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Zhewei Wei

Publications and source records attributed to Zhewei Wei.

At least 19 recordsLinked to original sources
arXiv2026

A Simple Active-Set Method for PageRank-Based Local Graph Clustering

Local graph clustering aims to find a well-connected cluster near a given seed node without exploring the entire graph. A key step in the classic local clustering algorithm of Andersen, Chung, and Lang (ACL; Internet Math. 2007) is to approximate the PageRank vector from the seed node. Their local push method computes an ACL $\varepsilon$-approximate PageRank vector with teleportation parameter $\alpha$ in $O\bigl(1/(\alpha\varepsilon)\bigr)$ time. We give an algorithm that computes an ACL $\varepsilon$-approximate PageRank vector in $\widetilde{O}\bigl(1 / \varepsilon^2\bigr)$ time with high probability. This bound is independent of the graph size and has only a polylogarithmic dependence on $1 / \alpha$, albeit with a quadratic dependence on $1 / \varepsilon$. As a direct consequence, we obtain a new running-time tradeoff between the target conductance and target volume in local graph clustering. Our method also applies to the optimization problem of $\ell_1$-regularized PageRank and computes an additive approximate minimizer with a polylogarithmic dependence on $1/\alpha$, improving the $1/\sqrt{\alpha}$ dependence in the previous bound of Mart\'inez-Rubio, Wirth, and Pokutta (COLT 2023). Our algorithm is based on an intuitive process that maintains a growing active set of nodes: it performs push operations on the current set until convergence and then expands the set and repeats the process if necessary. We show that for each active set, the corresponding limiting state is the solution to a symmetric diagonally dominant (SDD) linear system on the set. We apply nearly-linear-time SDD solvers to these systems and prove that the approximation preserves the properties of the push process.

cs.DS↗
arXiv2026

From Atomic Actions to Standard Operating Procedures: Iterative Tool Optimization for Self-Evolving LLM Agents

Tool utilization enables Large Language Model (LLM) agents to interact with the real world and resolve complex tasks. However, existing agent frameworks predominantly rely on static toolsets composed of granular atomic actions (e.g., basic file I/O or single-turn search), which forces agents to reinvent low-level logic for every recurring workflow, leading to increased reasoning overhead and failure rates. In this study, we propose that agents can achieve self-evolution by synthesizing these atomic actions into reusable Standard Operating Procedures (SOPs), which function as callable higher-order tools that encapsulate multi-step logic. We further introduce EvoSOP, a framework that empowers agents to extract SOPs from execution trajectories and iteratively optimize the toolset through a systematic lifecycle of construction, merging, evaluation, and pruning. Extensive experiments demonstrate that EvoSOP significantly boosts task success rates while substantially reducing the number of interaction rounds compared to baselines. Our analysis also reveals that iterative tool optimization fosters reliable and efficient tool-use patterns, providing a scalable pathway for the development of self-evolving agents.

cs.AI↗
arXiv2026

Back to Basics: Improving Molecular Understanding in LLMs via SMILES-Graph Translation

Recent advances in molecular large language models have led to strong performance on molecular understanding and generation tasks, yet these gains often come without reliable structural grounding. In particular, existing approaches conflict with the chemistry principle that structure determines function: despite their downstream success, current molecular LLMs perform poorly on basic structure recognition, suggesting that they fail to capture molecular graphs from canonical SMILES. To remedy this, we propose MolBasic, a structure-first framework that strengthens structural comprehension via SMILES-Graph translation. MolBasic is built around a multi-level structure perception benchmark, where bidirectional SMILES-Graph conversion serves as the core task to align sequential and topological representations. On top of this foundation, we employ a progressive learning scheme with a standardized Chain-of-Thought (CoT) to steer models from structure acquisition toward higher-level molecular reasoning. Experiments show that MolBasic substantially improves structural understanding and yields robust gains on downstream tasks, including property prediction and objective optimization, supporting our structure-first paradigm.

cs.LG↗
arXiv2026

MolSight: A Graph-Aware Vision-Language Model for Unified Chemical Image Understanding

Using molecular large language models (LLMs) as a unified framework for understanding molecular structures and functions is emerging as a new trend in tasks such as molecular design and drug discovery. However, these models struggle to fully capture the visual representation of molecular structures, limiting their potential. While existing molecular vision-language models (VLMs) show promise, they still face challenges in structural alignment and lack the necessary topological modeling for accurate molecular understanding. To address this, we propose MolSight, a graph-aware vision-language model framework designed to enhance the understanding of molecular images by VLMs. MolSight integrates a Molecular Topology Module to inject chemical-bond adjacency information into vision tokens, and a Molecular Grounding Module to align visual features with chemical symbolic semantics. Our experiments demonstrate that MolSight significantly outperforms existing VLMs, molecular LLMs, and task-specific models across multiple chemical visual understanding tasks, achieving a new level of molecular image reasoning in complex chemical scenarios.

cs.CV↗
arXiv2026

Visual Graph Scaffolds for Structural Reasoning in Large Language Models

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.

cs.AI↗
arXiv2026

Learning Agent-Compatible Context Management for Long-Horizon Tasks

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.

cs.AI↗
arXiv2026

Position: The Turing-Completeness of Autoregressive Transformers Relies Heavily on Context Management

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.

cs.AI↗
arXiv2026

FuseDiff: Symmetry-Preserving Joint Diffusion for Dual-Target Structure-Based Drug Design

Dual-target structure-based drug design aims to generate a single ligand together with two pocket-specific binding poses, each compatible with a corresponding target pocket, enabling polypharmacological therapies with improved efficacy and reduced resistance. Existing approaches typically rely on staged pipelines, which either decouple the two poses via conditional-independence assumptions or enforce overly rigid correlations, and therefore fail to jointly generate two target-specific binding modes. To address this, we propose FuseDiff, an end-to-end diffusion model that jointly generates a ligand molecular graph and two pocket-specific binding poses conditioned on both pockets. FuseDiff features a message-passing backbone with Dual-target Local Context Fusion (DLCF), which fuses each ligand atom's local context from both pockets to enable expressive joint modeling while preserving the desired symmetries. Together with explicit bond generation, FuseDiff enforces topological consistency across the two poses under a shared graph while allowing target-specific geometric adaptation in each pocket. To support principled training and evaluation, we derive a dual-target training set and use an independent held-out test set for evaluation. Experiments on the benchmark and a real-world dual-target system show that FuseDiff achieves state-of-the-art docking performance and enables the first systematic assessment of dual-target pose quality prior to docking-based pose search.

cs.LG↗
arXiv2026

Large Language Model-Enhanced Relational Operators: Taxonomy, Benchmark, and Analysis

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/.

cs.DB↗
arXiv2026

AbFlow : End-to-end Paratope-Centric Antibody Design by Interaction Enhanced Flow Matching

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.

q-bio.QM↗
arXiv2026

AeroSketch: Near-Optimal Time Matrix Sketch Framework for Persistent, Sliding Window, and Distributed Streams

Many real-world matrix datasets arrive as high-throughput vector streams, making it impractical to store or process them in their entirety. To enable real-time analytics under limited computational, memory, and communication resources, matrix sketching techniques have been developed over recent decades to provide compact approximations of such streaming data. Some algorithms have achieved optimal space and communication complexity. However, these approaches often require frequent time-consuming matrix factorization operations. In particular, under tight approximation error bounds, each matrix factorization computation incurs cubic time complexity, thereby limiting their update efficiency. In this paper, we introduce AeroSketch, a novel matrix sketching framework that leverages recent advances in randomized numerical linear algebra (RandNLA). AeroSketch achieves optimal communication and space costs while delivering near-optimal update time complexity (within logarithmic factors) across persistent, sliding window, and distributed streaming scenarios. Extensive experiments on both synthetic and real-world datasets demonstrate that AeroSketch consistently outperforms state-of-the-art methods in update throughput. In particular, under tight approximation error constraints, AeroSketch reduces the cubic time complexity to the quadratic level. Meanwhile, it maintains comparable approximation quality while retaining optimal communication and space costs.

cs.DB↗
arXiv2025

Multi-Alignment Contrastive Learning for Enzyme--Reaction Retrieval

Identifying enzymes that catalyze target biochemical reactions is a key step in computational enzyme discovery and biocatalyst design. Recent representation-learning methods formulate this problem as enzyme--reaction matching, where paired enzymes and reactions are embedded into a shared space. However, most existing approaches primarily rely on pairwise enzyme--reaction supervision and make limited use of the relationships within reaction sets or enzyme families. This work introduces a multi-alignment contrastive learning framework for biochemical retrieval. The framework jointly models cross-domain compatibility between enzymes and reactions and within-domain relationships induced by functional annotations. In addition, a Gromov--Wasserstein-inspired regularization objective encourages geometric consistency between the learned enzyme and reaction representation spaces. By combining pairwise catalytic supervision with higher-order relational alignment, the model captures both direct enzyme--reaction associations and broader functional organization. We evaluate the approach on enzyme virtual screening and bidirectional enzyme--reaction retrieval tasks. Experiments on EnzymeMap show improved early-recognition performance under BEDROC and enrichment-factor metrics compared with strong contrastive baselines. On ReactZyme, the method achieves consistent gains across time-based, enzyme-similarity, and reaction-similarity splits, demonstrating robustness to unseen enzymes and unseen reactions. Ablation studies further indicate that within-domain alignment, functional supervision, and the geometric regularization term each contribute to the observed improvements. These results suggest that modeling multiple forms of alignment can improve contrastive retrieval models for enzyme discovery, reaction annotation, and related computational biology applications.

q-bio.BM↗
arXiv2025

Leveraging LLM-based agents for social science research: insights from citation network simulations

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.

physics.soc-ph↗
arXiv2025

From Leakage to Fidelity: Reliable Benchmarking for Temporal Cascade Prediction

Temporal cascade prediction is widely studied, yet its empirical foundations remain fragile. Most existing works report results under random cascade splits that mix past and future signals, rely on datasets with limited features and no downstream conversion labels, and compare increasingly complex models without systematically examining whether benchmark conclusions are protocol-dependent. This paper argues that the field should move from leakage-prone evaluation toward fidelity-aware benchmarking. We introduce a protocol suite and renewed evaluation standard for temporal cascade prediction, centered on the Full Temporal protocol, overlap-based leakage diagnostics, and analyses of performance inflation and temporal drift. To broaden the scope of benchmark tasks, we also present Taoke, a real-world e-commerce cascade dataset with rich promoter/product features and observed purchase conversions, enabling both first-stage popularity forecasting and second-stage conversion forecasting under a shared benchmark asset. Finally, we include CasTemp as a lightweight reference method and additionally probe a larger same-task internal extension to verify that this pipeline remains operational at substantially greater scale. Together, these components turn cascade prediction from a protocol-sensitive leaderboard exercise into a more reliable analysis and benchmarking problem, while still providing a practical reference pipeline for large-scale evaluation and conversion-aware modeling.

cs.LG↗
arXiv2025

GRAPHIA: Harnessing Social Graph Data to Enhance LLM-Based Social Simulation

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.

cs.SI↗
arXiv2025

Robustness in Text-Attributed Graph Learning: Insights, Trade-offs, and New Defenses

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.

cs.LG↗
arXiv2025

Lighter-X: An Efficient and Plug-and-play Strategy for Graph-based Recommendation through Decoupled Propagation

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.

cs.LG↗
arXiv2025

Rethinking and Benchmarking Large Language Models for Graph Reasoning

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.

cs.AI↗