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Dongyuan Li

Publications and source records attributed to Dongyuan Li.

At least 19 recordsLinked to original sources
arXiv2026

BrainLinear: A Linear Model for Brain Network Analysis in Sparse Tangent Subspaces

Functional connectome analysis examines brain-region interactions to understand and identify disorders such as autism spectrum disorder and Alzheimer's disease. Existing methods typically use GNNs and Transformers to model the full functional connectivity matrix. However, processing tens of thousands of connections introduces redundancy and noise, increases computational cost, and limits connection-level interpretability. This raises a central question: do we really need complex interaction modeling, or is identifying a small set of disease-relevant connectivity patterns sufficient? To answer this question, we propose BrainLinear, a lightweight geometry-aware framework for mining disease-discriminative connectome patterns. BrainLinear first maps each functional connectivity matrix to a shared tangent space centered at the Fréchet mean of the training set, capturing subject-specific deviations while respecting matrix geometry. It then scores each ROI-pair tangent direction by its classification contribution and disease--control difference, retaining Top-$K$ directions as a compact representation. Finally, a shallow multilayer perceptron performs classification on the selected representation. Experiments on ABIDE and ADNI show that BrainLinear matches or exceeds strong GNN and Transformer baselines at a fraction of their cost: it improves AUC and ACC over the best baseline for each metric by up to $3.54$ and $1.39$ percentage points, while reducing runtime and peak GPU memory by $84.0\%$ and $68.4\%$ relative to the closest baseline in AUC. The selected directions are directionally consistent with between-group displacements and organized across major functional systems, supporting connection-level interpretation.

cs.GR↗
arXiv2026

HarnessSafe: Evaluating Safety Across Persistent Carriers in Agent Harnesses

Modern agent harnesses persist state across tasks and sessions through persistent carriers like memory, skills, tools, and shared artifacts. However, this capability creates delayed safety risks: attacker-influenced content can cross system boundaries and later affect the execution of a benign request. Existing benchmarks typically focus on a few carriers or harnesses, while end-to-end attack-success rates reveal little about how risks propagate. To this end, we present HarnessSafe, a benchmark comprising 328 executable cases across seven persistent-carrier families and evaluated on most mainstream agent harnesses. Each case is specified as a Persistent-Risk Lifecycle that traces attacker influence from its initial entry, through persistence across carriers and system boundaries, to a later benign trigger and an observable violation. We further introduce a multi-stage, trace-based evaluation that uses observable execution evidence to determine how far each attack chain progresses and where it is stopped. Experiments show that containment is carrier-specific and strongly depends on the harness-model configuration. Both the harness and model backend substantially shape containment outcomes, while attack success rates cannot reflect distinct lifecycle progression patterns.

cs.CR↗
arXiv2026

Can LLM design high-quality experiments? A Comprehensive and Systematic Benchmark on Autonomous Experimental Design

AI for Research (AI4Research) leverages AI to automate and improve scientific workflows. While experimental design is a critical stage of the research process, prior work has focused primarily on code implementation and execution, overlooking the importance of this stage, and no benchmark exists to evaluate AI's ability to conduct systematic experiment design. To bridge this gap, we propose SCOPE, a Scientific COmprehensive Planning Evaluation Benchmark constructed from 300 high-quality latest papers across 19 research domains from top-tier venues (e.g., ICML, NeurIPS, and ICLR),evaluating LLMs on two dimensions: High-Level planning completeness (main, ablation, and analysis experiments) and Low-Level configuration accuracy and rationality (datasets, baselines, and metrics). Benchmarking reveals three findings: (1) most LLMs cannot directly design high-quality experiments; (2) all LLMs exhibit a performance bottleneck in low-level configuration; and (3) search mode does not improve design quality. Furthermore, to address these challenges, we propose OptED, a novel agentic workflow to optimize LLM-based experimental design, that enhances LLM-based experimental planning through stage isolation, tool augmentation, and rule-based constraints, effectively alleviating the configuration bottleneck.

cs.AI↗
arXiv2026

HAS-Bench: Evaluating LLM-Based Human-Agent Systems under Configurable Human Participation

Large language models increasingly operate in settings where humans are active collaborators rather than passive task providers. We introduce HAS-Framework, a graph-based framework that represents humans and LLM-powered agents as first-class participants with explicit roles, permissions, communication paths, and action authority. Building on this framework, HAS-Bench evaluates Human-Agent Systems under configurable human participation across agency levels, interaction channels, and persona policies. The benchmark measures both task outcomes and process-level collaboration behavior, including clarification quality, feedback utilization, control calibration, safety, initiative, and interaction cost. Experiments across six domains show that human participation can substantially improve task completion and failure recovery, but the gains depend on when, how, and by whom human input is exercised.

cs.AI↗
arXiv2026

PaperClaw: Harnessing Agents for Autonomous Research and Human-in-the-Loop Refinement

Large language models have become capable reasoners and tool users that write and run code and search the literature, which makes automating the research process itself a realistic goal. We present PAPERCLAW, a harnessed multi-agent system that carries a project autonomously, from a field of study to a finished paper. PAPERCLAW curates a domain from a field's live literature, datasets, and code; brainstorms it into an idea with a pre-registered main-result contract; and drives a stoppable hypothesis map through an iterative propose, test, reflect loop that grows only from measured verdicts and halts once the evidence supports the idea, at which point it writes a venue-compliant paper. A full-lifecycle memory keeps each stage in a single living record, so a long run can be paused, inspected, and resumed without losing context. At the centre is an in-cycle research assistant with research tools and skills: it can drive the whole pipeline on its own, while the same interface lets a person step in at any stage, turning a first autonomous draft into a stronger paper through human-in-the-loop refinement. Throughout, PAPERCLAW keeps its output grounded and checkable, citing only references validated against open scholarly indexes and reporting results that genuinely ran. An evaluation with an LLM judge finds that PAPERCLAW produces strong papers both fully autonomously and with human-in-the-loop refinement.

cs.AI↗
arXiv2026

Understanding Fact Recall in Language Models: Why Two-Stage Training Encourages Memorization but Mixed Training Teaches Knowledge

While fine-tuning is the standard for injecting factual knowledge into large language models (LLMs), the mechanisms enabling reliable fact recall via unseen queries remain poorly understood. Common two-stage training strategies, which sequentially train on fact storage and query formats, often cause rote memorization. In contrast, mixed training jointly optimizes both formats and exhibits superior generalized recall. We investigate this success by comparing the two paradigms across 2.8$\sim$4B LLMs and identify the core mechanism: the joint optimization objective in mixed training induces gradient consistency across storage and query formats. This in turn drives the representation consistency between the two formats, establishing a format-invariant retrieval process that maps unseen queries to stored facts. In contrast, the lack of such an objective in two-stage training results in inconsistent representations and failed recall. The consistency further localizes to the parameters updated by both formats, a set that is substantially larger under mixed training than under two-stage training. At the input level, the consistency leaves an interpretable signature: mixed training encodes facts in storage format from subject-relation tokens, the same components available in queries, while two-stage training relies on the full context. Our findings characterize the mechanisms of fact recall and offer mechanistic foundation for optimizing knowledge injection in LLMs.

cs.CL↗
arXiv2026

Event-Aware Prompt Learning for Dynamic Graphs

Real-world graph typically evolve via a series of events, modeling dynamic interactions between objects across various domains. For dynamic graph learning, dynamic graph neural networks (DGNNs) have emerged as popular solutions. Recently, prompt learning methods have been explored on dynamic graphs. However, existing methods generally focus on capturing the relationship between nodes and time, while overlooking the impact of historical events. In this paper, we propose EVP, an event-aware dynamic graph prompt learning framework that can serve as a plug-in to existing methods, enhancing their ability to leverage historical events knowledge. First, we extract a series of historical events for each node and introduce an event adaptation mechanism to align the fine-grained characteristics of these events with downstream tasks. Second, we propose an event aggregation mechanism to effectively integrate historical knowledge into node representations. Finally, we conduct extensive experiments on four public datasets to evaluate and analyze EVP.

cs.LG↗
arXiv2026

TimeClaw: A Time-Series AI Agent with Exploratory Execution Learning

Time series analysis underpins forecasting, monitoring, and decision making in domains such as finance and weather, where solving a task often requires both numerical accuracy and contextual reasoning. Recent progress has moved from specialized neural predictors to approaches built on LLMs and foundation models that can reason over time series inputs and use external tools. However, most such systems remain execution-centric: they focus on solving the current instance but learn little from exploratory execution. This is especially limiting in verifiable numeric settings, where multiple candidate executions and tool-use procedures may all be task-valid yet differ sharply in quantitative quality, and where early success can trigger tool-prior collapse that suppresses further exploration. To address this limitation, we present TimeClaw, an exploratory execution learning framework that turns exploratory execution into reusable hierarchical distilled experience through a four-stage loop: Explore, Compare, Distill, and Reinject. TimeClaw combines metric-supervised exploratory execution learning, task-aware tool dropout, and hierarchical distilled experience for inference-time reinjection, while keeping the base model frozen and avoiding online test-time adaptation. In an MTBench-aligned evaluation with 17 tasks that span finance and weather prediction and reasoning tasks, TimeClaw delivers consistent gains over the baselines. These results suggest that, for scientific systems, the bottleneck is not only execution-time capability, but how exploratory experience is compared, distilled, and reused.

cs.AI↗
arXiv2026

LLM-Based Human-Agent Collaboration and Interaction Systems: A Survey

Recent advances in large language models (LLMs) have sparked growing interest in building fully autonomous agents. However, fully autonomous LLM-based agents still face significant challenges, including limited reliability due to hallucinations, difficulty in handling complex tasks, and substantial safety and ethical risks, all of which limit their feasibility and trustworthiness in real-world applications. To overcome these limitations, LLM-based human-agent systems (LLM-HAS) incorporate human-provided information, feedback, or control into the agent system to enhance system performance, reliability, and safety. These human-agent collaboration systems enable humans and LLM-based agents to collaborate effectively by leveraging their complementary strengths. This paper provides the first comprehensive and structured survey of LLM-HAS. It clarifies fundamental concepts, systematically presents core components shaping these systems, including environment and profiling, human feedback, interaction types, orchestration, and communication, explores emerging applications, and discusses unique challenges and opportunities arising from human-AI collaboration. By consolidating current knowledge and offering a structured overview, we aim to foster further research and innovation in this rapidly evolving interdisciplinary field. Paper lists and resources are available at https://github.com/HenryPengZou/Awesome-Human-Agent-Collaboration-Interaction-Systems.

cs.CL↗
arXiv2026

See2Refine: Vision-Language Feedback Improves LLM-Based eHMI Action Designers

Automated vehicles lack natural communication channels with other road users, making external Human-Machine Interfaces (eHMIs) essential for conveying intent and maintaining trust in shared environments. However, most eHMI studies rely on developer-crafted message-action pairs, which are difficult to adapt to diverse and dynamic traffic contexts. A promising alternative is to use Large Language Models (LLMs) as action designers that generate context-conditioned eHMI actions, yet such designers lack perceptual verification and typically depend on fixed prompts or costly human-annotated feedback for improvement. We present See2Refine, a human-free, closed-loop framework that uses vision-language model (VLM) perceptual evaluation as automated visual feedback to improve an LLM-based eHMI action designer. Given a driving context and a candidate eHMI action, the VLM evaluates the perceived appropriateness of the action, and this feedback is used to iteratively revise the designer's outputs, enabling systematic refinement without human supervision. We evaluate our framework across three eHMI modalities (lightbar, eyes, and arm) and multiple LLM model sizes. Across settings, our framework consistently outperforms prompt-only LLM designers and manually specified baselines in both VLM-based metrics and human-subject evaluations. Results further indicate that the improvements generalize across modalities and that VLM evaluations are well aligned with human preferences, supporting the robustness and effectiveness of See2Refine for scalable action design.

cs.HC↗
arXiv2026

Routing Channel-Patch Dependencies in Time Series Forecasting with Graph Spectral Decomposition

Time series forecasting has attracted significant attention in the field of AI. Previous works have revealed that the Channel-Independent (CI) strategy improves forecasting performance by modeling each channel individually, but it often suffers from poor generalization and overlooks meaningful inter-channel interactions. Conversely, Channel-Dependent (CD) strategies aggregate all channels, which may introduce irrelevant information and lead to oversmoothing. Despite recent progress, few existing methods offer the flexibility to adaptively balance CI and CD strategies in response to varying channel dependencies. To address this, we propose a generic plugin xCPD, that can adaptively model the channel-patch dependencies from the perspective of graph spectral decomposition. Specifically, xCPD first projects multivariate signals into the frequency domain using a shared graph Fourier basis, and groups patches into low-, mid-, and high-frequency bands based on their spectral energy responses. xCPD then applies a channel-adaptive routing mechanism that dynamically adjusts the degree of inter-channel interaction for each patch, enabling selective activation of frequency-specific experts. This facilitates fine-grained input-aware modeling of smooth trends, local fluctuations, and abrupt transitions. xCPD can be seamlessly integrated on top of existing CI and CD forecasting models, consistently enhancing both accuracy and generalization across benchmarks. The code is available https://github.com/Clearloveyuan/xCPD.

cs.LG↗
arXiv2026

Node Role-Guided LLMs for Dynamic Graph Clustering

Dynamic graph clustering aims to detect and track time-varying clusters in dynamic graphs, revealing how complex real-world systems evolve over time. However, existing methods are predominantly black-box models. They lack interpretability in their clustering decisions and fail to provide semantic explanations of why clusters form or how they evolve, severely limiting their use in safety-critical domains such as healthcare or transportation. To address these limitations, we propose an end-to-end interpretable framework that maps continuous graph embeddings into discrete semantic concepts through learnable prototypes. Specifically, we first decompose node representations into orthogonal role and clustering subspaces, so that nodes with similar roles (e.g., hubs, bridges) but different cluster affiliations can be properly distinguished. We then introduce five node role prototypes (Leader, Contributor, Wanderer, Connector, Newcomer) in the role subspace as semantic anchors, transforming continuous embeddings into discrete concepts to facilitate LLM understanding of node roles within communities. Finally, we design a hierarchical LLM reasoning mechanism to generate both clustering results and natural language explanations, while providing consistency feedback as weak supervision to refine node representations. Experimental results on four synthetic and six real-world benchmarks demonstrate the effectiveness, interpretability, and robustness of DyG-RoLLM. Code is available at https://github.com/Clearloveyuan/DyG-RoLLM.

cs.LG↗
arXiv2026

ELLMob: Event-Driven Human Mobility Generation with Self-Aligned LLM Framework

Human mobility generation aims to synthesize plausible trajectory data, which is widely used in urban system research. While Large Language Model-based methods excel at generating routine trajectories, they struggle to capture deviated mobility during large-scale societal events. This limitation stems from two critical gaps: (1) the absence of event-annotated mobility datasets for design and evaluation, and (2) the inability of current frameworks to reconcile competitions between users' habitual patterns and event-imposed constraints when making trajectory decisions. This work addresses these gaps with a twofold contribution. First, we construct the first event-annotated mobility dataset covering three major events: Typhoon Hagibis, COVID-19, and the Tokyo 2021 Olympics. Second, we propose ELLMob, a self-aligned LLM framework that first extracts competing rationales between habitual patterns and event constraints, based on Fuzzy-Trace Theory, and then iteratively aligns them to generate trajectories that are both habitually grounded and event-responsive. Extensive experiments show that ELLMob wins state-of-the-art baselines across all events, demonstrating its effectiveness. Our codes and datasets are available at https://github.com/deepkashiwa20/ELLMob.

cs.LG↗
arXiv2026

Deep Research with Open-Domain Evaluation and Multi-Stage Guardrails for Safety

Deep research frameworks have shown promising capabilities in synthesizing comprehensive reports from web sources. While deep research possesses significant potential to address complex issues through planning and research cycles, existing frameworks are deficient in sufficient evaluation procedures and stage-specific protections. They typically treat evaluation as exact match accuracy of question-answering, but overlook crucial aspects of report quality such as credibility, coherence, breadth, depth, and safety. This oversight may result in hazardous or malicious sources being integrated into the final report. To address this, we introduce DeepResearchGuard, a framework featuring four-stage safeguards with open-domain evaluation, and DRSafeBench, a novel stage-wise safety benchmark. Evaluating across GPT-4o, o4-mini, Gemini-2.5-flash, DeepSeek-v3, GPT-5, DeepResearchGuard improves defense success rates by 16.53% while reducing over-refusal to 6%. Through extensive experiments, we show that DRSafeBench enables comprehensive open-domain evaluation and stage-aware defenses that effectively block harmful content propagation, while systematically improving report quality without excessive over-refusal rates.

cs.CL↗
arXiv2025

DyG-Mamba: Continuous State Space Modeling on Dynamic Graphs

Dynamic graph modeling aims to uncover evolutionary patterns in real-world systems, enabling accurate social recommendation and early detection of cancer cells. Inspired by the success of recent state space models in efficiently capturing long-term dependencies, we propose DyG-Mamba by translating dynamic graph modeling into a long-term sequence modeling problem. Specifically, inspired by Ebbinghaus' forgetting curve, we treat the irregular timespans between events as control signals, allowing DyG-Mamba to dynamically adjust the forgetting of historical information. This mechanism ensures effective usage of irregular timespans, thereby improving both model effectiveness and inductive capability. In addition, inspired by Ebbinghaus' review cycle, we redefine core parameters to ensure that DyG-Mamba selectively reviews historical information and filters out noisy inputs, further enhancing the model's robustness. Through exhaustive experiments on 12 datasets covering dynamic link prediction and node classification tasks, we show that DyG-Mamba achieves state-of-the-art performance on most datasets, while demonstrating significantly improved computational and memory efficiency. Code is available at https://github.com/Clearloveyuan/DyG-Mamba.

cs.LG↗
arXiv2025

Do MLLMs Really Understand the Charts?

Although Multimodal Large Language Models (MLLMs) have demonstrated increasingly impressive performance in chart understanding, most of them exhibit alarming hallucinations and significant performance degradation when handling non-annotated charts. We argue that current MLLMs rely largely on visual recognition rather than visual reasoning to interpret the charts, and visual estimation of numerical values is one of the most fundamental capabilities in chart understanding that require complex visual reasoning. To prove this, we introduce ChartVRBench, a benchmark meticulously designed to isolate and evaluate visual reasoning ability in chart understanding. Furthermore, we propose ChartVR-3B/7B trained with a novel Visual Reasoning Reinforcement Finetuning (VR-RFT) strategy to strengthen genuine chart visual reasoning abilities. Extensive experiments show that ChartVR achieves superior performance on ChartVRBench, outperforming even powerful proprietary models. Moreover, the visual reasoning skills cultivated by the proposed VR-RFT demonstrate strong generalization, leading to significant performance gains across a diverse suite of public chart understanding benchmarks. The code and dataset will be publicly available upon publication.

cs.CL↗
arXiv2025

A Zero-shot Explainable Doctor Ranking Framework with Large Language Models

Online medical service provides patients convenient access to doctors, but effectively ranking doctors based on specific medical needs remains challenging. Current ranking approaches typically lack the interpretability crucial for patient trust and informed decision-making. Additionally, the scarcity of standardized benchmarks and labeled data for supervised learning impedes progress in expertise-aware doctor ranking. To address these challenges, we propose an explainable ranking framework for doctor ranking powered by large language models in a zero-shot setting. Our framework dynamically generates disease-specific ranking criteria to guide the large language model in assessing doctor relevance with transparency and consistency. It further enhances interpretability by generating step-by-step rationales for its ranking decisions, improving the overall explainability of the information retrieval process. To support rigorous evaluation, we built and released DrRank, a novel expertise-driven dataset comprising 38 disease-treatment pairs and 4,325 doctor profiles. On this benchmark, our framework significantly outperforms the strongest baseline by +6.45 NDCG@10. Comprehensive analyses also show our framework is fair across disease types, patient gender, and geographic regions. Furthermore, verification by medical experts confirms the reliability and interpretability of our approach, reinforcing its potential for trustworthy, real-world doctor recommendation. To demonstrate its broader applicability, we validate our framework on two datasets from BEIR benchmark, where it again achieves superior performance. The code and associated data are available at: https://github.com/YangLab-BUPT/DrRank.

cs.IR↗
arXiv2025

Multi-Agent Autonomous Driving Systems with Large Language Models: A Survey of Recent Advances

Autonomous Driving Systems (ADSs) are revolutionizing transportation by reducing human intervention, improving operational efficiency, and enhancing safety. Large Language Models (LLMs) have been integrated into ADSs to support high-level decision-making through their powerful reasoning, instruction-following, and communication abilities. However, LLM-based single-agent ADSs face three major challenges: limited perception, insufficient collaboration, and high computational demands. To address these issues, recent advances in LLM-based multi-agent ADSs leverage language-driven communication and coordination to enhance inter-agent collaboration. This paper provides a frontier survey of this emerging intersection between NLP and multi-agent ADSs. We begin with a background introduction to related concepts, followed by a categorization of existing LLM-based methods based on different agent interaction modes. We then discuss agent-human interactions in scenarios where LLM-based agents engage with humans. Finally, we summarize key applications, datasets, and challenges to support future research.

cs.MA↗