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Jingrui He

Publications and source records attributed to Jingrui He.

At least 37 records · Page 2Linked to original sources
arXiv2026

ReContext: Recursive Evidence Replay as LLM Harness for Long-Context Reasoning

Understanding and reasoning over long contexts has become a key requirement for deploying large language models (LLMs) in realistic applications. Although recent LLMs support increasingly long context windows, they often fail to use relevant evidence that is already present in the input, revealing a gap between context access and effective context utilization. In this work, we propose Recursive Evidence Replay as LLM Harness for Long-Context Reasoning (RECONTEXT), a training-free inference method for improving long-context reasoning. RECONTEXT uses model-internal relevance signals to construct a query-conditioned evidence pool and replays it before final generation while preserving the full original context. This recursive selection process separates evidence organization from answer generation without training, external memory, or context pruning. We also provide a theoretical analysis based on associative memory, which characterizes the context as a memory store, the question as a retrieval cue, attention as cue-trace association, and replay as trace reactivation. Experiments on eight long-context datasets with 128K context length show that RECONTEXT consistently improves evidence utilization across Qwen3-4B, Qwen3-8B, and Llama3-8B, achieving the best average rank on all three backbones. Code is available at https://github.com/Yanjun-Zhao/ReContext.

cs.AI↗
arXiv2026

AutoTool: Dynamic Tool Selection and Integration for Agentic Reasoning

Agentic reinforcement learning has advanced large language models (LLMs) to reason through long chain-of-thought trajectories while interleaving external tool use. Existing approaches assume a fixed inventory of tools, which limits the adaptability of LLM agents to new or evolving toolsets. We present AutoTool, a training framework that equips LLM agents with dynamic tool-selection capabilities throughout their reasoning trajectories. AutoTool employs a dual-phase optimization pipeline: (i) SFT and RL-based trajectory stabilization for coherent reasoning, and (ii) KL-regularized Plackett-Luce Ranking to refine consistent multi-step tool selection. We further build a 200k dataset with explicit tool-selection rationales across 1,000+ tools and 100+ tasks spanning mathematics, science, code generation, and multimodal reasoning. Across ten diverse benchmarks, we train two base models, Qwen3-8B and Qwen2.5-VL-7B, with AutoTool. With fewer parameters, AutoTool consistently outperforms advanced LLM agents and tool-integration methods, yielding average gains of 6.4% in math & science reasoning, 4.5% in search-based QA, 7.7% in code generation, and 6.9% in multimodal understanding. In addition, AutoTool exhibits stronger generalization by dynamically leveraging unseen tools from evolving toolsets during inference.

cs.CL↗
arXiv2026

TSAQA: Time Series Analysis Question And Answering Benchmark

Time series data are integral to critical applications across domains such as finance, healthcare, transportation, and environmental science. While recent work has begun to explore multi-task time series question answering (QA), current benchmarks remain limited to forecasting and anomaly detection tasks. We introduce TSAQA, a novel unified benchmark designed to broaden task coverage and evaluate diverse temporal analysis capabilities. TSAQA integrates six diverse tasks under a single framework ranging from conventional analysis, including anomaly detection and classification, to advanced analysis, such as characterization, comparison, data transformation, and temporal relationship analysis. Spanning 210k samples across 13 domains, the dataset employs diverse formats, including true-or-false (TF), multiple-choice (MC), and a novel puzzling (PZ), to comprehensively assess time series analysis. Zero-shot evaluation demonstrates that these tasks are challenging for current Large Language Models (LLMs): the best-performing commercial LLM, Gemini-2.5-Flash, achieves an average score of only 65.08. Although instruction tuning boosts open-source performance: the best-performing open-source model, LLaMA-3.1-8B, shows significant room for improvement, highlighting the complexity of temporal analysis for LLMs.

cs.AI↗
arXiv2026

Harnessing Generalist Agents for Contextualized Time Series

Time series are often embedded in rich contexts that are essential for holistic modeling. Moreover, real-world practitioners often require end-to-end workflows for analyzing temporal dynamics, where widely studied tasks such as forecasting are only one step in a broader solution loop. While generalist AI agents offer a promising interface for such workflows under complex contexts, they still operate primarily in textual spaces that are not fully aligned with structured temporal signals. In this work, we introduce TimeClaw, an agentic harness framework for time series that equips generalist LLM agents with the time series-native runtime support needed for contextualized temporal reasoning. TimeClaw integrates executable temporal tools for grounded and auditable analysis, experience-driven capability evolution for creating reusable analytical routines, and episodic multimodal memory for retrieving relevant reasoning traces. Together, these components unlock harnessed open-ended temporal reasoning with contextual information. Extensive evaluation on multiple benchmarks covering diverse tasks across energy, finance, weather, traffic, and other real-world domains demonstrates improved performance of TimeClaw. Code is available at https://github.com/iDEA-iSAIL-Lab-UIUC/TimeClaw.

cs.AI↗
arXiv2026

Local Clustering on Complex Graphs and Complex Hypergraphs

Local/seeded clustering aims to find a compact cluster near the given starting instances. While most existing studies on graph clustering assume a discrete graph setting (i.e., unweighted, undirected graphs without self-loops), real-world graphs can be more complex. In this paper, we extend the classic non-approximating Andersen-Chung-Lang (ACL) clustering algorithm beyond discrete graphs and generalize its quadratic optimality to a wider range of complex graphs, including weighted, directed, and self-looped graphs and hypergraphs with edge-dependent vertex weights. Specifically, by leveraging PageRank, we propose two algorithms: GeneralACL for graphs and HyperACL for hypergraphs. We prove that, under two mild conditions, both algorithms can identify a quadratically optimal cluster in terms of conductance. Additionally, we provide experiments to validate our theoretical findings. Our code is available at https://github.com/iDEA-iSAIL-Lab-UIUC/HyperACL.

cs.SI↗
arXiv2026

Evo-Memory: Benchmarking LLM Agent Test-time Learning with Self-Evolving Memory

Statefulness is essential for large language model (LLM) agents to perform long-term planning and problem-solving. This makes memory a critical component, yet its management and evolution remain largely underexplored. Existing evaluations mostly focus on static conversational settings, where memory is passively retrieved from dialogue to answer queries, overlooking the dynamic ability to accumulate and reuse experience across evolving task streams. In real-world environments such as interactive problem assistants or embodied agents, LLMs are required to handle continuous task streams, yet often fail to learn from accumulated interactions, losing valuable contextual insights, a limitation that calls for test-time evolution, where LLMs retrieve, integrate, and update memory continuously during deployment. To bridge this gap, we introduce Evo-Memory, a comprehensive streaming benchmark and framework for evaluating self-evolving memory in LLM agents. Evo-Memory structures datasets into sequential task streams, requiring LLMs to search, adapt, and evolve memory after each interaction. We unify and implement over ten representative memory modules and evaluate them across 10 diverse multi-turn goal-oriented and single-turn reasoning and QA datasets. To better benchmark experience reuse, we provide a baseline method, ExpRAG, for retrieving and utilizing prior experience, and further propose ReMem, an action-think-memory refine pipeline that tightly integrates reasoning, task actions, and memory updates to achieve continual improvement.

cs.CL↗
arXiv2026

Code as Agent Harness

Recent large language models (LLMs) have demonstrated strong capabilities in understanding and generating code, from competitive programming to repository-level software engineering. In emerging agentic systems, code is no longer only a target output. It increasingly serves as an operational substrate for agent reasoning, acting, environment modeling, and execution-based verification. We frame this shift through the lens of agent harnesses and introduce code as agent harness: a unified view that centers code as the basis for agent infrastructure. To systematically study this perspective, we organize the survey around three connected layers. First, we study the harness interface, where code connects agents to reasoning, action, and environment modeling. Second, we examine harness mechanisms: planning, memory, and tool use for long-horizon execution, together with feedback-driven control and optimization that make harness reliable and adaptive. Third, we discuss scaling the harness from single-agent systems to multi-agent settings, where shared code artifacts support multi-agent coordination, review, and verification. Across these layers, we summarize representative methods and practical applications of code as agent harness, spanning coding assistants, GUI/OS automation, embodied agents, scientific discovery, personalization and recommendation, DevOps, and enterprise workflows. We further outline open challenges for harness engineering, including evaluation beyond final task success, verification under incomplete feedback, regression-free harness improvement, consistent shared state across multiple agents, human oversight for safety-critical actions, and extensions to multimodal environments. By centering code as the harness of agentic AI, this survey provides a unified roadmap toward executable, verifiable, and stateful AI agent systems.

cs.CL↗
arXiv2026

Heterogeneous Scientific Foundation Model Collaboration

Agentic large language model systems have demonstrated strong capabilities. However, their reliance on language as the universal interface fundamentally limits their applicability to many real-world problems, especially in scientific domains where domain-specific foundation models have been developed to address specialized tasks beyond natural language. In this work, we introduce Eywa, a heterogeneous agentic framework designed to extend language-centric systems to a broader class of scientific foundation models. The key idea of Eywa is to augment domain-specific foundation models with a language-model-based reasoning interface, enabling language models to guide inference over non-linguistic data modalities. This design allows predictive foundation models, which are typically optimized for specialized data and tasks, to participate in higher-level reasoning and decision-making processes within agentic systems. Eywa can serve as a drop-in replacement for a single-agent pipeline (EywaAgent) or be integrated into existing multi-agent systems by replacing traditional agents with specialized agents (EywaMAS). We further investigate a planning-based orchestration framework in which a planner dynamically coordinates traditional agents and Eywa agents to solve complex tasks across heterogeneous data modalities (EywaOrchestra). We evaluate Eywa across a diverse set of scientific domains spanning physical, life, and social sciences. Experimental results demonstrate that Eywa improves performance on tasks involving structured and domain-specific data, while reducing reliance on language-based reasoning through effective collaboration with specialized foundation models.

cs.AI↗
arXiv2026

PaperMind: Benchmarking Agentic Reasoning and Critique over Scientific Papers in Multimodal LLMs

Understanding scientific papers requires more than answering isolated questions or summarizing content. It involves an integrated reasoning process that grounds textual and visual information, interprets experimental evidence, synthesizes information across sources, and critically evaluates scientific claims. However, existing benchmarks typically assess these abilities in isolation, making it difficult to evaluate scientific paper understanding as a unified set of interacting cognitive abilities. In this work, we introduce PaperMind, a benchmark designed to evaluate integrated and agent-oriented scientific reasoning over research papers. PaperMind is constructed from real scientific papers across seven domains, including agriculture, biology, chemistry, computer science, medicine, physics, and economics. It comprises four complementary task families that collectively operationalize distinct cognitive facets of scientific paper reasoning, including multimodal grounding, experimental interpretation, cross-source evidence reasoning, and critical assessment. By analyzing model behavior across multiple tasks, PaperMind enables a diagnostic evaluation of integrated scientific reasoning behaviors that are difficult to assess through isolated task evaluations. Extensive experiments on both opensource and closed-source multimodal LLMs reveal consistent performance gaps across tasks, highlighting persistent challenges in integrated scientific reasoning and critique. Our benchmark and dataset are available at https:// github.com/Yanjun-Zhao/PaperMind.

cs.IR↗
arXiv2026

Ramen: Robust Test-Time Adaptation of Vision-Language Models with Active Sample Selection

Pretrained vision-language models such as CLIP exhibit strong zero-shot generalization but remain sensitive to distribution shifts. Test-time adaptation adapts models during inference without access to source data or target labels, offering a practical way to handle such shifts. However, existing methods typically assume that test samples come from a single, consistent domain, while in practice, test data often include samples from mixed domains with distinct characteristics. Consequently, their performance degrades under mixed-domain settings. To address this, we present Ramen, a framework for robust test-time adaptation through active sample selection. For each incoming test sample, Ramen retrieves a customized batch of relevant samples from previously seen data based on two criteria: domain consistency, which ensures that adaptation focuses on data from similar domains, and prediction balance, which mitigates adaptation bias caused by skewed predictions. To improve efficiency, Ramen employs an embedding-gradient cache that stores the embeddings and sample-level gradients of past test images. The stored embeddings are used to retrieve relevant samples, and the corresponding gradients are aggregated for model updates, eliminating the need for any additional forward or backward passes. Our theoretical analysis provides insight into why the proposed adaptation mechanism is effective under mixed-domain shifts. Experiments on multiple image corruption and domain-shift benchmarks demonstrate that Ramen achieves strong and consistent performance, offering robust and efficient adaptation in complex mixed-domain scenarios. Our code is available at https://github.com/baowenxuan/Ramen .

cs.CV↗
arXiv2026

Neural Exploitation and Exploration of Contextual Bandits

In this paper, we study utilizing neural networks for the exploitation and exploration of contextual multi-armed bandits. Contextual multi-armed bandits have been studied for decades with various applications. To solve the exploitation-exploration trade-off in bandits, there are three main techniques: epsilon-greedy, Thompson Sampling (TS), and Upper Confidence Bound (UCB). In recent literature, a series of neural bandit algorithms have been proposed to adapt to the non-linear reward function, combined with TS or UCB strategies for exploration. In this paper, instead of calculating a large-deviation based statistical bound for exploration like previous methods, we propose, ``EE-Net,'' a novel neural-based exploitation and exploration strategy. In addition to using a neural network (Exploitation network) to learn the reward function, EE-Net uses another neural network (Exploration network) to adaptively learn the potential gains compared to the currently estimated reward for exploration. We provide an instance-based $\widetilde{\mathcal{O}}(\sqrt{T})$ regret upper bound for EE-Net and show that EE-Net outperforms related linear and neural contextual bandit baselines on real-world datasets.

cs.LG↗
arXiv2026

OWLEYE: Zero-Shot Learner for Cross-Domain Graph Data Anomaly Detection

Graph data is informative to represent complex relationships such as transactions between accounts, communications between devices, and dependencies among machines or processes. Correspondingly, graph anomaly detection (GAD) plays a critical role in identifying anomalies across various domains, including finance, cybersecurity, manufacturing, etc. Facing the large-volume and multi-domain graph data, nascent efforts attempt to develop foundational generalist models capable of detecting anomalies in unseen graphs without retraining. To the best of our knowledge, the different feature semantics and dimensions of cross-domain graph data heavily hinder the development of the graph foundation model, leaving further in-depth continual learning and inference capabilities a quite open problem. Hence, we propose OWLEYE, a novel zero-shot GAD framework that learns transferable patterns of normal behavior from multiple graphs, with a threefold contribution. First, OWLEYE proposes a cross-domain feature alignment module to harmonize feature distributions, which preserves domain-specific semantics during alignment. Second, with aligned features, to enable continuous learning capabilities, OWLEYE designs the multi-domain multi-pattern dictionary learning to encode shared structural and attribute-based patterns. Third, for achieving the in-context learning ability, OWLEYE develops a truncated attention-based reconstruction module to robustly detect anomalies without requiring labeled data for unseen graph-structured data. Extensive experiments on real-world datasets demonstrate that OWLEYE achieves superior performance and generalizability compared to state-of-the-art baselines, establishing a strong foundation for scalable and label-efficient anomaly detection.

cs.LG↗
arXiv2026

Prune as You Generate: Online Rollout Pruning for Faster and Better RLVR

Reinforcement Learning with Verifiable Rewards (RLVR) has significantly advanced the reasoning capabilities of Large Language Models (LLMs). However, methods such as GRPO and DAPO suffer from substantial computational cost, since they rely on sampling many rollouts for each prompt. Moreover, in RLVR the relative advantage is often sparse: many samples become nearly all-correct or all-incorrect, yielding low within-group reward variance and thus weak learning signals. In this paper, we introduce arrol (Accelerating RLVR via online Rollout Pruning), an online rollout pruning method that prunes rollouts during generation while explicitly steering the surviving ones more correctness-balanced to enhance learning signals. Specifically, arrol trains a lightweight quality head on-the-fly to predict the success probability of partial rollouts and uses it to make early pruning decisions. The learned quality head can further weigh candidates to improve inference accuracy during test-time scaling. To improve efficiency, we present a system design that prunes rollouts inside the inference engine and re-batches the remaining ones for log-probability computation and policy updates. Across GRPO and DAPO on Qwen-3 and LLaMA-3.2 models (1B-8B), arrol improves average accuracy by +2.30 to +2.99 while achieving up to 1.7x training speedup, and yielding up to +8.33 additional gains in average accuracy in test-time scaling. The code is available at https://github.com/Hsu1023/ARRoL.

cs.CL↗
arXiv2026

Flow Matching Meets Biology and Life Science: A Survey

Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule design, protein generation, catalysis discovery, drug discovery, and beyond. At the same time, biological applications have served as valuable testbeds for evaluating the capabilities of generative models. Recently, flow matching has emerged as a powerful and efficient alternative to diffusion-based generative modeling, with growing interest in its application to problems in biology and life sciences. This paper presents the first comprehensive survey of recent developments in flow matching and its applications in biological domains. We begin by systematically reviewing the foundations and variants of flow matching, and then categorize its applications into three major areas: biological sequence modeling, molecule generation and design, and peptide and protein generation. For each, we provide an in-depth review of recent progress. We also summarize commonly used datasets and software tools, and conclude with a discussion of potential future directions. The corresponding curated resources are available at https://github.com/Violet24K/Awesome-Flow-Matching-Meets-Biology.

cs.LG↗
arXiv2026

Language in the Flow of Time: Time-Series-Paired Texts Weaved into a Unified Temporal Narrative

While many advances in time series models focus exclusively on numerical data, research on multimodal time series, particularly those involving contextual textual information, remains in its infancy. With recent progress in large language models and time series learning, we revisit the integration of paired texts with time series through the Platonic Representation Hypothesis, which posits that representations of different modalities converge to shared spaces. In this context, we identify that time-series-paired texts may naturally exhibit periodic properties that closely mirror those of the original time series. Building on this insight, we propose a novel framework, Texts as Time Series (TaTS), which considers the time-series-paired texts to be auxiliary variables of the time series. TaTS can be plugged into any existing numerical-only time series models and effectively enable them to handle time series data with paired texts. Through extensive experiments on both multimodal time series forecasting and imputation tasks across benchmark datasets with various existing time series models, we demonstrate that TaTS can enhance multimodal predictive performance without modifying model architectures. Our Code is available at https://github.com/iDEA-iSAIL-Lab-UIUC/TaTS.

cs.LG↗
arXiv2026

MC-Search: Evaluating and Enhancing Multimodal Agentic Search with Structured Long Reasoning Chains

With the increasing demand for step-wise, cross-modal, and knowledge-grounded reasoning, multimodal large language models (MLLMs) are evolving beyond the traditional fixed retrieve-then-generate paradigm toward more sophisticated agentic multimodal retrieval-augmented generation (MM-RAG). Existing benchmarks, however, mainly focus on simplified QA with short retrieval chains, leaving adaptive planning and multimodal reasoning underexplored. We present MC-Search, the first benchmark for agentic MM-RAG with long, step-wise annotated reasoning chains spanning five representative reasoning structures. Each example specifies sub-questions, retrieval modalities, supporting facts, and intermediate answers, with fidelity ensured by HAVE (Hop-wise Attribution and Verification of Evidence), resulting in 3,333 high-quality examples averaging 3.7 hops. Beyond answer accuracy, MC-Search introduces new process-level metrics for reasoning quality, stepwise retrieval and planning accuracy. By developing a unified agentic MM-RAG pipeline, we benchmark six leading MLLMs and reveal systematic issues such as over- and under-retrieval and modality-misaligned planning. Finally, we introduce Search-Align, a process-supervised fine-tuning framework leveraging verified reasoning chains, showing that our data not only enables faithful evaluation but also improves planning and retrieval fidelity in open-source MLLMs.

cs.AI↗
arXiv2026

Hypergraphs as Weighted Directed Self-Looped Graphs: Spectral Properties, Clustering, Cheeger Inequality

Hypergraphs naturally arise when studying group relations and have been widely used in the field of machine learning. To the best of our knowledge, the recently proposed edge-dependent vertex weights (EDVW) modeling is one of the most generalized modeling methods of hypergraphs, i.e., most existing hypergraph conceptual modeling methods can be generalized as EDVW hypergraphs without information loss. However, the relevant algorithmic developments on EDVW hypergraphs remain nascent: compared to the spectral theories for graphs, its formulations are incomplete, the spectral clustering algorithms are not well-developed, and the hypergraph Cheeger Inequality is not well-defined. To this end, deriving a unified random walk-based formulation, we propose our definitions of hypergraph Rayleigh Quotient, NCut, boundary/cut, volume, and conductance, which are consistent with the corresponding definitions on graphs. Then, we prove that the normalized hypergraph Laplacian is associated with the NCut value, which inspires our proposed HyperClus-G algorithm for spectral clustering on EDVW hypergraphs. Finally, we prove that HyperClus-G can always find an approximately linearly optimal partitioning in terms of both NCut and conductance. Additionally, we provide extensive experiments to validate our theoretical findings from an empirical perspective. Code of HyperClus-G is available at https://github.com/iDEA-iSAIL-Lab-UIUC/HyperClus-G.

cs.SI↗
arXiv2026

Influence-Preserving Proxies for Gradient-Based Data Selection in LLM Fine-tuning

Supervised fine-tuning (SFT) relies critically on selecting training data that most benefits a model's downstream performance. Gradient-based data selection methods such as TracIn and Influence Functions leverage influence to identify useful samples, but their computational cost scales poorly, making them impractical for multi-billion-parameter large language models (LLMs). A common alternative is to use off-the-shelf smaller models as proxies, but they remain suboptimal since their learning dynamics are unclear, their sizes cannot be flexibly adjusted, and they cannot be further aligned with the target model in terms of gradient-based influence estimation. To address these challenges, we introduce Iprox, a two-stage framework that derives influence-preserving proxies directly from the target model. It first applies a low-rank compression stage to preserve influence information of the target model, and then an aligning stage to align both model gradients and logits, thereby constructing proxies that flexibly control computational cost while retaining the target model's influence. Experimental results across diverse LLM families and evaluation tasks show that Iprox consistently outperforms off-the-shelf proxies and baseline methods. On Qwen3-4B, a 1.5B proxy constructed with Iprox achieves stronger performance than the larger 1.7B off-the-shelf proxy. Notably, on Llama3.2, Iprox achieves better performance than baselines while reducing computational cost by more than half relative to the full 3B model. These results show that Iprox provides effective influence-preserving proxies, making gradient-based data selection more scalable for LLMs.

cs.LG↗