arXiv subjects

Junjie Wang

Publications and source records attributed to Junjie Wang.

At least 91 records · Page 5Linked to original sources

arXiv2026

NEPMaker: Active learning of neuroevolution machine learning potential for large cells

Machine learning potentials (MLPs) achieve near first-principles accuracy but often fail for atomic environments outside the training distribution. Active learning can mitigate this limitation; however, its application to large-scale simulations is hindered by the prohibitive cost of labeling entire configurations. Here, we develop a D-optimality-driven active learning framework for the neuroevolution potential (NEP) implemented within the GPUMD package, named NEPMaker. Extrapolative atomic environments are identified on-the-fly and embedded into locally periodic structures, where boundary atoms are optimized to remain close to the training distribution. This strategy enables large-scale simulations to directly contribute to dataset construction, significantly reducing extrapolation errors while improving model robustness and transferability. The proposed framework provides a scalable route for constructing reliable machine learning potentials in complex materials systems, including those involving defects, interfaces, and phase transitions.

physics.comp-ph↗

arXiv2026

One Shot Dominance: Knowledge Poisoning Attack on Retrieval-Augmented Generation Systems

Large Language Models (LLMs) enhanced with Retrieval-Augmented Generation (RAG) have shown improved performance in generating accurate responses. However, the dependence on external knowledge bases introduces potential security vulnerabilities, particularly when these knowledge bases are publicly accessible and modifiable. While previous studies have exposed knowledge poisoning risks in RAG systems, existing attack methods suffer from critical limitations: they either require injecting multiple poisoned documents (resulting in poor stealthiness) or can only function effectively on simplistic queries (limiting real-world applicability). This paper reveals a more realistic knowledge poisoning attack against RAG systems that achieves successful attacks by poisoning only a single document while remaining effective for complex multi-hop questions involving complex relationships between multiple elements. Our proposed AuthChain address three challenges to ensure the poisoned documents are reliably retrieved and trusted by the LLM, even against large knowledge bases and LLM's own knowledge. Extensive experiments across six popular LLMs demonstrate that AuthChain achieves significantly higher attack success rates while maintaining superior stealthiness against RAG defense mechanisms compared to state-of-the-art baselines.

cs.CR↗

arXiv2026

Know Thy Enemy: Securing LLMs Against Prompt Injection via Diverse Data Synthesis and Instruction-Level Chain-of-Thought Learning

Large language model (LLM)-integrated applications have become increasingly prevalent, yet face critical security vulnerabilities from prompt injection (PI) attacks. Defending against PI attacks faces two major issues: malicious instructions can be injected through diverse vectors, and injected instructions often lack clear semantic boundaries from the surrounding context, making them difficult to identify. To address these issues, we propose InstruCoT, a model enhancement method for PI defense that synthesizes diverse training data and employs instruction-level chain-of-thought fine-tuning, enabling LLMs to effectively identify and reject malicious instructions regardless of their source or position in the context. We evaluate InstruCoT across three critical dimensions: Behavior Deviation, Privacy Leakage, and Harmful Output. Experimental results across four LLMs demonstrate that InstruCoT significantly outperforms baselines in all dimensions while maintaining utility performance without degradation

cs.AI↗

arXiv2026

SpecQuant: Spectral Decomposition and Adaptive Truncation for Ultra-Low-Bit LLMs Quantization

The emergence of accurate open large language models (LLMs) has sparked a push for advanced quantization techniques to enable efficient deployment on end-user devices. In this paper, we revisit the challenge of extreme LLM compression -- targeting ultra-low-bit quantization for both activations and weights -- from a Fourier frequency domain perspective. We propose SpecQuant, a two-stage framework that tackles activation outliers and cross-channel variance. In the first stage, activation outliers are smoothed and transferred into the weight matrix to simplify downstream quantization. In the second stage, we apply channel-wise low-frequency Fourier truncation to suppress high-frequency components while preserving essential signal energy, improving quantization robustness. Our method builds on the principle that most of the weight energy is concentrated in low-frequency components, which can be retained with minimal impact on model accuracy. To enable runtime adaptability, we introduce a lightweight truncation module during inference that adjusts truncation thresholds based on channel characteristics. On LLaMA-3 8B, SpecQuant achieves 4-bit quantization for both weights and activations, narrowing the zero-shot accuracy gap to only 1.5% compared to full precision, while delivering 2 times faster inference and 3times lower memory usage. Code will be available at https://github.com/Kishon-zzx/SpecQuant.

cs.LG↗

arXiv2026

DIVER: A Multi-Stage Approach for Reasoning-intensive Information Retrieval

Retrieval-augmented generation has achieved strong performance on knowledge-intensive tasks where query-document relevance can be identified through direct lexical or semantic matches. However, many real-world queries involve abstract reasoning, analogical thinking, or multi-step inference, which existing retrievers often struggle to capture. To address this challenge, we present DIVER, a retrieval pipeline designed for reasoning-intensive information retrieval. It consists of four components. The document preprocessing stage enhances readability and preserves content by cleaning noisy texts and segmenting long documents. The query expansion stage leverages large language models to iteratively refine user queries with explicit reasoning and evidence from retrieved documents. The retrieval stage employs a model fine-tuned on synthetic data spanning medical and mathematical domains, along with hard negatives, enabling effective handling of reasoning-intensive queries. Finally, the reranking stage combines pointwise and listwise strategies to produce both fine-grained and globally consistent rankings. On the BRIGHT benchmark, DIVER achieves state-of-the-art nDCG@10 scores of 46.8 overall and 31.9 on original queries, consistently outperforming competitive reasoning-aware models. These results demonstrate the effectiveness of reasoning-aware retrieval strategies in complex real-world tasks.

cs.IR↗

arXiv2026

Efficient Reasoning with Balanced Thinking

Large Reasoning Models (LRMs) have shown remarkable reasoning capabilities, yet they often suffer from overthinking, expending redundant computational steps on simple problems, or underthinking, failing to explore sufficient reasoning paths despite inherent capabilities. These issues lead to inefficiencies and potential inaccuracies, limiting practical deployment in resource-constrained settings. Existing methods to mitigate overthinking, such as suppressing reflective keywords or adjusting reasoning length, may inadvertently induce underthinking, compromising accuracy. Therefore, we propose ReBalance, a training-free framework that achieves efficient reasoning with balanced thinking. ReBalance leverages confidence as a continuous indicator of reasoning dynamics, identifying overthinking through high confidence variance and underthinking via consistent overconfidence. By aggregating hidden states from a small-scale dataset into reasoning mode prototypes, we compute a steering vector to guide LRMs' reasoning trajectories. A dynamic control function modulates this vector's strength and direction based on real-time confidence, pruning redundancy during overthinking, and promoting exploration during underthinking. Extensive experiments conducted on four models ranging from 0.5B to 32B, and across nine benchmarks in math reasoning, general question answering, and coding tasks demonstrate that ReBalance effectively reduces output redundancy while improving accuracy, offering a general, training-free, and plug-and-play strategy for efficient and robust LRM deployment. Project page and code are available at https://rebalance-ai.github.io .

cs.AI↗

arXiv2026

Mapping generative AI use in the human brain: divergent neural, academic, and mental health profiles of functional versus socio emotional AI use

The widespread adoption of generative artificial intelligence conversational agents (AICAs) among university students constitutes a novel cognitive social environment whose impact on the maturing brain remains elusive. Combining surveys with high resolution structural MRI, we examined patterns of general, functional, and socio emotional AICA use, academic performance, mental health, and brain structural signatures in a comparatively large sample of 222 young individuals. Across computational anatomy, meta analytic network level, and behavioral decoding analyses, we observed use specific associations. Higher general and functional AICA use frequencies were linked to better academic outcomes (GPA), larger dorsolateral prefrontal and calcarine gray matter volume, and enhanced hippocampal network clustering and local efficiency. In contrast, more frequent socio emotional AICA use was associated with poorer mental health (depression, social anxiety) and lower volume of superior temporal and amygdalar regions central to social and affective processing. These findings indicate that the same class of AI tools exerts distinct effects depending on usage patterns and motivations, engaging prefrontal hippocampal systems that support cognition versus socio emotional systems that may track distress linked usage. These heterogeneities are crucial for designing environments that harness the educational benefits of AI while mitigating mental health risks.

q-bio.NC↗

arXiv2026

AutoEG: Exploiting Known Third-Party Vulnerabilities in Black-Box Web Applications

Large-scale web applications are widely deployed with complex third-party components, inheriting security risks arising from component vulnerabilities. Security assessment is therefore required to determine whether such known vulnerabilities remain practically exploitable in real applications. Penetration testing is a widely adopted approach that validates exploitability by launching concrete attacks against known vulnerabilities in real-world black-box systems. However, existing approaches often fail to automatically generate reliable exploits, limiting their effectiveness in practical security assessment. This limitation mainly stems from two issues: (1) precisely triggering vulnerabilities with correct technical details, and (2) adapting exploits to diverse real-world deployment settings. In this paper, we propose AutoEG, a fully automated multi-agent framework for exploit generation targeting black-box web applications. AutoEG has two phases: First, AutoEG extracts precise vulnerability trigger logic from unstructured vulnerability information and encapsulates it into reusable trigger functions. Second, AutoEG uses trigger functions for concrete attack objectives and iteratively refines exploits through feedback-driven interaction with the target application. We evaluate AutoEG on 104 real-world vulnerabilities with 29 attack objectives, resulting in 660 exploitation tasks and 55,440 exploit attempts. AutoEG achieves an average success rate of 82.41%, substantially outperforming state-of-the-art baselines, whose best performance reaches only 32.88%.

cs.CR↗

arXiv2026

NMRPeak: a ready-to-use intelligent system for molecular structure elucidation enabled by synergistic cross-modal learning

One-dimensional nuclear magnetic resonance (NMR) spectroscopy is essential for molecular structure elucidation in organic synthesis, drug discovery, natural product characterization, and metabolomics, yet its interpretation remains heavily dependent on expert knowledge and difficult to scale. Although machine learning has been applied to NMR spectrum prediction, library retrieval, and structure generation, these tasks have evolved in isolation using simulated data and incompatible spectral representations, limiting their utility under real experimental scenarios. Here we present NMRPeak, a unified cross-modal learning system that integrates these three tasks through experimentally grounded design. We curate approximately 1.8 million experimental and simulated spectra to construct the largest benchmark for NMR-based structure elucidation and systematically quantify the distribution shift between these domains. We introduce a chemically-aware adaptive tokenizer that dynamically balances discretization granularity to preserve spectral semantics while controlling vocabulary size, and an assignment-free peak-aware similarity metric that enables direct comparison between predicted and experimental spectra. Through a unified molecule-to-spectrum paradigm and synergistic coupling of prediction, retrieval, and generation modules, NMRPeak achieves transformative performance on experimental benchmarks: it overcomes the longstanding simulation-to-experiment gap in spectrum prediction while delivering over 95% top-1 accuracy in molecular retrieval and approximately 75% top-1 accuracy in stereochemistry-aware de novo structure generation. These capabilities establish a foundation for automated, high-throughput molecular structure elucidation in organic synthesis, drug discovery, and chemical biology.

cond-mat.mtrl-sci↗

arXiv2026

Mitigating the Reasoning Tax in Vision-Language Fine-Tuning with Input-Adaptive Depth Aggregation

Supervised fine-tuning (SFT) on visual instruction data often improves perceptual capabilities in vision-language models (VLMs) while degrading reasoning performance, creating a persistent reasoning tax during post-training. We investigate whether this degradation is related to disrupted access to depth-wise representations, and find that even fixed cross-depth aggregation substantially restores reasoning, suggesting that preserved cross-depth access is an important missing factor in VLM fine-tuning. Building on this observation, we propose Input-Adaptive Depth Aggregation (IADA), a lightweight mechanism that makes cross-depth retrieval input-adaptive, modality-aware, and efficiently parameterized through a low-rank bottleneck. On Qwen3-VL-2B, IADA improves the average reasoning score by 9.5 points and the average perception score by $3.3$ points over LoRA-only fine-tuning with only 0.14M additional parameters, with the strongest gains appearing in parameter-efficient low-rank settings.

cs.CV↗

arXiv2026

GPU-MetaD: Full-Life-Cycle GPU Accelerated Metadynamics with Machine Learning Potentials

Large-scale molecular dynamics simulations with high accuracy have been increasingly popular for their capability to bridge the gap between atomistic modeling and mesoscale phenomena. Both machine learning potentials and enhanced sampling approaches offer substantial improvements in high-accuracy simulation efficiency, which can be further boosted through GPU acceleration. However, an efficient framework combining these advances for extending simulations to large systems and long timescales remains elusive. In this work, we proposed a full-life-cycle GPU accelerated metadynamics simulations package GPU-MetaD. Benchmarking across molecular, interface, and bulk systems demonstrates that GPU-MetaD efficiently handles diverse atomic systems and delivers an order-of-magnitude performance improvement. Building on this demonstrated capability, it enables ab-initio-level rare-event sampling for systems comprising millions of atoms on a typical single GPU. This capability allows us to reveal a previously unknown size-dependent two-step nucleation mechanism in gallium nitride (GaN), highlighting the potential of GPU-MetaD for uncovering complex rare events in realistic large-scale materials systems.

physics.comp-ph↗

arXiv2026

Evontree: Ontology Rule-Guided Self-Evolution of Large Language Models

Although Large Language Models (LLMs) perform exceptionally well in general domains, the problem of hallucinations poses significant risks in specialized fields such as healthcare and law, where high interpretability is essential. Existing fine-tuning methods depend heavily on large-scale professional datasets, which are often hard to obtain due to the privacy regulations. Moreover, existing self-evolution methods are primarily designed for general domains, which may struggle to adapt to knowledge-intensive domains due to the lack of knowledge constraints. In this paper, we propose an ontology rule guided method Evontree to enable self-evolution of LLMs in low-resource specialized domains. Specifically, Evontree first extracts domain ontology knowledge from raw models, then detects knowledge inconsistencies using two core ontology rules, and finally reinforces gap knowledge into model via self-distilled fine-tuning. Extensive evaluations on medical QA benchmarks using Llama3-8B-Instruct and Med42-V2 demonstrate the effectiveness of Evontree, which outperforms both the base models and strong baselines, achieving up to a 3.7\% improvement in accuracy. Detailed ablation studies further validate the robustness of our approach.

cs.CL↗

arXiv2026

Uni-Parser Technical Report

This technical report introduces Uni-Parser, an industrial-grade document parsing engine tailored for scientific literature and patents, delivering high throughput, robust accuracy, and cost efficiency. Unlike pipeline-based document parsing methods, Uni-Parser employs a modular, loosely coupled multi-expert architecture that preserves fine-grained cross-modal alignments across text, equations, tables, figures, and chemical structures, while remaining easily extensible to emerging modalities. The system incorporates adaptive GPU load balancing, distributed inference, dynamic module orchestration, and configurable modes that support either holistic or modality-specific parsing. Optimized for large-scale cloud deployment, Uni-Parser achieves a processing rate of up to 20 PDF pages per second on 8 x NVIDIA RTX 4090D GPUs, enabling cost-efficient inference across billions of pages. This level of scalability facilitates a broad spectrum of downstream applications, ranging from literature retrieval and summarization to the extraction of chemical structures, reaction schemes, and bioactivity data, as well as the curation of large-scale corpora for training next-generation large language models and AI4Science models.

cs.CV↗

arXiv2026

A Survey of Reasoning in Autonomous Driving Systems: Open Challenges and Emerging Paradigms

The development of high-level autonomous driving (AD) is shifting from perception-centric limitations to a more fundamental bottleneck, namely, a deficit in robust and generalizable reasoning. Although current AD systems manage structured environments, they consistently falter in long-tail scenarios and complex social interactions that require human-like judgment. Meanwhile, the advent of large language and multimodal models (LLMs and MLLMs) presents a transformative opportunity to integrate a powerful cognitive engine into AD systems, moving beyond pattern matching toward genuine comprehension. However, a systematic framework to guide this integration is critically lacking. To bridge this gap, we provide a comprehensive review of this emerging field and argue that reasoning should be elevated from a modular component to the system's cognitive core. Specifically, we first propose a novel Cognitive Hierarchy to decompose the monolithic driving task according to its cognitive and interactive complexity. Building on this, we further derive and systematize seven core reasoning challenges, such as the responsiveness-reasoning trade-off and social-game reasoning. Furthermore, we conduct a dual-perspective review of the state-of-the-art, analyzing both system-centric approaches to architecting intelligent agents and evaluation-centric practices for their validation. Our analysis reveals a clear trend toward holistic and interpretable "glass-box" agents. In conclusion, we identify a fundamental and unresolved tension between the high-latency, deliberative nature of LLM-based reasoning and the millisecond-scale, safety-critical demands of vehicle control. For future work, a primary objective is to bridge the symbolic-to-physical gap by developing verifiable neuro-symbolic architectures, robust reasoning under uncertainty, and scalable models for implicit social negotiation.

cs.AI↗

arXiv2026

DynaTrust: Defending Multi-Agent Systems Against Sleeper Agents via Dynamic Trust Graphs

Large Language Model-based Multi-Agent Systems (MAS) have demonstrated remarkable collaborative reasoning capabilities but introduce new attack surfaces, such as the sleeper agent, which behave benignly during routine operation and gradually accumulate trust, only revealing malicious behaviors when specific conditions or triggers are met. Existing defense works primarily focus on static graph optimization or hierarchical data management, often failing to adapt to evolving adversarial strategies or suffering from high false-positive rates (FPR) due to rigid blocking policies. To address this, we propose DynaTrust, a novel defense method against sleeper agents. DynaTrust models MAS as a dynamic trust graph~(DTG), and treats trust as a continuous, evolving process rather than a static attribute. It dynamically updates the trust of each agent based on its historical behaviors and the confidence of selected expert agents. Instead of simply blocking, DynaTrust autonomously restructures the graph to isolate compromised agents and restore task connectivity to ensure the usability of MAS. To assess the effectiveness of DynaTrust, we evaluate it on mixed benchmarks derived from AdvBench and HumanEval. The results demonstrate that DynaTrust outperforms the state-of-the-art method AgentShield by increasing the defense success rate by 41.7%, achieving rates exceeding 86% under adversarial conditions. Furthermore, it effectively balances security with utility by significantly reducing FPR, ensuring uninterrupted system operations through graph adaptation.

cs.AI↗

arXiv2026

SemFuzz: A Semantics-Aware Fuzzing Framework for Network Protocol Implementations

Network protocols are the foundation of modern communication, yet their implementations often contain semantic vulnerabilities stemming from inadequate understanding of specification semantics. Existing gray-box and black-box testing approaches lack semantic modeling of protocols, making it difficult to precisely express testing intent and cover boundary conditions. Moreover, they typically rely on coarse-grained oracles such as crashes, which are inadequate for identifying deep semantic vulnerabilities. To address these limitations, we present a semantics-aware fuzzing framework, SemFuzz. The framework leverages large language models to extract structured semantic rules from RFC documents and generates test cases that intentionally violate these rules to encode specific testing intents. It then detects deep semantic vulnerabilities by comparing the observed responses with the expected ones. Evaluation on seven widely deployed protocol implementations shows that SemFuzz identified sixteen potential vulnerabilities, ten of which have been confirmed. Among the confirmed vulnerabilities, five were previously unknown and four have been assigned CVEs. These results demonstrate the effectiveness of SemFuzz in detecting semantic vulnerabilities.

cs.CR↗

arXiv2026

VeriWeb: Verifiable Long-Chain Web Benchmark for Agentic Information-Seeking

Recent advances have showcased the extraordinary capabilities of Large Language Model (LLM) agents in tackling web-based information-seeking tasks. However, existing efforts mainly focus on single-fact retrieval and rely on outcome-only verification, thereby limiting their scalability in realistic knowledge-intensive scenarios that involve long-horizon web tasks requiring large-scale retrieval and synthesis of information from diverse sources. In this work, we introduce VeriWeb, a novel verifiable long-chain web benchmark designed to facilitate the evaluation and development of web agents within realistic web environments. Our benchmark emphasizes two critical dimensions: (1) long-chain complexity, encompassing both breadth- and depth-oriented search tasks to assess how effectively web agents ensure comprehensive information coverage and consistent context tracking in multi-hop reasoning; and (2) subtask-level verifiability, where tasks are decomposed into a sequence of interdependent verifiable subtasks. This structure enables diverse exploration strategies within each subtask, while ensuring that each subtask-level answer remains unchanged and verifiable. The benchmark consists of 302 tasks across five real-world domains, each with a complete trajectory demonstration, annotated by human experts. Extensive experiments on VeriWeb using various agents powered by different foundation models reveal significant performance gaps in handling long-horizon web tasks, highlighting the need for more powerful agentic information-seeking capabilities.

cs.HC↗

arXiv2026

Demystifying the Lifecycle of Failures in Platform-Orchestrated Agentic Workflows

Agentic workflows built on low-code orchestration platforms enable rapid development of multi-agent systems, but they also introduce new and poorly understood failure modes that hinder reliability and maintainability. Unlike traditional software systems, failures in agentic workflows often propagate across heterogeneous nodes through natural-language interactions, tool invocations, and dynamic control logic, making failure attribution and repair particularly challenging. In this paper, we present an empirical study of platform-orchestrated agentic workflows from a failure lifecycle perspective, with the goal of characterizing failure manifestations, identifying underlying root causes, and examining corresponding repair strategies. We present AgentFail, a dataset of 307 real-world failure cases collected from two representative agentic workflow platforms. Based on this dataset, we analyze failure patterns, root causes, and repair difficulty for various failure root causes and nodes in the workflow. Our findings reveal key failure mechanisms in agentic workflows and provide actionable guidelines for reliable failure repair, and real-world agentic workflow design.

cs.AI↗