Zhewei Wei

Lei Wang, Chen Ma, Xueyang Feng et al.

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.

Gengmo Zhou, Zhifeng Gao, Zhewei Wei et al. · microsoft-research

Molecular conformation generation (MCG) is a fundamental and important problem in drug discovery. Many traditional methods have been developed to solve the MCG problem, such as systematic searching, model-building, random searching, distance geometry, molecular dynamics, Monte Carlo methods, etc. However, they have some limitations depending on the molecular structures. Recently, there are plenty of deep learning based MCG methods, which claim they largely outperform the traditional methods. However, to our surprise, we design a simple and cheap algorithm (parameter-free) based on the traditional methods and find it is comparable to or even outperforms deep learning based MCG methods in the widely used GEOM-QM9 and GEOM-Drugs benchmarks. In particular, our design algorithm is simply the clustering of the RDKIT-generated conformations. We hope our findings can help the community to revise the deep learning methods for MCG. The code of the proposed algorithm could be found at https://gist.github.com/ZhouGengmo/5b565f51adafcd911c0bc115b2ef027c.

Lu Yi, Runlin Lei, Liuyi Yao et al.

LLM agents increasingly face long-horizon tasks such as web search and deep research in real-world applications, where accumulated context can cause long-context degradation and reasoning failures. Prior work mitigates this through context management with agent-side context control or fixed strategies such as summarization, which require training the agent itself for adaptation - making it impractical for closed-source agents and ignoring that different agents may require different strategies. We introduce Adaptive Context Management (AdaCoM), which trains an external LLM to manage the context of a frozen agent through flexible modification actions and end-to-end reinforcement learning. Across diverse agents on web search and deep research benchmarks, AdaCoM substantially improves performance by preserving task constraints and progress while pruning stale content. The learned strategies reveal a Fidelity-Reliability Trade-off: agents with higher vanilla ReAct performance benefit from higher-fidelity context preservation, whereas lower-performing agents require more aggressive compression to stay within a reliable reasoning regime. Transfer experiments show that AdaCoM generalizes most effectively across agents with similar capability (measured by vanilla ReAct performance), suggesting a practical path toward reusable context managers for agent systems.

Yuhe Guo, Zhewei Wei

Polynomial filters, a kind of Graph Neural Networks, typically use a predetermined polynomial basis and learn the coefficients from the training data. It has been observed that the effectiveness of the model is highly dependent on the property of the polynomial basis. Consequently, two natural and fundamental questions arise: Can we learn a suitable polynomial basis from the training data? Can we determine the optimal polynomial basis for a given graph and node features? In this paper, we propose two spectral GNN models that provide positive answers to the questions posed above. First, inspired by Favard's Theorem, we propose the FavardGNN model, which learns a polynomial basis from the space of all possible orthonormal bases. Second, we examine the supposedly unsolvable definition of optimal polynomial basis from Wang & Zhang (2022) and propose a simple model, OptBasisGNN, which computes the optimal basis for a given graph structure and graph signal. Extensive experiments are conducted to demonstrate the effectiveness of our proposed models. Our code is available at https://github.com/yuziGuo/FarOptBasis.

Jie Chen, Zhipeng Chen, Jiapeng Wang et al.

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.

Xuchen Pan, Dawei Gao, Yuexiang Xie et al.

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.

Yang Zhang, Zhewei Wei, Ye Yuan et al.

Predicting the binding sites of target proteins plays a fundamental role in drug discovery. Most existing deep-learning methods consider a protein as a 3D image by spatially clustering its atoms into voxels and then feed the voxelized protein into a 3D CNN for prediction. However, the CNN-based methods encounter several critical issues: 1) defective in representing irregular protein structures; 2) sensitive to rotations; 3) insufficient to characterize the protein surface; 4) unaware of protein size shift. To address the above issues, this work proposes EquiPocket, an E(3)-equivariant Graph Neural Network (GNN) for binding site prediction, which comprises three modules: the first one to extract local geometric information for each surface atom, the second one to model both the chemical and spatial structure of protein and the last one to capture the geometry of the surface via equivariant message passing over the surface atoms. We further propose a dense attention output layer to alleviate the effect incurred by variable protein size. Extensive experiments on several representative benchmarks demonstrate the superiority of our framework to the state-of-the-art methods.

Runlin Lei, Zhen Wang, Yaliang Li et al.

Graph Neural Networks (GNNs) have received extensive research attention for their promising performance in graph machine learning. Despite their extraordinary predictive accuracy, existing approaches, such as GCN and GPRGNN, are not robust in the face of homophily changes on test graphs, rendering these models vulnerable to graph structural attacks and with limited capacity in generalizing to graphs of varied homophily levels. Although many methods have been proposed to improve the robustness of GNN models, most of these techniques are restricted to the spatial domain and employ complicated defense mechanisms, such as learning new graph structures or calculating edge attentions. In this paper, we study the problem of designing simple and robust GNN models in the spectral domain. We propose EvenNet, a spectral GNN corresponding to an even-polynomial graph filter. Based on our theoretical analysis in both spatial and spectral domains, we demonstrate that EvenNet outperforms full-order models in generalizing across homophilic and heterophilic graphs, implying that ignoring odd-hop neighbors improves the robustness of GNNs. We conduct experiments on both synthetic and real-world datasets to demonstrate the effectiveness of EvenNet. Notably, EvenNet outperforms existing defense models against structural attacks without introducing additional computational costs and maintains competitiveness in traditional node classification tasks on homophilic and heterophilic graphs.

Runlin Lei, Xiaokui Xiao, Zhewei Wei

Graphs have been used to enhance large language models (LLMs) for structured reasoning, mostly as external knowledge sources are provided to models at test time. In this paper, we take a different view: the value of graphs for LLMs lie not only in supplying information, but also in organizing reasoning. Inspired by how humans use graph-structured mind maps to organize branching and converging thoughts, we ask whether graphs can serve as an internal form of reasoning assistance. We study this question on multi-hop question answering tasks, where teacher-provided reasoning traces are rewritten as graph mind maps and used to guide a student model. Our experiments reveal a clear modality gap. When graph structures are flattened into text, their benefits become limited once direct answer hints are removed. Under this abstract guidance setting, both reasoning efficiency and answer quality degrade substantially. In contrast, visual graph guidance remains effective without direct answer clues, and its advantage persists after supervised fine-tuning and KL-based distillation. The above findings support the claim that graphs should be studied not only as external knowledge structures for LLMs, but also as visual scaffolds for organizing reasoning.

Yunxiang Su, Tianjing Zeng, Zhongjun Ding et al.

With the development of large language models (LLMs), numerous studies integrate LLMs through operator-like components to enhance relational data processing tasks, e.g., filters with semantic predicates, knowledge-augmented table imputation, reasoning-driven entity matching and more challenging semantic query processing. These components invoke LLMs while preserving a relational input/output interface, which we refer to as LLM-Enhanced Relational Operators (LROs). From an operator perspective, unfortunately, these existing LROs suffer from fragmented definition, various implementation strategies and inadequate evaluation benchmarks. To this end, in this paper, we first establish a unified LRO taxonomy to align existing LROs, and categorize them into: Select, Match, Impute, Cluster and Order, along with their operands and implementation variants. Second, we design LROBench, a comprehensive benchmark featuring 290 single-LRO queries and 60 multi-LRO queries, spanning 27 databases across more than 10 domains. LROBench covers all operating logics and operand granularities in its single-LRO workload, and provides challenging multi-LRO queries stratified by query complexity. Based on these, we evaluate individual LROs under various implementations, deriving practical insights into LRO design choices and summarizing our empirical best practices. We further compare the end-to-end performance of existing multi-LRO systems against an LRO suite instantiated with these best practices, in order to investigate how to design an effective LRO set for multi-LRO systems targeting complex semantic queries. Last, to facilitate future work, we outline promising future directions and open-source all benchmark data and evaluation code, available at https://github.com/LROBench/LROBench/.

Yang Zhang, Gengmo Zhou, Zhewei Wei et al.

The prediction of protein-ligand binding affinity is of great significance for discovering lead compounds in drug research. Facing this challenging task, most existing prediction methods rely on the topological and/or spatial structure of molecules and the local interactions while ignoring the multi-level inter-molecular interactions between proteins and ligands, which often lead to sub-optimal performance. To solve this issue, we propose a novel global-local interaction (GLI) framework to predict protein-ligand binding affinity. In particular, our GLI framework considers the inter-molecular interactions between proteins and ligands, which involve not only the high-energy short-range interactions between closed atoms but also the low-energy long-range interactions between non-bonded atoms. For each pair of protein and ligand, our GLI embeds the long-range interactions globally and aggregates local short-range interactions, respectively. Such a joint global-local interaction modeling strategy helps to improve prediction accuracy, and the whole framework is compatible with various neural network-based modules. Experiments demonstrate that our GLI framework outperforms state-of-the-art methods with simple neural network architectures and moderate computational costs.

Xuwei Xu, Sen Wang, Yudong Chen et al.

Vision Transformers (ViTs) have revolutionized the field of computer vision, yet their deployments on resource-constrained devices remain challenging due to high computational demands. To expedite pre-trained ViTs, token pruning and token merging approaches have been developed, which aim at reducing the number of tokens involved in the computation. However, these methods still have some limitations, such as image information loss from pruned tokens and inefficiency in the token-matching process. In this paper, we introduce a novel Graph-based Token Propagation (GTP) method to resolve the challenge of balancing model efficiency and information preservation for efficient ViTs. Inspired by graph summarization algorithms, GTP meticulously propagates less significant tokens' information to spatially and semantically connected tokens that are of greater importance. Consequently, the remaining few tokens serve as a summarization of the entire token graph, allowing the method to reduce computational complexity while preserving essential information of eliminated tokens. Combined with an innovative token selection strategy, GTP can efficiently identify image tokens to be propagated. Extensive experiments have validated GTP's effectiveness, demonstrating both efficiency and performance improvements. Specifically, GTP decreases the computational complexity of both DeiT-S and DeiT-B by up to 26% with only a minimal 0.3% accuracy drop on ImageNet-1K without finetuning, and remarkably surpasses the state-of-the-art token merging method on various backbones at an even faster inference speed. The source code is available at https://github.com/Ackesnal/GTP-ViT.

Qian Tao, Zhen Wang, Wenyuan Yu et al.

In recent years, a plethora of spectral graph neural networks (GNN) methods have utilized polynomial basis with learnable coefficients to achieve top-tier performances on many node-level tasks. Although various kinds of polynomial bases have been explored, each such method adopts a fixed polynomial basis which might not be the optimal choice for the given graph. Besides, we identify the so-called over-passing issue of these methods and show that it is somewhat rooted in their less-principled regularization strategy and unnormalized basis. In this paper, we make the first attempts to address these two issues. Leveraging Jacobi polynomials, we design a novel spectral GNN, LON-GNN, with Learnable OrthoNormal bases and prove that regularizing coefficients becomes equivalent to regularizing the norm of learned filter function now. We conduct extensive experiments on diverse graph datasets to evaluate the fitting and generalization capability of LON-GNN, where the results imply its superiority.

Yanping Zheng, Hanzhi Wang, Zhewei Wei et al.

Graph Neural Networks (GNNs) have been widely used for modeling graph-structured data. With the development of numerous GNN variants, recent years have witnessed groundbreaking results in improving the scalability of GNNs to work on static graphs with millions of nodes. However, how to instantly represent continuous changes of large-scale dynamic graphs with GNNs is still an open problem. Existing dynamic GNNs focus on modeling the periodic evolution of graphs, often on a snapshot basis. Such methods suffer from two drawbacks: first, there is a substantial delay for the changes in the graph to be reflected in the graph representations, resulting in losses on the model's accuracy; second, repeatedly calculating the representation matrix on the entire graph in each snapshot is predominantly time-consuming and severely limits the scalability. In this paper, we propose Instant Graph Neural Network (InstantGNN), an incremental computation approach for the graph representation matrix of dynamic graphs. Set to work with dynamic graphs with the edge-arrival model, our method avoids time-consuming, repetitive computations and allows instant updates on the representation and instant predictions. Graphs with dynamic structures and dynamic attributes are both supported. The upper bounds of time complexity of those updates are also provided. Furthermore, our method provides an adaptive training strategy, which guides the model to retrain at moments when it can make the greatest performance gains. We conduct extensive experiments on several real-world and synthetic datasets. Empirical results demonstrate that our model achieves state-of-the-art accuracy while having orders-of-magnitude higher efficiency than existing methods.

Jiahong Ma, Mingguo He, Zhewei Wei

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.

Yuhe Guo, Zhewei Wei

Graph Convolutional Networks (GCNs), which use a message-passing paradigm with stacked convolution layers, are foundational methods for learning graph representations. Recent GCN models use various residual connection techniques to alleviate the model degradation problem such as over-smoothing and gradient vanishing. Existing residual connection techniques, however, fail to make extensive use of underlying graph structure as in the graph spectral domain, which is critical for obtaining satisfactory results on heterophilic graphs. In this paper, we introduce ClenshawGCN, a GNN model that employs the Clenshaw Summation Algorithm to enhance the expressiveness of the GCN model. ClenshawGCN equips the standard GCN model with two straightforward residual modules: the adaptive initial residual connection and the negative second-order residual connection. We show that by adding these two residual modules, ClenshawGCN implicitly simulates a polynomial filter under the Chebyshev basis, giving it at least as much expressive power as polynomial spectral GNNs. In addition, we conduct comprehensive experiments to demonstrate the superiority of our model over spatial and spectral GNN models.

Lu Yi, Zhewei Wei

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.

Jiarui Ji, Zehua Zhang, Zhewei Wei et al.

Large language models (LLMs) have shown promise in simulating human-like social behaviors. Social graphs provide high-quality supervision signals that encode both local interactions and global network structure, yet they remain underutilized for LLM training. To address this gap, we propose Graphia, the first general LLM-based social graph simulation framework that leverages graph data as supervision for LLM post-training via reinforcement learning. With GNN-based structural rewards, Graphia trains specialized agents to predict whom to interact with (destination selection) and how to interact (edge generation), followed by designed graph generation pipelines. We evaluate Graphia under two settings: Transductive Dynamic Graph Generation (TDGG), a micro-level task with our proposed node-wise interaction alignment metrics; and Inductive Dynamic Graph Generation (IDGG), a macro-level task with our proposed metrics for aligning emergent network properties. On three real-world networks, Graphia improves micro-level alignment by 6.1% in the composite destination selection score, 12% in edge classification accuracy, and 27.9% in edge content BERTScore over the strongest baseline. For macro-level alignment, it achieves 35.98% higher structural similarity and 28.71% better replication of social phenomena such as power laws and echo chambers. Our results show that social graphs can serve as high-quality supervision signals for LLM post-training, closing the gap between agent behaviors and network dynamics for LLM-based simulation. Code is available at https://github.com/Ji-Cather/Graphia.git.

Guanyu Cui, Yuhe Guo, Zhewei Wei et al.

Message-passing graph neural networks (MPGNNs) are commonly compared with the Weisfeiler-Lehman (WL) color-refinement procedure, but this comparison does not quantify the resource parameters a network needs to realize color refinement with bounded-size messages and finite numerical precision. We study the cost of simulating a single color-refinement step on unattributed graphs. We distinguish input-independent, or oblivious, simulation from instance-dependent simulation. In the former, the parameters, or their distributions in randomized models, are fixed before the input instance is known. Our results show that the local form of WL color refinement hides a global relabeling problem. In the oblivious setting, deterministic and zero-error randomized MPGNNs cannot solve this problem in the worst case using only shallow networks with small messages. We complement this lower bound with a nearly matching construction in a stronger rooted, port-aware model. By contrast, when the color set is large, bounded-error randomness can greatly reduce the cost, and a one-layer MPGNN with messages of logarithmic size and a logarithmic number of random bits suffices. We show that this logarithmic number of random bits is essentially necessary for shallow, small-message simulations. When the color set is small, we still obtain a rooted, port-aware simulation, but this construction requires more layers or larger messages. We also prove that this extra cost is partly unavoidable, as small color sets force a nontrivial trade-off between the number of layers and the message size. Finally, instance-dependent simulation can be much shallower, but the required instance-specific parameters are not necessarily easy to find. Together, these results reveal quantitative structure hidden behind the statement that MPGNNs match WL color refinement.

Gengmo Zhou, Zhen Wang, Feng Yu et al.

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.

Guanyu Cui, Zhewei Wei, Kun He

Many works make the eye-catching claim that Transformers are Turing-complete. However, the literature often conflates two distinct settings: (i) a fixed Transformer system setting, in which a fixed autoregressive Transformer is coupled with a fixed context-management method to process inputs of different lengths step by step, and (ii) a scaling-family setting, in which a family of different models (with increasing context-window length or numerical precision) is used to handle different input lengths. Existing proofs of Transformer Turing-completeness are frequently established in setting (ii), whereas real-world LLM deployment and the standard notion of Turing-completeness correspond more naturally to setting (i). In this paper, we first formalize the fixed-system setting, thereby providing a concrete characterization of how real-world LLMs operate. We then argue that results proved in the scaling-family setting provide theoretically meaningful resource bounds but do not establish Turing-completeness, thereby clarifying a common misinterpretation of existing results. Finally, we show that different context-management methods can yield sharply different computational power, and we advocate the position that context management is a central component that critically determines the computational power of real-world autoregressive Transformers.

Jie Peng, Runlin Lei, Zhewei Wei

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.

Jiarui Ji, Runlin Lei, Xuchen Pan et al.

The emergence of Large Language Models (LLMs) demonstrates their potential to encapsulate the logic and patterns inherent in human behavior simulation by leveraging extensive web data pre-training. However, the boundaries of LLM capabilities in social simulation remain unclear. To further explore the social attributes of LLMs, we introduce the CiteAgent framework, designed to generate citation networks based on human-behavior simulation with LLM-based agents. CiteAgent successfully captures predominant phenomena in real-world citation networks, including power-law distribution, citational distortion, and shrinking diameter. Building on this realistic simulation, we establish two LLM-based research paradigms in social science: LLM-SE (LLM-based Survey Experiment) and LLM-LE (LLM-based Laboratory Experiment). These paradigms facilitate rigorous analyses of citation network phenomena, allowing us to validate and challenge existing theories. Additionally, we extend the research scope of traditional science of science studies through idealized social experiments, with the simulation experiment results providing valuable insights for real-world academic environments. Our work demonstrates the potential of LLMs for advancing science of science research in social science.

Gengmo Zhou, Feng Yu, Wenda Wang et al.

Enzymes are crucial catalysts that enable a wide range of biochemical reactions. Efficiently identifying specific enzymes from vast protein libraries is essential for advancing biocatalysis. Traditional computational methods for enzyme screening and retrieval are time-consuming and resource-intensive. Recently, deep learning approaches have shown promise. However, these methods focus solely on the interaction between enzymes and reactions, overlooking the inherent hierarchical relationships within each domain. To address these limitations, we introduce FGW-CLIP, a novel contrastive learning framework based on optimizing the fused Gromov-Wasserstein distance. FGW-CLIP incorporates multiple alignments, including inter-domain alignment between reactions and enzymes and intra-domain alignment within enzymes and reactions. By introducing a tailored regularization term, our method minimizes the Gromov-Wasserstein distance between enzyme and reaction spaces, which enhances information integration across these domains. Extensive evaluations demonstrate the superiority of FGW-CLIP in challenging enzyme-reaction tasks. On the widely-used EnzymeMap benchmark, FGW-CLIP achieves state-of-the-art performance in enzyme virtual screening, as measured by BEDROC and EF metrics. Moreover, FGW-CLIP consistently outperforms across all three splits of ReactZyme, the largest enzyme-reaction benchmark, demonstrating robust generalization to novel enzymes and reactions. These results position FGW-CLIP as a promising framework for enzyme discovery in complex biochemical settings, with strong adaptability across diverse screening scenarios.

Jiarui Ji, Yang Li, Hongtao Liu et al.

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

Jiarui Ji, Runlin Lei, Jialing Bi et al.

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.

Runlin Lei, Lu Yi, Mingguo He et al.

While Graph Neural Networks (GNNs) and Large Language Models (LLMs) are powerful approaches for learning on Text-Attributed Graphs (TAGs), a comprehensive understanding of their robustness remains elusive. Current evaluations are fragmented, failing to systematically investigate the distinct effects of textual and structural perturbations across diverse models and attack scenarios. To address these limitations, we introduce a unified and comprehensive framework to evaluate robustness in TAG learning. Our framework evaluates classical GNNs, robust GNNs (RGNNs), and GraphLLMs across ten datasets from four domains, under diverse text-based, structure-based, and hybrid perturbations in both poisoning and evasion scenarios. Our extensive analysis reveals multiple findings, among which three are particularly noteworthy: 1) models have inherent robustness trade-offs between text and structure, 2) the performance of GNNs and RGNNs depends heavily on the text encoder and attack type, and 3) GraphLLMs are particularly vulnerable to training data corruption. To overcome the identified trade-offs, we introduce SFT-auto, a novel framework that delivers superior and balanced robustness against both textual and structural attacks within a single model. Our work establishes a foundation for future research on TAG security and offers practical solutions for robust TAG learning in adversarial environments. Our code is available at: https://github.com/Leirunlin/TGRB.

Yutao Zhu, Kun Zhou, Kelong Mao et al.

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.

Tianjing Zeng, Junwei Lan, Jiahong Ma et al.

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.

Mingguo He, Zhewei Wei, Shikun Feng et al.

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.

Mingguo He, Zhewei Wei, Ji-Rong Wen

Designing spectral convolutional networks is a challenging problem in graph learning. ChebNet, one of the early attempts, approximates the spectral graph convolutions using Chebyshev polynomials. GCN simplifies ChebNet by utilizing only the first two Chebyshev polynomials while still outperforming it on real-world datasets. GPR-GNN and BernNet demonstrate that the Monomial and Bernstein bases also outperform the Chebyshev basis in terms of learning the spectral graph convolutions. Such conclusions are counter-intuitive in the field of approximation theory, where it is established that the Chebyshev polynomial achieves the optimum convergent rate for approximating a function. In this paper, we revisit the problem of approximating the spectral graph convolutions with Chebyshev polynomials. We show that ChebNet's inferior performance is primarily due to illegal coefficients learnt by ChebNet approximating analytic filter functions, which leads to over-fitting. We then propose ChebNetII, a new GNN model based on Chebyshev interpolation, which enhances the original Chebyshev polynomial approximation while reducing the Runge phenomenon. We conducted an extensive experimental study to demonstrate that ChebNetII can learn arbitrary graph convolutions and achieve superior performance in both full- and semi-supervised node classification tasks. Most notably, we scale ChebNetII to a billion graph ogbn-papers100M, showing that spectral-based GNNs have superior performance. Our code is available at https://github.com/ivam-he/ChebNetII.

Guanyu Cui, Zhewei Wei

Graph Neural Networks (GNNs) have emerged as a prominent research topic in the field of machine learning. Existing GNN models are commonly categorized into two types: spectral GNNs, which are designed based on polynomial graph filters, and spatial GNNs, which utilize a message-passing scheme as the foundation of the model. For the expressive power and universality of spectral GNNs, a natural approach is to improve the design of basis functions for better approximation ability. As for spatial GNNs, models like Graph Isomorphism Networks (GIN) analyze their expressive power based on Graph Isomorphism Tests. Recently, there have been attempts to establish connections between spatial GNNs and geometric concepts like curvature and cellular sheaves, as well as physical phenomena like oscillators. However, despite the recent progress, there is still a lack of comprehensive analysis regarding the universality of spatial GNNs from the perspectives of geometry and physics. In this paper, we propose MetricGNN (MGNN), a spatial GNN model inspired by the congruent-insensitivity property of classifiers in the classification phase of GNNs. We demonstrate that a GNN model is universal in the spatial domain if it can generate embedding matrices that are congruent to any given embedding matrix. This property is closely related to the Distance Geometry Problem (DGP). Since DGP is an NP-Hard combinatorial optimization problem, we propose optimizing an energy function derived from spring networks and the Multi-Dimensional Scaling (MDS) problem. This approach also allows our model to handle both homophilic and heterophilic graphs. Finally, we propose employing the iteration method to optimize our energy function. We extensively evaluate the effectiveness of our model through experiments conducted on both synthetic and real-world datasets. Our code is available at: https://github.com/GuanyuCui/MGNN.

Mingguo He, Zhewei Wei, Zengfeng Huang et al.

Many representative graph neural networks, e.g., GPR-GNN and ChebNet, approximate graph convolutions with graph spectral filters. However, existing work either applies predefined filter weights or learns them without necessary constraints, which may lead to oversimplified or ill-posed filters. To overcome these issues, we propose BernNet, a novel graph neural network with theoretical support that provides a simple but effective scheme for designing and learning arbitrary graph spectral filters. In particular, for any filter over the normalized Laplacian spectrum of a graph, our BernNet estimates it by an order-$K$ Bernstein polynomial approximation and designs its spectral property by setting the coefficients of the Bernstein basis. Moreover, we can learn the coefficients (and the corresponding filter weights) based on observed graphs and their associated signals and thus achieve the BernNet specialized for the data. Our experiments demonstrate that BernNet can learn arbitrary spectral filters, including complicated band-rejection and comb filters, and it achieves superior performance in real-world graph modeling tasks. Code is available at https://github.com/ivam-he/BernNet.

Yongyi Yang, Tang Liu, Yangkun Wang et al.

Despite the recent success of graph neural networks (GNN), common architectures often exhibit significant limitations, including sensitivity to oversmoothing, long-range dependencies, and spurious edges, e.g., as can occur as a result of graph heterophily or adversarial attacks. To at least partially address these issues within a simple transparent framework, we consider a new family of GNN layers designed to mimic and integrate the update rules of two classical iterative algorithms, namely, proximal gradient descent and iterative reweighted least squares (IRLS). The former defines an extensible base GNN architecture that is immune to oversmoothing while nonetheless capturing long-range dependencies by allowing arbitrary propagation steps. In contrast, the latter produces a novel attention mechanism that is explicitly anchored to an underlying end-to-end energy function, contributing stability with respect to edge uncertainty. When combined we obtain an extremely simple yet robust model that we evaluate across disparate scenarios including standardized benchmarks, adversarially-perturbated graphs, graphs with heterophily, and graphs involving long-range dependencies. In doing so, we compare against SOTA GNN approaches that have been explicitly designed for the respective task, achieving competitive or superior node classification accuracy. Our code is available at https://github.com/FFTYYY/TWIRLS.

Ming Chen, Zhewei Wei, Bolin Ding et al.

Graph Neural Networks (GNN) is an emerging field for learning on non-Euclidean data. Recently, there has been increased interest in designing GNN that scales to large graphs. Most existing methods use "graph sampling" or "layer-wise sampling" techniques to reduce training time. However, these methods still suffer from degrading performance and scalability problems when applying to graphs with billions of edges. This paper presents GBP, a scalable GNN that utilizes a localized bidirectional propagation process from both the feature vectors and the training/testing nodes. Theoretical analysis shows that GBP is the first method that achieves sub-linear time complexity for both the precomputation and the training phases. An extensive empirical study demonstrates that GBP achieves state-of-the-art performance with significantly less training/testing time. Most notably, GBP can deliver superior performance on a graph with over 60 million nodes and 1.8 billion edges in less than half an hour on a single machine. The codes of GBP can be found at https://github.com/chennnM/GBP .

Ming Chen, Zhewei Wei, Zengfeng Huang et al.

Graph convolutional networks (GCNs) are a powerful deep learning approach for graph-structured data. Recently, GCNs and subsequent variants have shown superior performance in various application areas on real-world datasets. Despite their success, most of the current GCN models are shallow, due to the {\em over-smoothing} problem. In this paper, we study the problem of designing and analyzing deep graph convolutional networks. We propose the GCNII, an extension of the vanilla GCN model with two simple yet effective techniques: {\em Initial residual} and {\em Identity mapping}. We provide theoretical and empirical evidence that the two techniques effectively relieves the problem of over-smoothing. Our experiments show that the deep GCNII model outperforms the state-of-the-art methods on various semi- and full-supervised tasks. Code is available at https://github.com/chennnM/GCNII .

Jiaqi Han, Jiacheng Cen, Liming Wu et al.

Geometric graphs are a special kind of graph with geometric features, which are vital to model many scientific problems. Unlike generic graphs, geometric graphs often exhibit physical symmetries of translations, rotations, and reflections, making them ineffectively processed by current Graph Neural Networks (GNNs). To address this issue, researchers proposed a variety of geometric GNNs equipped with invariant/equivariant properties to better characterize the geometry and topology of geometric graphs. Given the current progress in this field, it is imperative to conduct a comprehensive survey of data structures, models, and applications related to geometric GNNs. In this paper, based on the necessary but concise mathematical preliminaries, we formalize geometric graph as the data structure, on top of which we provide a unified view of existing models from the geometric message passing perspective. Additionally, we summarize the applications as well as the related datasets to facilitate later research for methodology development and experimental evaluation. We also discuss the challenges and future potential directions of geometric GNNs at the end of this survey.

Yanping Zheng, Lu Yi, Zhewei Wei

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.

Wenda Wang, Yang Zhang, Zhewei Wei et al.

Antigen-antibody binding is a critical process in the immune response. Although recent progress has advanced antibody design, current methods lack a generative framework for end-to-end modeling of full-atom antibody structures and struggle to fully exploit antigen-specific geometric information for optimizing local binding interfaces and global structures. To overcome these limitations, we introduce AbFlow, a flow-matching framework that leverages optimal transport to design full-atom antibodies end-to-end. AbFlow incorporates an extended velocity field network featuring an equivariant Surface Multi-channel Encoder, which uses surface-level antigen interaction data to refine the antibody structure, particularly the CDR-H3 region. Extensive experiments in paratoep-centric antibody design, multi-CDRs and full-atom antibody design, binding affinity optimization, and complex structure prediction show that AbFlow produces superior antigen-antibody complexes, especially at the contact interface, and markedly improves the binding affinity of generated antibodies.

Lu Yi, Jie Peng, Yanping Zheng et al.

Future link prediction is a fundamental challenge in various real-world dynamic systems. To address this, numerous temporal graph neural networks (temporal GNNs) and benchmark datasets have been developed. However, these datasets often feature excessive repeated edges and lack complex sequential dynamics, a key characteristic inherent in many real-world applications such as recommender systems and ``Who-To-Follow'' on social networks. This oversight has led existing methods to inadvertently downplay the importance of learning sequential dynamics, focusing primarily on predicting repeated edges. In this study, we demonstrate that existing methods, such as GraphMixer and DyGFormer, are inherently incapable of learning simple sequential dynamics, such as ``a user who has followed OpenAI and Anthropic is more likely to follow AI at Meta next.'' Motivated by this issue, we introduce the Temporal Graph Benchmark with Sequential Dynamics (TGB-Seq), a new benchmark carefully curated to minimize repeated edges, challenging models to learn sequential dynamics and generalize to unseen edges. TGB-Seq comprises large real-world datasets spanning diverse domains, including e-commerce interactions, movie ratings, business reviews, social networks, citation networks and web link networks. Benchmarking experiments reveal that current methods usually suffer significant performance degradation and incur substantial training costs on TGB-Seq, posing new challenges and opportunities for future research. TGB-Seq datasets, leaderboards, and example codes are available at https://tgb-seq.github.io/.

Jie Peng, Zhewei Wei, Yuhang Ye

Due to the proficiency of self-attention mechanisms (SAMs) in capturing dependencies in sequence modeling, several existing dynamic graph neural networks (DGNNs) utilize Transformer architectures with various encoding designs to capture sequential evolutions of dynamic graphs. However, the effectiveness and efficiency of these Transformer-based DGNNs vary significantly, highlighting the importance of properly defining the SAM on dynamic graphs and comprehensively encoding temporal and interactive dynamics without extra complex modules. In this work, we propose TIDFormer, a dynamic graph TransFormer that fully exploits Temporal and Interactive Dynamics in an efficient manner. We clarify and verify the interpretability of our proposed SAM, addressing the open problem of its uninterpretable definitions on dynamic graphs in previous works. To model the temporal and interactive dynamics, respectively, we utilize the calendar-based time partitioning information and extract informative interaction embeddings for both bipartite and non-bipartite graphs using merely the sampled first-order neighbors. In addition, we jointly model temporal and interactive features by capturing potential changes in historical interaction patterns through a simple decomposition. We conduct extensive experiments on several dynamic graph datasets to verify the effectiveness and efficiency of TIDFormer. The experimental results demonstrate that TIDFormer excels, outperforming state-of-the-art models across most datasets and experimental settings. Furthermore, TIDFormer exhibits significant efficiency advantages compared to previous Transformer-based methods.

Haipeng Ding, Zhewei Wei, Yuhang Ye

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).

Hanyan Yin, Dongxie Wen, Jiajun Li et al.

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.

Yuwei Hu, Xinyi Huang, Zhewei Wei et al.

Large Language Models (LLMs) for Graph Reasoning have been extensively studied over the past two years, involving enabling LLMs to understand graph structures and reason on graphs to solve various graph problems, with graph algorithm problems being the most prevalent. Recent studies underscore the potential of LLMs in handling graph reasoning tasks, but their performance is underwhelming. In this work, we point out issues with existing methods and benchmarks, and rethink the direction that LLMs for graph reasoning should strive toward. We find that base models, e.g., GPT-4o-mini, are largely underestimated due to improper reasoning focus. Base models with reasoning focus redirected from replicating graph algorithms to designing them can easily solve most graph reasoning tasks in existing benchmarks. To truly evaluate the graph reasoning capabilities of LLMs, we construct a more challenging GraphAlgorithm benchmark, comprising 239 different graph problems and 3,041 test instances collected from 4 competition platforms. Finally, we introduce a simple and strong baseline Simple-Reasoning-Then-Coding (Simple-RTC)-which guides LLMs to design graph algorithms first and then code to address graph reasoning tasks. Simple-RTC achieves near-perfect accuracy on existing benchmarks and significantly outperforms GPT-4o-mini and all prior methods on the GraphAlgorithm benchmark. This strong baseline encourages further advancements in LLMs for Graph Reasoning in the future.

Yule Li, Yifeng Lu, Zhen Wang et al.

In recent years, graph neural networks (GNN) have achieved unprecedented successes in node classification tasks. Although GNNs inherently encode specific inductive biases (e.g., acting as low-pass or high-pass filters), most existing methods implicitly assume conditional independence among node labels in their optimization objectives. While this assumption is suitable for traditional classification tasks such as image recognition, it contradicts the intuitive observation that node labels in graphs remain correlated, even after conditioning on the graph structure. To make structured predictions for node labels, we propose ReDiSC, namely, Reparameterized masked Diffusion model for Structured node Classification. ReDiSC estimates the joint distribution of node labels using a reparameterized masked diffusion model, which is learned through the variational expectation-maximization (EM) framework. Our theoretical analysis shows the efficiency advantage of ReDiSC in the E-step compared to DPM-SNC, a state-of-the-art model that relies on a manifold-constrained diffusion model in continuous domain. Meanwhile, we explicitly link ReDiSC's M-step objective to popular GNN and label propagation hybrid approaches. Extensive experiments demonstrate that ReDiSC achieves superior or highly competitive performance compared to state-of-the-art GNN, label propagation, and diffusion-based baselines across both homophilic and heterophilic graphs of varying sizes. Notably, ReDiSC scales effectively to large-scale datasets on which previous structured diffusion methods fail due to computational constraints, highlighting its significant practical advantage in structured node classification tasks.

Jie Peng, Jiarui Ji, Runlin Lei et al.

Dynamic Text-Attributed Graphs (DyTAGs), which intricately integrate structural, temporal, and textual attributes, are crucial for modeling complex real-world systems. However, most of the existing DyTAG datasets exhibit poor textual quality, which severely limits their utility for DyTAG generation tasks requiring semantically rich inputs. Additionally, prior work mainly focuses on discriminative tasks on DyTAGs, resulting in a lack of standardized task formulations and evaluation protocols tailored for DyTAG generation. To address these critical issues, we propose Generative DyTAG Benchmark (GDGB), which comprises eight meticulously curated DyTAG datasets with high-quality textual features for both nodes and edges, overcoming limitations of prior datasets. Building on GDGB, we define two novel DyTAG generation tasks: Transductive Dynamic Graph Generation (TDGG) and Inductive Dynamic Graph Generation (IDGG). TDGG transductively generates a target DyTAG based on the given source and destination node sets, while the more challenging IDGG introduces new node generation to inductively model the dynamic expansion of real-world graph data. To enable holistic evaluation, we design multifaceted metrics that assess the structural, temporal, and textual quality of the generated DyTAGs. We further propose GAG-General, an LLM-based multi-agent generative framework tailored for reproducible and robust benchmarking of DyTAG generation. Experimental results demonstrate that GDGB enables rigorous evaluation of TDGG and IDGG, with key insights revealing the critical interplay of structural and textual features in DyTAG generation. These findings establish GDGB as a foundational resource for advancing generative DyTAG research and unlocking further practical applications in DyTAG generation. GDGB datasets, source codes, and leaderboards are available at \href{https://gdgb-algo.github.io/}{here}.

Runlin Lei, Jiarui Ji, Haipeng Ding et al.

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.

Dongxie Wen, Hanyan Yin, Xiao Zhang et al.

The utilization of sketching techniques has progressively emerged as a pivotal method for enhancing the efficiency of online learning. In linear bandit settings, current sketch-based approaches leverage matrix sketching to reduce the per-round time complexity from \(Ω\left(d^2\right)\) to \(O(d)\), where \(d\) is the input dimension. Despite this improved efficiency, these approaches encounter critical pitfalls: if the spectral tail of the covariance matrix does not decrease rapidly, it can lead to linear regret. In this paper, we revisit the regret analysis and algorithm design concerning approximating the covariance matrix using matrix sketching in linear bandits. We illustrate how inappropriate sketch sizes can result in unbounded spectral loss, thereby causing linear regret. To prevent this issue, we propose Dyadic Block Sketching, an innovative streaming matrix sketching approach that adaptively manages sketch size to constrain global spectral loss. This approach effectively tracks the best rank-\( k \) approximation in an online manner, ensuring efficiency when the geometry of the covariance matrix is favorable. Then, we apply the proposed Dyadic Block Sketching to linear bandits and demonstrate that the resulting bandit algorithm can achieve sublinear regret without prior knowledge of the covariance matrix, even under the worst case. Our method is a general framework for efficient sketch-based linear bandits, applicable to all existing sketch-based approaches, and offers improved regret bounds accordingly. Additionally, we conduct comprehensive empirical studies using both synthetic and real-world data to validate the accuracy of our theoretical findings and to highlight the effectiveness of our algorithm.

Jie Peng, Rui Wang, Qiang Wang et al.

Information cascade popularity prediction is a key problem in analyzing content diffusion in social networks. However, current related works suffer from three critical limitations: (1) temporal leakage in current evaluation--random cascade-based splits allow models to access future information, yielding unrealistic results; (2) feature-poor datasets that lack downstream conversion signals (e.g., likes, comments, or purchases), which limits more practical applications; (3) computational inefficiency of complex graph-based methods that require days of training for marginal gains. We systematically address these challenges from three perspectives: task setup, dataset construction, and model design. First, we propose a time-ordered splitting strategy that chronologically partitions data into consecutive windows, ensuring models are evaluated on genuine forecasting tasks without future information leakage. Second, we introduce Taoke, a large-scale e-commerce cascade dataset featuring rich promoter/product attributes and ground-truth purchase conversions--capturing the complete diffusion lifecycle from promotion to monetization. Third, we develop CasTemp, a lightweight framework that efficiently models cascade dynamics through temporal walks, Jaccard-based neighbor selection for inter-cascade dependencies, and GRU-based encoding with time-aware attention. Under leak-free evaluation, CasTemp achieves state-of-the-art performance across four datasets with orders-of-magnitude speedup. Notably, it excels at predicting second-stage popularity conversions--a practical task critical for real-world applications.

Yanping Zheng, Zhewei Wei, Frank de Hoog et al.

Graph Neural Networks (GNNs) have demonstrated remarkable effectiveness in recommendation systems. However, conventional graph-based recommenders, such as LightGCN, require maintaining embeddings of size $d$ for each node, resulting in a parameter complexity of $\mathcal{O}(n \times d)$, where $n$ represents the total number of users and items. This scaling pattern poses significant challenges for deployment on large-scale graphs encountered in real-world applications. To address this scalability limitation, we propose \textbf{Lighter-X}, an efficient and modular framework that can be seamlessly integrated with existing GNN-based recommender architectures. Our approach substantially reduces both parameter size and computational complexity while preserving the theoretical guarantees and empirical performance of the base models, thereby enabling practical deployment at scale. Specifically, we analyze the original structure and inherent redundancy in their parameters, identifying opportunities for optimization. Based on this insight, we propose an efficient compression scheme for the sparse adjacency structure and high-dimensional embedding matrices, achieving a parameter complexity of $\mathcal{O}(h \times d)$, where $h \ll n$. Furthermore, the model is optimized through a decoupled framework, reducing computational complexity during the training process and enhancing scalability. Extensive experiments demonstrate that Lighter-X achieves comparable performance to baseline models with significantly fewer parameters. In particular, on large-scale interaction graphs with millions of edges, we are able to attain even better results with only 1\% of the parameter over LightGCN.