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Xiaorui Wang

Publications and source records attributed to Xiaorui Wang.

At least 19 recordsLinked to original sources
arXiv2026

DeepResearch Bench II: Diagnosing Deep Research Agents via Rubrics from Expert Reports

Deep Research Agents (DRA) aim to help users search the web, synthesize information, and deliver comprehensive investigative reports. Prior benchmarks often either under-evaluate a system's ability to produce meaningful insights and high-quality writing, or adopt coarse or LLM-defined criteria that are hard to verify and can diverge from human expert judgment. To address these issues, we introduce Deep Research Bench II, a new benchmark for evaluating DRAs. It contains 132 grounded research tasks across 22 domains; for each task, an agent must produce a research report that is evaluated by a set of 9,430 fine-grained binary rubrics in total, covering three dimensions: information recall, analysis, and presentation. All rubrics are derived from carefully selected expert-written investigative articles and are constructed through a four-stage LLM+human pipeline that combines automatic extraction with over 400 human-hours of expert review, ensuring that the criteria are verifiable and aligned with human expert judgment. We evaluate several state-of-the-art deep-research agents on Deep Research Bench II and find that even the strongest models satisfy fewer than 50% of the rubrics, revealing a substantial gap between current DRAs and human experts. We release the benchmark, evaluation scripts, and all rubrics at https://github.com/imlrz/DeepResearch-Bench-II to facilitate future research on deep-rearch agents.

cs.CL↗
arXiv2026

Causal Inference for Heterogeneous Extreme Quantiles with Heavy-Tailed Outcomes

We propose a framework for estimating conditional extreme quantile treatment effects (CEQTEs) in observational studies with heavy-tailed outcomes. Our procedure first estimates intermediate conditional quantiles using inverse-probability-weighted (IPW) quantile regression and then extrapolates them to extreme levels using extreme value theory. Under a linear conditional quantile model, we show that the conditional and marginal distributions of each potential outcome share a common extreme value index (EVI), motivating two complementary Hill-type EVI estimators based on conditional and marginal information, respectively. On the theoretical front, we introduce an IPW tail quantile score process that bridges regression quantile score processes and uniform tail empirical processes while accounting for treatment assignment. We establish its functional weak convergence under mild regularity conditions, without requiring a max-domain-of-attraction condition. This result provides the probabilistic foundation for the asymptotic analysis of the proposed CEQTE estimators. Simulation studies demonstrate favorable finite-sample performance, and an application to NLSY79 data reveals substantial heterogeneity in the effect of college education on extremely high hourly wages across confounder-defined subpopulations.

stat.ME↗
arXiv2026

Learning Reduced-Order Dynamics with Singularity via Latent-Augmented Neural Ordinary Differential Equations

This paper addresses the issue of self-intersecting trajectories (in phase space) in industrial reduced-order modeling and proposes the Latent-Augmented Neural Ordinary Differential Equations (LA-NODEs) framework. From the perspective of artificial intelligence, the proposed method augments conventional neural ordinary differential equations to enhance model expressiveness, enabling the representation of conflicting vector fields that may arise in reduced-order systems, thereby improving learning accuracy. Through theoretical analysis, the underlying mechanism of the framework is established, and a condition for determining the minimum required augmentation dimension is derived. From the perspective of engineering applications, the effectiveness of the proposed method is validated on the reduced-order system of two representative industrial models, namely an interior permanent magnet synchronous motor (IPMSM) drive and a distributed energy system (DES). Experimental results demonstrate that the proposed method can recover system features that are difficult to capture using conventional approaches and achieve superior performance in terms of prediction accuracy and modeling fidelity, thereby providing an effective approach for high-precision data-driven modeling of complex industrial systems.

cs.LG↗
arXiv2026

AMR-Pose: An Active LED Marker-Based Relative Pose Estimation Framework With Probabilistic Switching PnP for Cooperative AUVs

Reliable relative pose estimation between autonomous underwater vehicles (AUVs) is critical for cooperative ocean exploration, sampling, and multi-robot coordination. However, achieving robust vision-based relative localization in underwater environments remains challenging due to severe optical degradation, including turbidity, illumination variations, reflections, and intermittent feature occlusions. This paper presents AMR-Pose, an active LED marker-based relative pose estimation framework for cooperative AUVs. A compact marker module consisting of one red central LED and three blue peripheral LEDs is developed and integrated onto the leader AUV to provide distinctive visual features under complex underwater conditions. Building upon the detected marker observations, a probabilistic switching Perspective-n-Point estimator (PSwPnP) is developed by combining Lie-group pose propagation on $SE(3)$, probabilistic marker association, and visibility-adaptive measurement fusion for robust six-degree-of-freedom relative pose estimation. The proposed framework dynamically adapts the estimation process according to marker visibility, maintaining geometric consistency and temporal stability during partial observations and visibility transitions. Extensive water-tank experiments with motion-capture ground truth validate that AMR-Pose achieves accurate, smooth, and robust relative pose estimation under challenging underwater conditions. Closed-loop leader-follower experiments further demonstrate its feasibility for real-time relative pose feedback in cooperative underwater robotics.

cs.RO↗
arXiv2026

CombinationTS: A Modular Framework for Understanding Time-Series Forecasting Models

Recent progress in time-series forecasting has led to rapidly increasing architectural complexity, yet many reported State-of-the-Art gains are statistically fragile or misattributed. We argue that progress requires a shift from model selection to modular attribution, identifying which components truly drive performance. We propose CombinationTS, a self-contained probabilistic evaluation framework that decomposes forecasting models into orthogonal modules--Input Transformation, Embedding, Encoder, Decoder, and Output Transformation--and evaluates them under a shared evaluation condition space. By quantifying each component via marginalized performance ($μ$) and stability ($σ$), CombinationTS enables robust attribution beyond fragile point estimates. Through large-scale paired evaluation, we uncover the Identity Paradox: once the data view (Embedding) is well-designed, a parameter-free Identity Encoder often matches or outperforms complex backbones. We further show that explicit structural priors introduced via Input Transformations yield a more favorable performance-stability trade-off than increasing Encoder complexity, establishing a principled baseline for architectural necessity.

cs.LG↗
arXiv2026

Bi-Level Reinforcement Learning Control for an Underactuated Blimp via Center-of-Mass Reconfiguration

This paper investigates goal-directed tracking control of underactuated blimps with center-of-mass (CoM) reconfiguration. Unlike conventional overactuated blimp designs that rely on redundant actuation for simplified control, this paper focuses on a compact architecture consisting of two thrusters and a movable internal slider, aiming to improve energy efficiency and payload capacity. This hardware-efficient configuration introduces significant underactuation and strong nonlinear coupling between CoM dynamics and vehicle motion. To address these challenges, this paper proposes a bi-level reinforcement learning framework that explicitly decouples task-level CoM planning from continuous thrust control. The outer policy determines a target-dependent CoM configuration prior to flight, while the inner policy generates thrust commands to track straight-line references. To ensure stable learning, this paper introduces a two-stage learning strategy, supported by a convergence analysis of the resulting bi-level process. Extensive simulations and real-world experiments on a 27-goal evaluation set demonstrate that the proposed method consistently outperforms fixed-CoM baselines and PID-based controllers, achieving higher tracking accuracy, enhanced robustness, and reliable sim-to-real transfer.

cs.RO↗
arXiv2026

FS-Researcher: Test-Time Scaling for Long-Horizon Research Tasks with File-System-Based Agents

Deep research is emerging as a representative long-horizon task for large language model (LLM) agents. However, long trajectories in deep research often exceed model context limits, compressing token budgets for both evidence collection and report writing, and preventing effective test-time scaling. We introduce FS-Researcher, a file-system-based, dual-agent framework that scales deep research beyond the context window via a persistent workspace. Specifically, a Context Builder agent acts as a librarian which browses the internet, writes structured notes, and archives raw sources into a hierarchical knowledge base that can grow far beyond context length. A Report Writer agent then composes the final report section by section, treating the knowledge base as the source of facts. In this framework, the file system serves as a durable external memory and a shared coordination medium across agents and sessions, enabling iterative refinement beyond the context window. Experiments on two open-ended benchmarks (DeepResearch Bench and DeepConsult) show that FS-Researcher achieves state-of-the-art report quality across different backbone models. Further analyses demonstrate a positive correlation between final report quality and the computation allocated to the Context Builder, validating effective test-time scaling under the file-system paradigm. The code and data are open-sourced at https://github.com/Ignoramus0817/FS-Researcher.

cs.CL↗
arXiv2026

Bi-TEAM: A Unified Cross-Scale Representation Learning Framework for Chemically Modified Biomolecules

Representation learning for protein biochemical space faces a difficult trade-off: protein language models excel at capturing long-range biological semantics but often miss fine-grained chemical details. Conversely, chemical language models encode atomic information but lack broader sequence context. To address this, we introduce Bi-TEAM (Bi-gated Residual Space Modification), a general framework that injects localized chemical variation into global protein contexts. By ensuring robustness against perturbations such as non-canonical amino acids, post-translational modifications (PTMs), and topological constraints, Bi-TEAM uncovers functional chemical dependencies often missed by evolutionary baselines. Mechanistically, Bi-TEAM maps non-canonical residues to their natural counterparts and injects atomic-level data via a bi-gated residual fusion mechanism. Crucially, this process uses modification-aware prompts to ensure that local structural changes influence global functional representations without requiring alphabet expansion. We evaluated Bi-TEAM on ten datasets spanning chemically modified peptides, PTMs, and natural proteins. The model consistently outperformed state-of-the-art baselines, achieving up to a 66 percent improvement in Matthews correlation coefficient (MCC) on scaffold-similarity splits and a 350 percent increase in hemolysis prediction accuracy. Furthermore, when deployed as an oracle for generative modeling, Bi-TEAM nearly quadrupled the success rate for designing cell-penetrating cyclic peptides. By unifying biological semantics with chemical precision, Bi-TEAM provides a versatile foundation for machine learning driven exploration of peptide and protein biochemical space.

q-bio.BM↗
arXiv2026

Designing the Haystack: Programmable Chemical Space for Generative Molecular Discovery

Chemical space exploration underlies drug discovery, yet most generative models treat chemical space as a fixed, implicitly learned distribution, focusing on sampling molecules rather than deliberately designing the space itself. We introduce SpaceGFN, a generative framework that elevates chemical space to a programmable computational object: a controllable degree of freedom enabling explicit construction and adaptive traversal of structured molecular universes. SpaceGFN decouples space definition from exploration. Users specify building blocks and reaction rules to construct chemically and synthetically coherent spaces, while a GFlowNet performs efficient, property-biased sampling within them. In Discovery mode, we demonstrate programmable space design through two strategies. A pseudo-natural product space assembles natural product-like architectures. An evolution-inspired (Evo) space recombines endogenous metabolite fragments via enzyme-consistent transformations, introducing an evolutionary prior into chemical generation. This bias yields favorable shifts in predicted metabolic and toxicological profiles while preserving pharmacological diversity, supported by broad docking enrichment across therapeutic targets. In Editing mode, SpaceGFN enables reaction-consistent lead optimization through a curated toolkit of executable synthetic transformations, allowing local, synthesis-aware modification of existing compounds instead of unrestricted graph mutation. Across 96 drug targets, SpaceGFN achieves strong optimization performance while maintaining structural diversity under synthetic constraints. By integrating programmable chemical universe construction with flow-based exploration and reaction-level editing, SpaceGFN establishes a general paradigm for deliberate navigation of therapeutic chemical space.

physics.chem-ph↗
arXiv2026

Dual-Regime Hybrid Aerodynamic Modeling of Winged Blimps With Neural Mixing

Winged blimps operate across distinct aerodynamic regimes that cannot be adequately captured by a single model. At high speeds and small angles of attack, their dynamics exhibit strong coupling between lift and attitude, resembling fixed-wing aircraft behavior. At low speeds or large angles of attack, viscous effects and flow separation dominate, leading to drag-driven and damping-dominated dynamics. Accurately representing transitions between these regimes remains a fundamental challenge. This paper presents a hybrid aerodynamic modeling framework that integrates a fixed-wing Aerodynamic Coupling Model (ACM) and a Generalized Drag Model (GDM) using a learned neural network mixer with explicit physics-based regularization. The mixer enables smooth transitions between regimes while retaining explicit, physics-based aerodynamic representation. Model parameters are identified through a structured three-phase pipeline tailored for hybrid aerodynamic modeling. The proposed approach is validated on the RGBlimp platform through a large-scale experimental campaign comprising 1,320 real-world flight trajectories across 330 thruster and moving mass configurations, spanning a wide range of speeds and angles of attack. Experimental results demonstrate that the proposed hybrid model consistently outperforms single-model and predefined-mixer baselines, establishing a practical and robust aerodynamic modeling solution for winged blimps.

cs.RO↗
arXiv2026

Wiki Live Challenge: Challenging Deep Research Agents with Expert-Level Wikipedia Articles

Deep Research Agents (DRAs) have demonstrated remarkable capabilities in autonomous information retrieval and report generation, showing great potential to assist humans in complex research tasks. Current evaluation frameworks primarily rely on LLM-generated references or LLM-derived evaluation dimensions. While these approaches offer scalability, they often lack the reliability of expert-verified content and struggle to provide objective, fine-grained assessments of critical dimensions. To bridge this gap, we introduce Wiki Live Challenge (WLC), a live benchmark that leverages the newest Wikipedia Good Articles (GAs) as expert-level references. Wikipedia's strict standards for neutrality, comprehensiveness, and verifiability serve as a great challenge for DRAs, with GAs representing the pinnacle of which. We curate a dataset of 100 recent Good Articles and propose Wiki Eval, a comprehensive evaluation framework comprising a fine-grained evaluation method with 39 criteria for writing quality and rigorous metrics for factual verifiability. Extensive experiments on various DRA systems demonstrate a significant gap between current DRAs and human expert-level Wikipedia articles, validating the effectiveness of WLC in advancing agent research. We release our benchmark at https://github.com/WangShao2000/Wiki_Live_Challenge

cs.CL↗
arXiv2026

A-RAG: Scaling Agentic Retrieval-Augmented Generation via Hierarchical Retrieval Interfaces

Frontier language models have demonstrated strong reasoning and long-horizon tool-use capabilities. However, existing RAG systems fail to leverage these capabilities. They still rely on two paradigms: (1) designing an algorithm that retrieves passages in a single shot and concatenates them into the model's input, or (2) predefining a workflow and prompting the model to execute it step-by-step. Neither paradigm allows the model to participate in retrieval decisions, preventing efficient scaling with model improvements. In this paper, we introduce A-RAG, an Agentic RAG framework that exposes hierarchical retrieval interfaces directly to the model. A-RAG provides three retrieval tools: keyword search, semantic search, and chunk read, enabling the agent to adaptively search and retrieve information across multiple granularities. Experiments on multiple open-domain QA benchmarks show that A-RAG consistently outperforms existing approaches with comparable or lower retrieved tokens, demonstrating that A-RAG effectively leverages model capabilities and dynamically adapts to different RAG tasks. We further systematically study how A-RAG scales with model size and test-time compute. We will release our code and evaluation suite to facilitate future research. Code and evaluation suite are available at https://github.com/Ayanami0730/arag.

cs.CL↗
arXiv2025

Multiscale Cross-Modal Mapping of Molecular, Pathologic, and Radiologic Phenotypes in Lipid-Deficient Clear Cell Renal CellCarcinoma

Clear cell renal cell carcinoma (ccRCC) exhibits extensive intratumoral heterogeneity on multiple biological scales, contributing to variable clinical outcomes and limiting the effectiveness of conventional TNM staging, which highlights the urgent need for multiscale integrative analytic frameworks. The lipid-deficient de-clear cell differentiated (DCCD) ccRCC subtype, defined by multi-omics analyses, is associated with adverse outcomes even in early-stage disease. Here, we establish a hierarchical cross-scale framework for the preoperative identification of DCCD-ccRCC. At the highest layer, cross-modal mapping transferred molecular signatures to histological and CT phenotypes, establishing a molecular-to-pathology-to-radiology supervisory bridge. Within this framework, each modality-specific model is designed to mirror the inherent hierarchical structure of tumor biology. PathoDCCD captured multi-scale microscopic features, from cellular morphology and tissue architecture to meso-regional organization. RadioDCCD integrated complementary macroscopic information by combining whole-tumor and its habitat-subregions radiomics with a 2D maximal-section heterogeneity metric. These nested models enabled integrated molecular subtype prediction and clinical risk stratification. Across five cohorts totaling 1,659 patients, PathoDCCD reliably recapitulated molecular subtypes, while RadioDCCD provided reliable preoperative prediction. The consistent predictions identified patients with the poorest clinical outcomes. This cross-scale paradigm unifies molecular biology, computational pathology, and quantitative radiology into a biologically grounded strategy for preoperative noninvasive molecular phenotyping of ccRCC.

q-bio.QM↗
arXiv2025

An Index-based Approach for Efficient and Effective Web Content Extraction

As web agents (e.g., Deep Research) routinely consume massive volumes of web pages to gather and analyze information, LLM context management -- under large token budgets and low signal density -- emerges as a foundational, high-importance, and technically challenging problem for agentic and RAG pipelines. Existing solutions for extracting relevant content are inadequate: generative extraction models suffer from high latency, rule-based heuristics lack adaptability, and chunk-and-rerank methods are blind to webpage structure. To overcome these issues, we introduce Index-based Web Content Extraction to reframe the extraction process from slow, token-by-token generation into a highly efficient, discriminative task of index prediction, achieving both effectiveness and efficiency. We partition HTML into structure-aware, addressable segments, and extract only the positional indices of content relevant to a given query. This method decouples extraction latency from content length, enabling rapid, query-relevant extraction. We first evaluate our method as a post-retrieval processing component within an RAG QA system and find that it improves QA accuracy. Then we directly measure its match rate with the target content in two scenarios: main content extraction (ME) and query-relevant extraction (QE). Experimental results show that our method outperforms existing works in both accuracy and speed, effectively bridging the gap between LLMs and the vast webpages.

cs.IR↗
arXiv2025

CONFIDE: Hallucination Assessment for Reliable Biomolecular Structure Prediction and Design

Reliable evaluation of protein structure predictions remains challenging, as metrics like pLDDT capture energetic stability but often miss subtle errors such as atomic clashes or conformational traps reflecting topological frustration within the protein folding energy landscape. We present CODE (Chain of Diffusion Embeddings), a self evaluating metric empirically found to quantify topological frustration directly from the latent diffusion embeddings of the AlphaFold3 series of structure predictors in a fully unsupervised manner. Integrating this with pLDDT, we propose CONFIDE, a unified evaluation framework that combines energetic and topological perspectives to improve the reliability of AlphaFold3 and related models. CODE strongly correlates with protein folding rates driven by topological frustration, achieving a correlation of 0.82 compared to pLDDT's 0.33 (a relative improvement of 148\%). CONFIDE significantly enhances the reliability of quality evaluation in molecular glue structure prediction benchmarks, achieving a Spearman correlation of 0.73 with RMSD, compared to pLDDT's correlation of 0.42, a relative improvement of 73.8\%. Beyond quality assessment, our approach applies to diverse drug design tasks, including all-atom binder design, enzymatic active site mapping, mutation induced binding affinity prediction, nucleic acid aptamer screening, and flexible protein modeling. By combining data driven embeddings with theoretical insight, CODE and CONFIDE outperform existing metrics across a wide range of biomolecular systems, offering robust and versatile tools to refine structure predictions, advance structural biology, and accelerate drug discovery.

q-bio.BM↗
arXiv2025

Thinker: Training LLMs in Hierarchical Thinking for Deep Search via Multi-Turn Interaction

Efficient retrieval of external knowledge bases and web pages is crucial for enhancing the reasoning abilities of LLMs. Previous works on training LLMs to leverage external retrievers for solving complex problems have predominantly employed end-to-end reinforcement learning. However, these approaches neglect supervision over the reasoning process, making it difficult to guarantee logical coherence and rigor. To address these limitations, we propose Thinker, a hierarchical thinking model for deep search through multi-turn interaction, making the reasoning process supervisable and verifiable. It decomposes complex problems into independently solvable sub-problems, each dually represented in both natural language and an equivalent logical function to support knowledge base and web searches. Concurrently, dependencies between sub-problems are passed as parameters via these logical functions, enhancing the logical coherence of the problem-solving process. To avoid unnecessary external searches, we perform knowledge boundary determination to check if a sub-problem is within the LLM's intrinsic knowledge, allowing it to answer directly. Experimental results indicate that with as few as several hundred training samples, the performance of Thinker is competitive with established baselines. Furthermore, when scaled to the full training set, Thinker significantly outperforms these methods across various datasets and model sizes. The source code is available at https://github.com/OpenSPG/KAG-Thinker.

cs.AI↗
arXiv2025

GRIP: A Graph-Based Reasoning Instruction Producer

Large-scale, high-quality data is essential for advancing the reasoning capabilities of large language models (LLMs). As publicly available Internet data becomes increasingly scarce, synthetic data has emerged as a crucial research direction. However, existing data synthesis methods often suffer from limited scalability, insufficient sample diversity, and a tendency to overfit to seed data, which constrains their practical utility. In this paper, we present \textit{\textbf{GRIP}}, a \textbf{G}raph-based \textbf{R}easoning \textbf{I}nstruction \textbf{P}roducer that efficiently synthesizes high-quality and diverse reasoning instructions. \textit{GRIP} constructs a knowledge graph by extracting high-level concepts from seed data, and uniquely leverages both explicit and implicit relationships within the graph to drive large-scale and diverse instruction data synthesis, while employing open-source multi-model supervision to ensure data quality. We apply \textit{GRIP} to the critical and challenging domain of mathematical reasoning. Starting from a seed set of 7.5K math reasoning samples, we construct \textbf{GRIP-MATH}, a dataset containing 2.1 million synthesized question-answer pairs. Compared to similar synthetic data methods, \textit{GRIP} achieves greater scalability and diversity while also significantly reducing costs. On mathematical reasoning benchmarks, models trained with GRIP-MATH demonstrate substantial improvements over their base models and significantly outperform previous data synthesis methods.

cs.CL↗
arXiv2025

DualSG: A Dual-Stream Explicit Semantic-Guided Multivariate Time Series Forecasting Framework

Multivariate Time Series Forecasting plays a key role in many applications. Recent works have explored using Large Language Models for MTSF to take advantage of their reasoning abilities. However, many methods treat LLMs as end-to-end forecasters, which often leads to a loss of numerical precision and forces LLMs to handle patterns beyond their intended design. Alternatively, methods that attempt to align textual and time series modalities within latent space frequently encounter alignment difficulty. In this paper, we propose to treat LLMs not as standalone forecasters, but as semantic guidance modules within a dual-stream framework. We propose DualSG, a dual-stream framework that provides explicit semantic guidance, where LLMs act as Semantic Guides to refine rather than replace traditional predictions. As part of DualSG, we introduce Time Series Caption, an explicit prompt format that summarizes trend patterns in natural language and provides interpretable context for LLMs, rather than relying on implicit alignment between text and time series in the latent space. We also design a caption-guided fusion module that explicitly models inter-variable relationships while reducing noise and computation. Experiments on real-world datasets from diverse domains show that DualSG consistently outperforms 15 state-of-the-art baselines, demonstrating the value of explicitly combining numerical forecasting with semantic guidance.

cs.AI↗