains uncertain as these scalable approaches introduce approximation errors into node embeddings. In contrast, certified graph unlearning demands bounded model error on exact node embeddings to maintain its certified guarantee. To address this challenge, we present ScaleGUN, the first approach to scale certified graph unlearning to billion-edge graphs. ScaleGUN integrates the approximate graph propagation technique into certified graph unlearning, offering certified guarantees for three unlearning scenarios: node feature, edge, and node unlearning. Extensive experiments on real-world datasets demonstrate the efficiency and unlearning efficacy of ScaleGUN. Remarkably, ScaleGUN accomplishes $(ε,δ)=(1,10^{-4})$ certified unlearning on the billion-edge graph ogbn-papers100M in 20 seconds for a 5,000 random edge removal request -- of which only 5 seconds are required for updating the node embeddings -- compared to 1.91 hours for retraining and 1.89 hours for re-propagation. Our code is available at https://github.com/luyi256/ScaleGUN.

cs.LG↗

Large-Scale Spectral Graph Neural Networks via Laplacian Sparsification: Technical Report

Graph Neural Networks (GNNs) play a pivotal role in graph-based tasks for their proficiency in representation learning. Among the various GNN methods, spectral GNNs employing polynomial filters have shown promising performance on tasks involving both homophilous and heterophilous graph structures. However, The scalability of spectral GNNs on large graphs is limited because they learn the polynomial coefficients through multiple forward propagation executions during forward propagation. Existing works have attempted to scale up spectral GNNs by eliminating the linear layers on the input node features, a change that can disrupt end-to-end training, potentially impact performance, and become impractical with high-dimensional input features. To address the above challenges, we propose "Spectral Graph Neural Networks with Laplacian Sparsification (SGNN-LS)", a novel graph spectral sparsification method to approximate the propagation patterns of spectral GNNs. We prove that our proposed method generates Laplacian sparsifiers that can approximate both fixed and learnable polynomial filters with theoretical guarantees. Our method allows the application of linear layers on the input node features, enabling end-to-end training as well as the handling of raw text features. We conduct an extensive experimental analysis on datasets spanning various graph scales and properties to demonstrate the superior efficiency and effectiveness of our method. The results show that our method yields superior results in comparison with the corresponding approximated base models, especially on dataset Ogbn-papers100M(111M nodes, 1.6B edges) and MAG-scholar-C (2.8M features).

cs.LG↗

LLM-Based Multi-Agent Systems are Scalable Graph Generative Models

The structural properties of naturally arising social graphs are extensively studied to understand their evolution. Prior approaches for modeling network dynamics typically rely on rule-based models, which lack realism and generalizability, or deep learning-based models, which require large-scale training datasets. Social graphs, as abstract graph representations of entity-wise interactions, present an opportunity to explore network evolution mechanisms through realistic simulations of human-item interactions. Leveraging the pre-trained social consensus knowledge embedded in large language models (LLMs), we present GraphAgent-Generator (GAG), a novel simulation-based framework for dynamic, text-attributed social graph generation. GAG simulates the temporal node and edge generation processes for zero-shot social graph generation. The resulting graphs exhibit adherence to seven key macroscopic network properties, achieving an 11% improvement in microscopic graph structure metrics. Through the node classification benchmarking task, we validate GAG effectively captures the intricate text-structure correlations in graph generation. Furthermore, GAG supports generating graphs with up to nearly 100,000 nodes or 10 million edges through large-scale LLM-based agent simulation with parallel acceleration, achieving a minimum speed-up of 90.4%. The source code is available at https://github.com/Ji-Cather/GraphAgent.

cs.CL↗

S-MolSearch: 3D Semi-supervised Contrastive Learning for Bioactive Molecule Search

Virtual Screening is an essential technique in the early phases of drug discovery, aimed at identifying promising drug candidates from vast molecular libraries. Recently, ligand-based virtual screening has garnered significant attention due to its efficacy in conducting extensive database screenings without relying on specific protein-binding site information. Obtaining binding affinity data for complexes is highly expensive, resulting in a limited amount of available data that covers a relatively small chemical space. Moreover, these datasets contain a significant amount of inconsistent noise. It is challenging to identify an inductive bias that consistently maintains the integrity of molecular activity during data augmentation. To tackle these challenges, we propose S-MolSearch, the first framework to our knowledge, that leverages molecular 3D information and affinity information in semi-supervised contrastive learning for ligand-based virtual screening. Drawing on the principles of inverse optimal transport, S-MolSearch efficiently processes both labeled and unlabeled data, training molecular structural encoders while generating soft labels for the unlabeled data. This design allows S-MolSearch to adaptively utilize unlabeled data within the learning process. Empirically, S-MolSearch demonstrates superior performance on widely-used benchmarks LIT-PCBA and DUD-E. It surpasses both structure-based and ligand-based virtual screening methods for AUROC, BEDROC and EF.

q-bio.BM↗

Optimal Matrix Sketching over Sliding Windows

Matrix sketching, aimed at approximating a matrix $\boldsymbol{A} \in \mathbb{R}^{N\times d}$ consisting of vector streams of length $N$ with a smaller sketching matrix $\boldsymbol{B} \in \mathbb{R}^{\ell\times d}, \ell \ll N$, has garnered increasing attention in fields such as large-scale data analytics and machine learning. A well-known deterministic matrix sketching method is the Frequent Directions algorithm, which achieves the optimal $O\left(\frac{d}{\varepsilon}\right)$ space bound and provides a covariance error guarantee of $\varepsilon = \lVert \boldsymbol{A}^\top \boldsymbol{A} - \boldsymbol{B}^\top \boldsymbol{B} \rVert_2/\lVert \boldsymbol{A} \rVert_F^2$. The matrix sketching problem becomes particularly interesting in the context of sliding windows, where the goal is to approximate the matrix $\boldsymbol{A}_W$, formed by input vectors over the most recent $N$ time units. However, despite recent efforts, whether achieving the optimal $O\left(\frac{d}{\varepsilon}\right)$ space bound on sliding windows is possible has remained an open question. In this paper, we introduce the DS-FD algorithm, which achieves the optimal $O\left(\frac{d}{\varepsilon}\right)$ space bound for matrix sketching over row-normalized, sequence-based sliding windows. We also present matching upper and lower space bounds for time-based and unnormalized sliding windows, demonstrating the generality and optimality of \dsfd across various sliding window models. This conclusively answers the open question regarding the optimal space bound for matrix sketching over sliding windows. Furthermore, we conduct extensive experiments with both synthetic and real-world datasets, validating our theoretical claims and thus confirming the correctness and effectiveness of our algorithm, both theoretically and empirically.

cs.DB↗

Intruding with Words: Towards Understanding Graph Injection Attacks at the Text Level

Graph Neural Networks (GNNs) excel across various applications but remain vulnerable to adversarial attacks, particularly Graph Injection Attacks (GIAs), which inject malicious nodes into the original graph and pose realistic threats. Text-attributed graphs (TAGs), where nodes are associated with textual features, are crucial due to their prevalence in real-world applications and are commonly used to evaluate these vulnerabilities. However, existing research only focuses on embedding-level GIAs, which inject node embeddings rather than actual textual content, limiting their applicability and simplifying detection. In this paper, we pioneer the exploration of GIAs at the text level, presenting three novel attack designs that inject textual content into the graph. Through theoretical and empirical analysis, we demonstrate that text interpretability, a factor previously overlooked at the embedding level, plays a crucial role in attack strength. Among the designs we investigate, the Word-frequency-based Text-level GIA (WTGIA) is particularly notable for its balance between performance and interpretability. Despite the success of WTGIA, we discover that defenders can easily enhance their defenses with customized text embedding methods or large language model (LLM)--based predictors. These insights underscore the necessity for further research into the potential and practical significance of text-level GIAs.

cs.LG↗

Very Large-Scale Multi-Agent Simulation in AgentScope

Recent advances in large language models (LLMs) have opened new avenues for applying multi-agent systems in very large-scale simulations. However, there remain several challenges when conducting multi-agent simulations with existing platforms, such as limited scalability and low efficiency, unsatisfied agent diversity, and effort-intensive management processes. To address these challenges, we develop several new features and components for AgentScope, a user-friendly multi-agent platform, enhancing its convenience and flexibility for supporting very large-scale multi-agent simulations. Specifically, we propose an actor-based distributed mechanism as the underlying technological infrastructure towards great scalability and high efficiency, and provide flexible environment support for simulating various real-world scenarios, which enables parallel execution of multiple agents, automatic workflow conversion for distributed deployment, and both inter-agent and agent-environment interactions. Moreover, we integrate an easy-to-use configurable tool and an automatic background generation pipeline in AgentScope, simplifying the process of creating agents with diverse yet detailed background settings. Last but not least, we provide a web-based interface for conveniently monitoring and managing a large number of agents that might deploy across multiple devices. We conduct a comprehensive simulation to demonstrate the effectiveness of these proposed enhancements in AgentScope, and provide detailed observations and insightful discussions to highlight the great potential of applying multi-agent systems in large-scale simulations. The source code is released on GitHub at https://github.com/modelscope/agentscope/tree/main/examples/paper_large_scale_simulation to inspire further research and development in large-scale multi-agent simulations.

cs.MA↗

SRAP-Agent: Simulating and Optimizing Scarce Resource Allocation Policy with LLM-based Agent

Public scarce resource allocation plays a crucial role in economics as it directly influences the efficiency and equity in society. Traditional studies including theoretical model-based, empirical study-based and simulation-based methods encounter limitations due to the idealized assumption of complete information and individual rationality, as well as constraints posed by limited available data. In this work, we propose an innovative framework, SRAP-Agent (Simulating and Optimizing Scarce Resource Allocation Policy with LLM-based Agent), which integrates Large Language Models (LLMs) into economic simulations, aiming to bridge the gap between theoretical models and real-world dynamics. Using public housing allocation scenarios as a case study, we conduct extensive policy simulation experiments to verify the feasibility and effectiveness of the SRAP-Agent and employ the Policy Optimization Algorithm with certain optimization objectives. The source code can be found in https://github.com/jijiarui-cather/SRAPAgent_Framework

cs.CL↗

Beyond Over-smoothing: Uncovering the Trainability Challenges in Deep Graph Neural Networks

The drastic performance degradation of Graph Neural Networks (GNNs) as the depth of the graph propagation layers exceeds 8-10 is widely attributed to a phenomenon of Over-smoothing. Although recent research suggests that Over-smoothing may not be the dominant reason for such a performance degradation, they have not provided rigorous analysis from a theoretical view, which warrants further investigation. In this paper, we systematically analyze the real dominant problem in deep GNNs and identify the issues that these GNNs towards addressing Over-smoothing essentially work on via empirical experiments and theoretical gradient analysis. We theoretically prove that the difficult training problem of deep MLPs is actually the main challenge, and various existing methods that supposedly tackle Over-smoothing actually improve the trainability of MLPs, which is the main reason for their performance gains. Our further investigation into trainability issues reveals that properly constrained smaller upper bounds of gradient flow notably enhance the trainability of GNNs. Experimental results on diverse datasets demonstrate consistency between our theoretical findings and empirical evidence. Our analysis provides new insights in constructing deep graph models.

cs.LG↗

Towards Effective and Efficient Continual Pre-training of Large Language Models

Continual pre-training (CPT) has been an important approach for adapting language models to specific domains or tasks. To make the CPT approach more traceable, this paper presents a technical report for continually pre-training Llama-3 (8B), which significantly enhances the Chinese language ability and scientific reasoning ability of the backbone model. To enhance the new abilities while retaining the original abilities, we design specific data mixture and curriculum strategies by utilizing existing datasets and synthesizing high-quality datasets. Specifically, we synthesize multidisciplinary scientific question and answer (QA) pairs based on related web pages, and subsequently incorporate these synthetic data to improve the scientific reasoning ability of Llama-3. We refer to the model after CPT as Llama-3-SynE (Synthetic data Enhanced Llama-3). We also present the tuning experiments with a relatively small model -- TinyLlama, and employ the derived findings to train the backbone model. Extensive experiments on a number of evaluation benchmarks show that our approach can largely improve the performance of the backbone models, including both the general abilities (+8.81 on C-Eval and +6.31 on CMMLU) and the scientific reasoning abilities (+12.00 on MATH and +4.13 on SciEval), without hurting the original capacities. Our model, data, and codes are available at https://github.com/RUC-GSAI/Llama-3-SynE.

cs.CL↗

PolyFormer: Scalable Node-wise Filters via Polynomial Graph Transformer

Spectral Graph Neural Networks have demonstrated superior performance in graph representation learning. However, many current methods focus on employing shared polynomial coefficients for all nodes, i.e., learning node-unified filters, which limits the filters' flexibility for node-level tasks. The recent DSF attempts to overcome this limitation by learning node-wise coefficients based on positional encoding. However, the initialization and updating process of the positional encoding are burdensome, hindering scalability on large-scale graphs. In this work, we propose a scalable node-wise filter, PolyAttn. Leveraging the attention mechanism, PolyAttn can directly learn node-wise filters in an efficient manner, offering powerful representation capabilities. Building on PolyAttn, we introduce the whole model, named PolyFormer. In the lens of Graph Transformer models, PolyFormer, which calculates attention scores within nodes, shows great scalability. Moreover, the model captures spectral information, enhancing expressiveness while maintaining efficiency. With these advantages, PolyFormer offers a desirable balance between scalability and expressiveness for node-level tasks. Extensive experiments demonstrate that our proposed methods excel at learning arbitrary node-wise filters, showing superior performance on both homophilic and heterophilic graphs, and handling graphs containing up to 100 million nodes. The code is available at https://github.com/air029/PolyFormer.

cs.LG↗

YuLan: An Open-source Large Language Model

Large language models (LLMs) have become the foundation of many applications, leveraging their extensive capabilities in processing and understanding natural language. While many open-source LLMs have been released with technical reports, the lack of training details hinders further research and development. This paper presents the development of YuLan, a series of open-source LLMs with $12$ billion parameters. The base model of YuLan is pre-trained on approximately $1.7$T tokens derived from a diverse corpus, including massive English, Chinese, and multilingual texts. We design a three-stage pre-training method to enhance YuLan's overall capabilities. Subsequent phases of training incorporate instruction-tuning and human alignment, employing a substantial volume of high-quality synthesized data. To facilitate the learning of complex and long-tail knowledge, we devise a curriculum-learning framework throughout across these stages, which helps LLMs learn knowledge in an easy-to-hard manner. YuLan's training is finished on Jan, 2024 and has achieved performance on par with state-of-the-art LLMs across various English and Chinese benchmarks. This paper outlines a comprehensive technical roadmap for developing LLMs from scratch. Our model and codes are available at https://github.com/RUC-GSAI/YuLan-Chat.

cs.CL↗

PRICE: A Pretrained Model for Cross-Database Cardinality Estimation

Cardinality estimation (CardEst) is essential for optimizing query execution plans. Recent ML-based CardEst methods achieve high accuracy but face deployment challenges due to high preparation costs and lack of transferability across databases. In this paper, we propose PRICE, a PRetrained multI-table CardEst model, which addresses these limitations. PRICE takes low-level but transferable features w.r.t. data distributions and query information and elegantly applies self-attention models to learn meta-knowledge to compute cardinality in any database. It is generally applicable to any unseen new database to attain high estimation accuracy, while its preparation cost is as little as the basic one-dimensional histogram-based CardEst methods. Moreover, PRICE can be finetuned to further enhance its performance on any specific database. We pretrained PRICE using 30 diverse datasets, completing the process in about 5 hours with a resulting model size of only about 40MB. Evaluations show that PRICE consistently outperforms existing methods, achieving the highest estimation accuracy on several unseen databases and generating faster execution plans with lower overhead. After finetuning with a small volume of databasespecific queries, PRICE could even find plans very close to the optimal ones. Meanwhile, PRICE is generally applicable to different settings such as data updates, data scaling, and query workload shifts. We have made all of our data and codes publicly available at https://github.com/StCarmen/PRICE.

cs.DB↗

Spectral Heterogeneous Graph Convolutions via Positive Noncommutative Polynomials

Heterogeneous Graph Neural Networks (HGNNs) have gained significant popularity in various heterogeneous graph learning tasks. However, most existing HGNNs rely on spatial domain-based methods to aggregate information, i.e., manually selected meta-paths or some heuristic modules, lacking theoretical guarantees. Furthermore, these methods cannot learn arbitrary valid heterogeneous graph filters within the spectral domain, which have limited expressiveness. To tackle these issues, we present a positive spectral heterogeneous graph convolution via positive noncommutative polynomials. Then, using this convolution, we propose PSHGCN, a novel Positive Spectral Heterogeneous Graph Convolutional Network. PSHGCN offers a simple yet effective method for learning valid heterogeneous graph filters. Moreover, we demonstrate the rationale of PSHGCN in the graph optimization framework. We conducted an extensive experimental study to show that PSHGCN can learn diverse heterogeneous graph filters and outperform all baselines on open benchmarks. Notably, PSHGCN exhibits remarkable scalability, efficiently handling large real-world graphs comprising millions of nodes and edges. Our codes are available at https://github.com/ivam-he/PSHGCN.

cs.LG↗

A survey of dynamic graph neural networks

Graph neural networks (GNNs) have emerged as a powerful tool for effectively mining and learning from graph-structured data, with applications spanning numerous domains. However, most research focuses on static graphs, neglecting the dynamic nature of real-world networks where topologies and attributes evolve over time. By integrating sequence modeling modules into traditional GNN architectures, dynamic GNNs aim to bridge this gap, capturing the inherent temporal dependencies of dynamic graphs for a more authentic depiction of complex networks. This paper provides a comprehensive review of the fundamental concepts, key techniques, and state-of-the-art dynamic GNN models. We present the mainstream dynamic GNN models in detail and categorize models based on how temporal information is incorporated. We also discuss large-scale dynamic GNNs and pre-training techniques. Although dynamic GNNs have shown superior performance, challenges remain in scalability, handling heterogeneous information, and lack of diverse graph datasets. The paper also discusses possible future directions, such as adaptive and memory-enhanced models, inductive learning, and theoretical analysis.

cs.LG↗