arXiv subjects

Wei Ruan

Publications and source records attributed to Wei Ruan.

At least 19 recordsLinked to original sources

arXiv2026

ASTELD: A Six-Axis Classification Framework for Autonomous AI Agents - Design, Evaluation, and an OpenClaw Case Study

Autonomous AI agent platforms differ substantially in architecture, security, tool integration, execution, autonomy, and deployment, yet the field lacks a common classification scheme for comparing these design choices. We propose ASTELD, an operational six-axis classification framework for autonomous AI agents: Architecture pattern, Security posture, Tool integration model, Execution paradigm, Level of autonomy and human control, and Deployment topology. ASTELD is constructed by synthesizing prior agent taxonomies with observable platform properties and explicit category-assignment rules. We evaluate its discriminative and explanatory utility by mapping eight representative frameworks and by using OpenClaw as an in-depth case study. The resulting profiles separate all eight platforms under their dominant configurations and reveal three cross-platform patterns: a security-accessibility diagonal, strong execution-architecture coupling, and capability convergence with persistent architectural differentiation. We further classify 50+ OpenClaw derivatives and find that innovation concentrates on the Security, Execution, and Deployment axes, indicating that ASTELD can explain where ecosystem fragmentation occurs. The OpenClaw case study also supplies a six-category vulnerability taxonomy, evidence from five institutional assessments, and adoption and governance analyses that connect platform coordinates to observed risks. These results position ASTELD as a reproducible method for comparing agent platforms, identifying unoccupied design regions, guiding framework selection, and organizing future empirical research. The analysis also exposes a consequential empty region: none of the evaluated systems combines local-first deployment with enterprise-grade security.

cs.CR↗

arXiv2026

World Models: A Comprehensive Survey of Architectures, Methodologies, Reasoning Paradigms, and Applications

World models, internal simulators that learn the structure and dynamics of an environment, have emerged as a central paradigm in the pursuit of artificial general intelligence, enabling agents to predict, plan, and reason within learned representations. Despite rapid progress across reinforcement learning, robotics, autonomous driving, and video generation, the field lacks a unified framework integrating its diverse architectural choices, training methods, reasoning mechanisms, and application settings. This survey addresses that gap with a multi-axis taxonomy organized along four dimensions: (i) architecture, encompassing representation format, dynamics formulation, input modality, learning paradigm, and downstream application; (ii) methodological family, including state-space and recurrent approaches, transformer-based models, diffusion-based generators, physics-informed networks, and language-augmented multimodal systems; (iii) reasoning strategy, covering imagination-based planning, latent policy learning, counterfactual reasoning, and planning under uncertainty; and (iv) application domain, spanning robotics, autonomous driving, video prediction, multimodal agents, reinforcement learning, scientific modeling, medical imaging, educational measurement, and business and finance. Tracing the field from early cognitive-science foundations to milestone systems such as PlaNet, the Dreamer family, MuZero, Sora, Cosmos, and Genie, we examine how these dimensions interact and highlight the recent convergence of chain-of-thought reasoning with world-model imagination. We review evaluation protocols and benchmarks, identify persistent challenges such as compounding prediction errors, sim-to-real transfer, and fragmented evaluation, and outline future directions toward unified multimodal world models, foundation-scale interactive simulators, and safe deployment in safety-critical domains.

cs.LG↗

arXiv2026

Vibe Medicine: Redefining Biomedical Research Through Human-AI Co-Work

With the emergence of large language models (LLMs) and AI agent frameworks, the human-AI co-work paradigm known as Vibe Coding is changing how people code, making it more accessible and productive. In scientific research, where workflows are more complex and the burden of specialized labor limits independent researchers and those in low-resource areas, the potential impact is even greater, particularly in biomedicine, which involves heterogeneous data modalities and multi-step analytical pipelines. In this paper, we introduce Vibe Medicine, a co-work paradigm in which clinicians and researchers direct skill-augmented AI agents through natural language to execute complex, multi-step biomedical workflows, while retaining the role of research director who specifies objectives, reviews intermediate results, and makes domain-informed decisions. The enabling infrastructure consists of three layers: capable LLMs, agent frameworks such as OpenClaw and Hermes Agent, and the OpenClaw medical skills collection, which includes more than 1,000 curated skills from multiple open-source repositories. We analyze the architecture and skill categories of this collection across ten biomedical domains, and present case studies covering rare disease diagnosis, drug repurposing, and clinical trial design that demonstrate end-to-end workflows in practice. We also identify the principal risks, such as hallucination, data privacy, and over-reliance, and outline directions toward more reliable, trustworthy, and clinically integrated agent-assisted research that advances research and technological equity and reduces health care resource disparities.

cs.AI↗

arXiv2026

Unveiling the impact of anti-site defects in magnetic transitions of few-layer MnBi2Te4 by operando heating

As the first experimentally discovered intrinsic magnetic topological insulator, MnBi2Te4 has attracted widespread attentions, providing a unique platform for the exploration of topological quantum phases, such as quantum anomalous Hall effect and axion insulator state. Despite the increasing number of potential factors affecting samples being identified, obtaining the high-quality device performance with desired topological quantum phases remains a challenge. In this work, by comparing the reflective magnetic circular dichroism (RMCD) of crystals with different defect densities that are characterized by atomically resolved scanning tunneling microscopy, we demonstrate that anti-site defects play an essential role in achieving ideal magnetic states. By measuring RMCD hysteresis loops with operando heating, we find that MnBi2Te4 few-layer samples are highly susceptible to thermal impact, even at temperature as low as 45{\deg}C. The magnetic behavior of heating-treated samples is akin to that of samples fabricated into devices, revealing the thermal impact on devices as well. Starting from few-layers with ideal layer-dependent magnetic order, thermal heating leads to the convergence of magnetization and transition fields between odd- and even-layers. The observed heating-induced magnetic evolution can serve as a valuable reference for assessing the sample quality or the density of anti-site defects. Our findings not only point out the long-standing hidden factor that arose controversies in MnBi2Te4, but also pave the way for controllably engineering the topological quantum phenomena.

cond-mat.mtrl-sci↗

arXiv2026

Large Language Models for Assisting American College Applications

American college applications require students to navigate fragmented admissions policies, repetitive and conditional forms, and ambiguous questions that often demand cross-referencing multiple sources. We present EZCollegeApp, a large language model (LLM)-powered system that assists high-school students by structuring application forms, grounding suggested answers in authoritative admissions documents, and maintaining full human control over final responses. The system introduces a mapping-first paradigm that separates form understanding from answer generation, enabling consistent reasoning across heterogeneous application portals. EZCollegeApp integrates document ingestion from official admissions websites, retrieval-augmented question answering, and a human-in-the-loop chatbot interface that presents suggestions alongside application fields without automated submission. We describe the system architecture, data pipeline, internal representations, security and privacy measures, and evaluation through automated testing and human quality assessment. Our source code is released on GitHub (https://github.com/ezcollegeapp-public/ezcollegeapp-public) to facilitate the broader impact of this work.

cs.CL↗

arXiv2025

Nanbeige4-3B Technical Report: Exploring the Frontier of Small Language Models

We present Nanbeige4-3B, a family of small-scale but high-performing language models. Pretrained on 23T high-quality tokens and finetuned on over 30 million diverse instructions, we extend the boundary of the scaling law for small language models. In pre-training, we design a Fine-Grained Warmup-Stable-Decay (FG-WSD) training scheduler, which progressively refines data mixtures across stages to boost model performance. In post-training, to improve the quality of the SFT data, we design a joint mechanism that integrates deliberative generation refinement and chain-of-thought reconstruction, yielding substantial gains on complex tasks. Following SFT, we employ our flagship reasoning model to distill Nanbeige4-3B through our proposed Dual Preference Distillation (DPD) method, which leads to further performance gains. Finally, a multi-stage reinforcement learning phase was applied, leveraging verifiable rewards and preference modeling to strengthen abilities on both reasoning and human alignment. Extensive evaluations show that Nanbeige4-3B not only significantly outperforms models of comparable parameter scale but also rivals much larger models across a wide range of benchmarks. The model checkpoints are available at https://huggingface.co/Nanbeige.

cs.CL↗

arXiv2025

Alignment and Safety in Large Language Models: Safety Mechanisms, Training Paradigms, and Emerging Challenges

Due to the remarkable capabilities and growing impact of large language models (LLMs), they have been deeply integrated into many aspects of society. Thus, ensuring their alignment with human values and intentions has emerged as a critical challenge. This survey provides a comprehensive overview of practical alignment techniques, training protocols, and empirical findings in LLM alignment. We analyze the development of alignment methods across diverse paradigms, characterizing the fundamental trade-offs between core alignment objectives. Our analysis shows that while supervised fine-tuning enables basic instruction-following, preference-based methods offer more flexibility for aligning with nuanced human intent. We discuss state-of-the-art techniques, including Direct Preference Optimization (DPO), Constitutional AI, brain-inspired methods, and alignment uncertainty quantification (AUQ), highlighting their approaches to balancing quality and efficiency. We review existing evaluation frameworks and benchmarking datasets, emphasizing limitations such as reward misspecification, distributional robustness, and scalable oversight. We summarize strategies adopted by leading AI labs to illustrate the current state of practice. We conclude by outlining open problems in oversight, value pluralism, robustness, and continuous alignment. This survey aims to inform both researchers and practitioners navigating the evolving landscape of LLM alignment.

cs.AI↗

arXiv2025

Quantized Topological States and Parity Anomaly in Intrinsic Quantum Anomalous Hall Insulator MnBi2Te4

When thinned down to just a few atomic layers, the layered magnetic topological insulator MnBi2Te4 offers an exceptional platform for exploring a wide range of topological phenomena. In this work, we overcome longstanding challenges in synthesizing high-purity MnBi2Te4 crystals and report the observation of a myriad of quantized topological states in high-quality five-septuple-layer (5-SL) samples under magnetic fields up to 45 Tesla. We show that the nontrivial topology of 5-SL MnBi2Te4, in the presence of Landau quantization, is governed by a generalized topological index rooted in the parity anomaly of Dirac fermions in (2+1) dimensions. The anomaly manifests as an anomalous Landau level, giving rise to gate-tunable helical edge transport. Our results establish high-quality MnBi2Te4 as a robust platform for exploring emergent topological states and for advancing novel quantum device applications.

cond-mat.mes-hall↗

arXiv2025

FractionalDiffEq.jl: High Performance Fractional Differential Equation Solver in Julia

We present FractionalDiffEq.jl, a comprehensive solver suite for solving fractional differential equations, featuring high-performance numerical algorithms in the Julia programming language. FractionalDiffEq.jl is designed to be user-friendly and scalable, tackling different types of fractional differential equations, encompassing powerful numerical algorithms including predictor-corrector methods, product-integral methods, and linear multistep methods, etc, and providing a unifying API to accommodate diverse solver features. This paper illustrates the convenient usage of FractionalDiffEq.jl in modeling various scientific problems, accompanied by detailed examples and applications. FractionalDiffEq.jl leverages best practices in Julia to ensure the high performance of numerical solvers. To validate the efficiency of FractionalDiffEq.jl , we conducted extensive benchmarks that prove the superiority of FractionalDiffEq.jl against other implementations on both stiff and non-stiff problems. We further demonstrate its capability on several challenging real-life scenarios including parameter estimation in fractional-order tequila fermentation processes, and harmonic oscillator problems, etc, emphasizing the robustness and flexibility of FractionalDiffEq.jl.

math.NA↗

arXiv2025

MolQAE: Quantum Autoencoder for Molecular Representation Learning

We introduce Quantum Molecular Autoencoder (MolQAE), the first quantum autoencoder to leverage the complete molecular structures. MolQAE uniquely maps SMILES strings directly to quantum states using parameterized rotation gates, preserving vital structural information. Its quantum encoder-decoder framework enables latent space compression and reconstruction. A dual-objective strategy optimizes fidelity and minimizes trash state deviation. Our evaluations demonstrate effective capture of molecular characteristics and a remarkable preservation of fidelity, approaching robust molecular reconstruction even with substantial dimensionality reduction. Our model establishes a quantum pathway in cheminformatics by being the first to process complete molecular structural information with a dedicated quantum architecture considering the Noisy Intermediate-Scale Quantum (NISQ)-era development and promising significant advances in drug and materials discovery.

quant-ph↗

arXiv2025

Knowledge Distillation and Dataset Distillation of Large Language Models: Emerging Trends, Challenges, and Future Directions

The exponential growth of Large Language Models (LLMs) continues to highlight the need for efficient strategies to meet ever-expanding computational and data demands. This survey provides a comprehensive analysis of two complementary paradigms: Knowledge Distillation (KD) and Dataset Distillation (DD), both aimed at compressing LLMs while preserving their advanced reasoning capabilities and linguistic diversity. We first examine key methodologies in KD, such as task-specific alignment, rationale-based training, and multi-teacher frameworks, alongside DD techniques that synthesize compact, high-impact datasets through optimization-based gradient matching, latent space regularization, and generative synthesis. Building on these foundations, we explore how integrating KD and DD can produce more effective and scalable compression strategies. Together, these approaches address persistent challenges in model scalability, architectural heterogeneity, and the preservation of emergent LLM abilities. We further highlight applications across domains such as healthcare and education, where distillation enables efficient deployment without sacrificing performance. Despite substantial progress, open challenges remain in preserving emergent reasoning and linguistic diversity, enabling efficient adaptation to continually evolving teacher models and datasets, and establishing comprehensive evaluation protocols. By synthesizing methodological innovations, theoretical foundations, and practical insights, our survey charts a path toward sustainable, resource-efficient LLMs through the tighter integration of KD and DD principles.

cs.CL↗

arXiv2025

AD-GPT: Large Language Models in Alzheimer's Disease

Large language models (LLMs) have emerged as powerful tools for medical information retrieval, yet their accuracy and depth remain limited in specialized domains such as Alzheimer's disease (AD), a growing global health challenge. To address this gap, we introduce AD-GPT, a domain-specific generative pre-trained transformer designed to enhance the retrieval and analysis of AD-related genetic and neurobiological information. AD-GPT integrates diverse biomedical data sources, including potential AD-associated genes, molecular genetic information, and key gene variants linked to brain regions. We develop a stacked LLM architecture combining Llama3 and BERT, optimized for four critical tasks in AD research: (1) genetic information retrieval, (2) gene-brain region relationship assessment, (3) gene-AD relationship analysis, and (4) brain region-AD relationship mapping. Comparative evaluations against state-of-the-art LLMs demonstrate AD-GPT's superior precision and reliability across these tasks, underscoring its potential as a robust and specialized AI tool for advancing AD research and biomarker discovery.

cs.CL↗

arXiv2025

From Task-Specific Models to Unified Systems: A Review of Model Merging Approaches

Model merging has achieved significant success, with numerous innovative methods proposed to enhance capabilities by combining multiple models. However, challenges persist due to the lack of a unified framework for classification and systematic comparative analysis, leading to inconsistencies in terminologies and categorizations. Meanwhile, as an increasing number of fine-tuned models are publicly available, their original training data often remain inaccessible due to privacy concerns or intellectual property restrictions. This makes traditional multi-task learning based on shared training data impractical. In scenarios where direct access to training data is infeasible, merging model parameters to create a unified model with broad generalization across multiple domains becomes crucial, further underscoring the importance of model merging techniques. Despite the rapid progress in this field, a comprehensive taxonomy and survey summarizing recent advances and predicting future directions are still lacking. This paper addresses these gaps by establishing a new taxonomy of model merging methods, systematically comparing different approaches, and providing an overview of key developments. By offering a structured perspective on this evolving area, we aim to help newcomers quickly grasp the field's landscape and inspire further innovations.

cs.LG↗

arXiv2025

Unveiling resilient superconducting fluctuations in atomically thin NbSe$_2$ through Higgs mode spectroscopy

We report a combined electrical transport and optical study of the superconductivity in atomically thin NbSe$_2$. When subjected to an out-of-plane magnetic field, an anomalous metallic state emerges, characterized by a finite longitudinal resistance and a vanishing Hall resistance, suggesting the presence of particle-hole symmetry. We establish a superconducting Higgs mode in atomically thin samples, which reveals enduring superconducting fluctuations that withstand unexpectedly high reduced magnetic fields. These findings provide evidence of robust locally paired electrons in the anomalous metallic state, affirming its bosonic nature.

cond-mat.supr-con↗

arXiv2025

Large Language Models for Bioinformatics

With the rapid advancements in large language model (LLM) technology and the emergence of bioinformatics-specific language models (BioLMs), there is a growing need for a comprehensive analysis of the current landscape, computational characteristics, and diverse applications. This survey aims to address this need by providing a thorough review of BioLMs, focusing on their evolution, classification, and distinguishing features, alongside a detailed examination of training methodologies, datasets, and evaluation frameworks. We explore the wide-ranging applications of BioLMs in critical areas such as disease diagnosis, drug discovery, and vaccine development, highlighting their impact and transformative potential in bioinformatics. We identify key challenges and limitations inherent in BioLMs, including data privacy and security concerns, interpretability issues, biases in training data and model outputs, and domain adaptation complexities. Finally, we highlight emerging trends and future directions, offering valuable insights to guide researchers and clinicians toward advancing BioLMs for increasingly sophisticated biological and clinical applications.

q-bio.QM↗

arXiv2024

PentestAgent: Incorporating LLM Agents to Automated Penetration Testing

Penetration testing is a critical technique for identifying security vulnerabilities, traditionally performed manually by skilled security specialists. This complex process involves gathering information about the target system, identifying entry points, exploiting the system, and reporting findings. Despite its effectiveness, manual penetration testing is time-consuming and expensive, often requiring significant expertise and resources that many organizations cannot afford. While automated penetration testing methods have been proposed, they often fall short in real-world applications due to limitations in flexibility, adaptability, and implementation. Recent advancements in large language models (LLMs) offer new opportunities for enhancing penetration testing through increased intelligence and automation. However, current LLM-based approaches still face significant challenges, including limited penetration testing knowledge and a lack of comprehensive automation capabilities. To address these gaps, we propose PentestAgent, a novel LLM-based automated penetration testing framework that leverages the power of LLMs and various LLM-based techniques like Retrieval Augmented Generation (RAG) to enhance penetration testing knowledge and automate various tasks. Our framework leverages multi-agent collaboration to automate intelligence gathering, vulnerability analysis, and exploitation stages, reducing manual intervention. We evaluate PentestAgent using a comprehensive benchmark, demonstrating superior performance in task completion and overall efficiency. This work significantly advances the practical applicability of automated penetration testing systems.

cs.CR↗

arXiv2024

Evaluation of OpenAI o1: Opportunities and Challenges of AGI

This comprehensive study evaluates the performance of OpenAI's o1-preview large language model across a diverse array of complex reasoning tasks, spanning multiple domains, including computer science, mathematics, natural sciences, medicine, linguistics, and social sciences. Through rigorous testing, o1-preview demonstrated remarkable capabilities, often achieving human-level or superior performance in areas ranging from coding challenges to scientific reasoning and from language processing to creative problem-solving. Key findings include: -83.3% success rate in solving complex competitive programming problems, surpassing many human experts. -Superior ability in generating coherent and accurate radiology reports, outperforming other evaluated models. -100% accuracy in high school-level mathematical reasoning tasks, providing detailed step-by-step solutions. -Advanced natural language inference capabilities across general and specialized domains like medicine. -Impressive performance in chip design tasks, outperforming specialized models in areas such as EDA script generation and bug analysis. -Remarkable proficiency in anthropology and geology, demonstrating deep understanding and reasoning in these specialized fields. -Strong capabilities in quantitative investing. O1 has comprehensive financial knowledge and statistical modeling skills. -Effective performance in social media analysis, including sentiment analysis and emotion recognition. The model excelled particularly in tasks requiring intricate reasoning and knowledge integration across various fields. While some limitations were observed, including occasional errors on simpler problems and challenges with certain highly specialized concepts, the overall results indicate significant progress towards artificial general intelligence.

cs.CL↗

arXiv2024

GP-GPT: Large Language Model for Gene-Phenotype Mapping

Pre-trained large language models(LLMs) have attracted increasing attention in biomedical domains due to their success in natural language processing. However, the complex traits and heterogeneity of multi-sources genomics data pose significant challenges when adapting these models to the bioinformatics and biomedical field. To address these challenges, we present GP-GPT, the first specialized large language model for genetic-phenotype knowledge representation and genomics relation analysis. Our model is fine-tuned in two stages on a comprehensive corpus composed of over 3,000,000 terms in genomics, proteomics, and medical genetics, derived from multiple large-scale validated datasets and scientific publications. GP-GPT demonstrates proficiency in accurately retrieving medical genetics information and performing common genomics analysis tasks, such as genomics information retrieval and relationship determination. Comparative experiments across domain-specific tasks reveal that GP-GPT outperforms state-of-the-art LLMs, including Llama2, Llama3 and GPT-4. These results highlight GP-GPT's potential to enhance genetic disease relation research and facilitate accurate and efficient analysis in the fields of genomics and medical genetics. Our investigation demonstrated the subtle changes of bio-factor entities' representations in the GP-GPT, which suggested the opportunities for the application of LLMs to advancing gene-phenotype research.

cs.CL↗