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Yaorui Shi

Publications and source records attributed to Yaorui Shi.

At least 19 recordsLinked to original sources
arXiv2026

Escaping the Self-Confirmation Trap: An Execute-Distill-Verify Paradigm for Agentic Experience Learning

Experience-driven self-evolution is critical for large language model (LLM) agents to improve through open-world interaction. However, existing experience learning methods mostly rely on single-agent loops, where the same agent executes tasks, summarizes outcomes, and determines memory content. This setup makes agents vulnerable to the Self-Confirmation Trap: wrong-but-self-consistent trajectories are misidentified as successful experience, leading to cumulative errors during retrieval and reuse. To address this issue, we propose EDV, an Execute-Distill-Verify framework for reliable experience learning. In the Execute stage, multiple heterogeneous agents explore the same task space in parallel to generate diverse candidate trajectories. In the Distill stage, a dedicated third-party agent comparatively analyzes these trajectories to produce candidate experiences, reducing executor-centric summarization bias. In the Verify stage, the execution group validates candidates via a consensus mechanism, and only approved experiences are written into shared or private memory. By decoupling the three stages, EDV transforms experience learning from isolated self-reflection into collaborative construction, filtering erroneous and noisy content before memory insertion. We evaluate EDV on three challenging long-horizon benchmarks: tau2-bench, Mind2Web and MMTB. Results show EDV consistently outperforms strong baselines, validating that reliable experience construction is essential for robust agent self-evolution. Our code is available at https://github.com/shidingz/EDV.

cs.CL↗
arXiv2026

VitaBench 2.0: Evaluating Personalized and Proactive Agents in Long-Term User Interactions

Large language models (LLMs) have evolved into interactive agents that collaborate with users in real-world tasks. Effective collaboration in such settings increasingly depends on understanding the user beyond what is explicitly stated, as user intent is often reflected in fragmented daily interactions and requires both personalized modeling and proactive interaction. However, existing agent benchmarks primarily evaluate reasoning and tool use, largely overlooking the challenges of inferring and leveraging user preferences in realistic scenarios. To address this gap, we introduce VitaBench 2.0, a benchmark for evaluating personalized and proactive agent behavior in long-term user interactions. In VitaBench 2.0, tasks are organized as temporally ordered sequences for individual users, where preferences are embedded in fragmented and heterogeneous interactions. Successful completion of tasks requires the agent to continuously extract, utilize, and update user preferences from these interactions. We further evaluate proactiveness through tasks that require agents to recognize missing information and actively acquire it from users or environments before making decisions. To support systematic analysis, we provide an extensible memory interface that enables controlled comparison across different memory architectures. We benchmark a diverse set of frontier proprietary and open-source LLMs. Results show that real-world personalization remains highly challenging even for state-of-the-art models, revealing a substantial gap between current capabilities and practical requirements. Extensive analysis further reveals the failure modes and capability bottlenecks of current agents in real-world personalized decision-making, providing insights for future model improvements.

cs.AI↗
arXiv2026

Learning to Act under Noise: Enhancing Agent Robustness via Noisy Environments

Recent advances in large language models (LLMs) have facilitated the widespread deployment of LLMs as interactive agents capable of reasoning, planning, and tool use. Despite strong performance on existing benchmarks, such agents often exhibit notable degradation when deployed in real-world settings, where environments are inherently stochastic and imperfect. We argue that this discrepancy arises from a fundamental mismatch between idealized training settings and real-world interaction dynamics, where current paradigms rely on carefully curated task instructions and stable, well-controlled environments. To address this gap, we propose NoisyAgent, an agentic training framework that explicitly incorporates environmental imperfections into the agent learning process. We identify two major sources of interaction noise in real-world scenarios: user noise, which captures ambiguity and variability in user interaction, and tool noise, which reflects failures and anomalies in tool execution. We introduce such perturbations into the training pipeline by modifying user interaction patterns and simulating tool execution results within the training environment. To stabilize training while encouraging agents to handle increasingly challenging imperfections, noise is applied to only a subset of rollouts and progressively increased in difficulty as the model adapts to the current noise level. Extensive experiments demonstrate that our approach consistently improves agent robustness under noisy and dynamic environments. Our analysis reveals that training under noise conditions also yields performance gains on idealized benchmarks, suggesting that controlled exposure to environmental noise promotes more generalizable reasoning and decision-making behaviors. Our findings highlight the importance of modeling interaction imperfections for bridging the gap between agent training and real-world deployment.

cs.AI↗
arXiv2026

When to Stop Reusing: Dynamic Gradient Gating for Sample-Efficient RLVR

Reinforcement Learning with Verifiable Rewards (RLVR) has become the dominant paradigm for advanced reasoning in Large Language Models (LLMs), but rollout samples are expensive to obtain, making sample efficiency a critical bottleneck. A natural remedy is to reuse each rollout batch for multiple gradient updates, a standard practice in classical RL. Yet in RLVR, this amplifies policy shift, leading to severe performance degradation. Detecting the onset of degradation early enough to stop reuse remains an open and challenging problem. We close this gap by identifying the \textit{Disproportionate Weight Divergence (DWD)} phenomenon: performance degradation is synchronized with a sharp surge in the \texttt{lm\_head} weight change, while intermediate layers remain stable. Empirically, we verify that DWD emerges consistently across diverse LLMs and tasks. Theoretically, we prove that (i) harmful gradients concentrate at the \texttt{lm\_head} while intermediate layers are structurally attenuated, and (ii) the \texttt{lm\_head} gradient norm lower-bounds the policy divergence. These results establish the \texttt{lm\_head} gradient norm as a principled, real-time signal of catastrophic policy shift. Guided by this insight, we propose \textit{Dynamic Gradient Gating (DGG)}, a lightweight intervention that monitors the \texttt{lm\_head} gradient norm in real time and intercepts harmful gradients before they corrupt the optimizer. DGG consistently matches or exceeds the standard single-use baseline, achieving up to $2.93\times$ sample efficiency and $2.14\times$ wall-clock speedup across math, ALFWorld, WebShop, and search-augmented QA tasks.

cs.LG↗
arXiv2026

Look Before You Leap: Autonomous Exploration for LLM Agents

Large language model based agents often fail in unfamiliar environments due to premature exploitation: a tendency to act on prior knowledge before acquiring sufficient environment-specific information. We identify autonomous exploration as a critical yet underexplored capability for building adaptive agents. To formalize and quantify this capability, we introduce Exploration Checkpoint Coverage, a verifiable metric that measures how broadly an agent discovers key states, objects, and affordances. Our systematic evaluation reveals that agents trained with standard task-oriented reinforcement learning consistently exhibit narrow and repetitive behaviors that impede downstream performance. To address this limitation, we develop a training strategy that interleaves task-execution rollouts and exploration rollouts, with each type of rollout optimized by its corresponding verifiable reward. Building on this training strategy, we propose the Explore-then-Act paradigm, which decouples information-gathering from task execution: agents first utilize an interaction budget to acquire grounded environmental knowledge, then leverage it for task resolution. Our results demonstrate that learning to systematically explore is imperative for building generalizable and real-world-ready agents.

cs.AI↗
arXiv2026

Skill1: Unified Evolution of Skill-Augmented Agents via Reinforcement Learning

A persistent skill library allows language model agents to reuse successful strategies across tasks. Maintaining such a library requires three coupled capabilities. The agent selects a relevant skill, utilizes it during execution, and distills new skills from experience. Existing methods optimize these capabilities in isolation or with separate reward sources, resulting in partial and conflicting evolution. We propose Skill1, a framework that trains a single policy to co-evolve skill selection, utilization, and distillation toward a shared task-outcome objective. The policy generates a query to search the skill library, re-ranks candidates to select one, solves the task conditioned on it, and distills a new skill from the trajectory. All learning derives from a single task-outcome signal. Its low-frequency trend credits selection and its high-frequency variation credits distillation. Experiments on ALFWorld and WebShop show that Skill1 outperforms prior skill-based and reinforcement learning baselines. Training dynamics confirm the co-evolution of the three capabilities, and ablations show that removing any credit signal degrades the evolution.

cs.AI↗
arXiv2026

Joint Optimization of Multi-agent Memory System

Memory systems are critical for LLMs, mitigating context window limitations and supporting long-horizon user-LLM interactions. Such systems typically comprise multiple agents responsible for memory construction and retrieval. Existing approaches often optimize each agent independently under a shared global objective (e.g., downstream QA accuracy), treating other agents as a static environment. However, this design has two key limitations: (1) independent optimization ignores inter-agent dependencies and lacks agents' co-adaptation, and (2) relying solely on sparse global rewards provides limited guidance for optimizing specialized agents and causes ambiguous credit assignment. These may ultimately limit agents' effective collaboration in the memory system. To address these limitations, we propose CoMAM, a joint optimization framework that promotes collaboration among agents via end-to-end reinforcement learning and an adaptive credit assignment mechanism. Specifically, we model the multi-agent pipeline as a Markov decision process (MDP) to expose inter-agent dependencies during end-to-end training. Agents are then jointly optimized using a combination of their local task reward and an adaptively weighted global reward, enabling agents to co-adapt while receiving targeted feedback for their respective roles. Experiments show that CoMAM consistently outperforms leading memory systems, validating the effectiveness of the joint optimization framework.

cs.MA↗
arXiv2026

When to Memorize and When to Stop: Gated Recurrent Memory for Long-Context Reasoning

While reasoning over long context is crucial for various real-world applications, it remains challenging for large language models (LLMs) as they suffer from performance degradation as the context length grows. Recent work MemAgent has tried to tackle this by processing context chunk-by-chunk in an RNN-like loop and updating a textual memory for final answering. However, this naive recurrent memory update faces two crucial drawbacks: (i) memory can quickly explode because it can update indiscriminately, even on evidence-free chunks; and (ii) the loop lacks an exit mechanism, leading to unnecessary computation after even sufficient evidence is collected. To address these issues, we propose GRU-Mem, which incorporates two text-controlled gates for more stable and efficient long-context reasoning. Specifically, in GRU-Mem, the memory only updates when the update gate is open and the recurrent loop will exit immediately once the exit gate is open. To endow the model with such capabilities, we introduce two reward signals $r^{\text{update}}$ and $r^{\text{exit}}$ within end-to-end RL, rewarding the correct updating and exiting behaviors respectively. Experiments on various long-context reasoning tasks demonstrate the effectiveness and efficiency of GRU-Mem, which generally outperforms the vanilla MemAgent with up to 400\% times inference speed acceleration.

cs.CL↗
arXiv2026

Learning to Self-Verify Makes Language Models Better Reasoners

Recent large language models (LLMs) achieve strong performance in generating promising reasoning paths for complex tasks. However, despite powerful generation ability, LLMs remain weak at verifying their own answers, revealing a persistent capability asymmetry between generation and self-verification. In this work, we conduct an in-depth investigation of this asymmetry throughout training evolution and show that, even on the same task, improving generation does not lead to corresponding improvements in self-verification. Interestingly, we find that the reverse direction of this asymmetry behaves differently: learning to self-verify can effectively improve generation performance, achieving accuracy comparable to standard generation training while yielding more efficient and effective reasoning traces. Building on this observation, we further explore integrating self-verification into generation training by formulating a multi-task reinforcement learning framework, where generation and self-verification are optimized as two independent but complementary objectives. Extensive experiments across benchmarks and models demonstrate performance gains over generation-only training in both generation and verification capabilities.

cs.CL↗
arXiv2026

MemOCR: Layout-Aware Visual Memory for Efficient Long-Horizon Reasoning

Long-horizon agentic reasoning necessitates effectively compressing growing interaction histories into a limited context window. Most existing memory systems serialize history as text, where token-level cost is uniform and scales linearly with length, often spending scarce budget on low-value details. To this end, we introduce MemOCR, a multimodal memory agent that improves long-horizon reasoning under tight context budgets by allocating memory space with adaptive information density through visual layout. Concretely, MemOCR maintains a structured rich-text memory (e.g., headings, highlights) and renders it into an image that the agent consults for memory access, visually prioritizing crucial evidence while aggressively compressing auxiliary details. To ensure robustness across varying memory budgets, we train MemOCR with reinforcement learning under budget-aware objectives that expose the agent to diverse compression levels. Across long-context multi-hop and single-hop question-answering benchmarks, MemOCR outperforms strong text-based baselines and achieves more effective context utilization under extreme budgets.

cs.AI↗
arXiv2025

Reasoning-Enhanced Large Language Models for Molecular Property Prediction

Molecular property prediction is crucial for drug discovery and materials science, yet existing approaches suffer from limited interpretability, poor cross-task generalization, and lack of chemical reasoning capabilities. Traditional machine learning models struggle with task transferability, while specialized molecular language models provide little insight into their decision-making processes. To address these limitations, we propose \textbf{MPPReasoner}, a multimodal large language model that incorporates chemical reasoning for molecular property prediction. Our approach, built upon Qwen2.5-VL-7B-Instruct, integrates molecular images with SMILES strings to enable comprehensive molecular understanding. We develop a two-stage training strategy: supervised fine-tuning (SFT) using 16,000 high-quality reasoning trajectories generated through expert knowledge and multiple teacher models, followed by Reinforcement Learning from Principle-Guided Rewards (RLPGR). RLPGR employs verifiable, rule-based rewards that systematically evaluate chemical principle application, molecular structure analysis, and logical consistency through computational verification. Extensive experiments across 8 datasets demonstrate significant performance improvements, with MPPReasoner outperforming the best baselines by 7.91\% and 4.53\% on in-distribution and out-of-distribution tasks respectively. MPPReasoner exhibits exceptional cross-task generalization and generates chemically sound reasoning paths that provide valuable insights into molecular property analysis, substantially enhancing both interpretability and practical utility for chemists. Code is available at https://anonymous.4open.science/r/MPPReasoner-12687.

cs.LG↗
arXiv2025

Look Back to Reason Forward: Revisitable Memory for Long-Context LLM Agents

Large language models face challenges in long-context question answering, where key evidence of a query may be dispersed across millions of tokens. Existing works equip large language models with a memory buffer that is dynamically updated via a linear document scan, also known as the "memorize while reading" methods. While this approach scales efficiently, it suffers from pruning of latent evidence, information loss through overwriting, and sparse reinforcement learning signals. To tackle these challenges, we present ReMemR1, which integrates the mechanism of memory retrieval into the memory update process, enabling the agent to selectively callback historical memories for non-linear reasoning. To further strengthen training, we propose a multi-level reward design, which combines final-answer rewards with dense, step-level signals that guide effective memory use. Together, these contributions mitigate information degradation, improve supervision, and support complex multi-hop reasoning. Extensive experiments demonstrate that ReMemR1 significantly outperforms state-of-the-art baselines on long-context question answering while incurring negligible computational overhead, validating its ability to trade marginal cost for robust long-context reasoning.

cs.CL↗
arXiv2025

Search and Refine During Think: Facilitating Knowledge Refinement for Improved Retrieval-Augmented Reasoning

Large language models have demonstrated impressive reasoning capabilities but are inherently limited by their knowledge reservoir. Retrieval-augmented reasoning mitigates this limitation by allowing LLMs to query external resources, but existing methods often retrieve irrelevant or noisy information, hindering accurate reasoning. In this paper, we propose AutoRefine, a reinforcement learning post-training framework that adopts a new "search-and-refine-during-think" paradigm. AutoRefine introduces explicit knowledge refinement steps between successive search calls, enabling the model to iteratively filter, distill, and organize evidence before generating an answer. Furthermore, we incorporate tailored retrieval-specific rewards alongside answer correctness rewards using group relative policy optimization. Experiments on single-hop and multi-hop QA benchmarks demonstrate that AutoRefine significantly outperforms existing approaches, particularly in complex, multi-hop reasoning scenarios. Detailed analysis shows that AutoRefine issues frequent, higher-quality searches and synthesizes evidence effectively.

cs.CL↗
arXiv2025

Language-Enhanced Representation Learning for Single-Cell Transcriptomics

Single-cell RNA sequencing (scRNA-seq) offers detailed insights into cellular heterogeneity. Recent advancements leverage single-cell large language models (scLLMs) for effective representation learning. These models focus exclusively on transcriptomic data, neglecting complementary biological knowledge from textual descriptions. To overcome this limitation, we propose scMMGPT, a novel multimodal framework designed for language-enhanced representation learning in single-cell transcriptomics. Unlike existing methods, scMMGPT employs robust cell representation extraction, preserving quantitative gene expression data, and introduces an innovative two-stage pre-training strategy combining discriminative precision with generative flexibility. Extensive experiments demonstrate that scMMGPT significantly outperforms unimodal and multimodal baselines across key downstream tasks, including cell annotation and clustering, and exhibits superior generalization in out-of-distribution scenarios.

cs.LG↗
arXiv2025

NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation

3D molecule generation is crucial for drug discovery and material design. While prior efforts focus on 3D diffusion models for their benefits in modeling continuous 3D conformers, they overlook the advantages of 1D SELFIES-based Language Models (LMs), which can generate 100% valid molecules and leverage the billion-scale 1D molecule datasets. To combine these advantages for 3D molecule generation, we propose a foundation model -- NExT-Mol: 3D Diffusion Meets 1D Language Modeling for 3D Molecule Generation. NExT-Mol uses an extensively pretrained molecule LM for 1D molecule generation, and subsequently predicts the generated molecule's 3D conformers with a 3D diffusion model. We enhance NExT-Mol's performance by scaling up the LM's model size, refining the diffusion neural architecture, and applying 1D to 3D transfer learning. Notably, our 1D molecule LM significantly outperforms baselines in distributional similarity while ensuring validity, and our 3D diffusion model achieves leading performances in conformer prediction. Given these improvements in 1D and 3D modeling, NExT-Mol achieves a 26% relative improvement in 3D FCD for de novo 3D generation on GEOM-DRUGS, and a 13% average relative gain for conditional 3D generation on QM9-2014. Our codes and pretrained checkpoints are available at https://github.com/acharkq/NExT-Mol.

q-bio.QM↗
arXiv2024

Intelligent System for Automated Molecular Patent Infringement Assessment

Automated drug discovery offers significant potential for accelerating the development of novel therapeutics by substituting labor-intensive human workflows with machine-driven processes. However, molecules generated by artificial intelligence may unintentionally infringe on existing patents, posing legal and financial risks that impede the full automation of drug discovery pipelines. This paper introduces PatentFinder, a novel multi-agent and tool-enhanced intelligence system that can accurately and comprehensively evaluate small molecules for patent infringement. PatentFinder features five specialized agents that collaboratively analyze patent claims and molecular structures with heuristic and model-based tools, generating interpretable infringement reports. To support systematic evaluation, we curate MolPatent-240, a benchmark dataset tailored for patent infringement assessment algorithms. On this benchmark, PatentFinder outperforms baseline methods that rely solely on large language models or specialized chemical tools, achieving a 13.8% improvement in F1-score and a 12% increase in accuracy. Additionally, PatentFinder autonomously generates detailed and interpretable patent infringement reports, showcasing enhanced accuracy and improved interpretability. The high accuracy and interpretability of PatentFinder make it a valuable and reliable tool for automating patent infringement assessments, offering a practical solution for integrating patent protection analysis into the drug discovery pipeline.

cs.LG↗
arXiv2024

SciLitLLM: How to Adapt LLMs for Scientific Literature Understanding

Scientific literature understanding is crucial for extracting targeted information and garnering insights, thereby significantly advancing scientific discovery. Despite the remarkable success of Large Language Models (LLMs), they face challenges in scientific literature understanding, primarily due to (1) a lack of scientific knowledge and (2) unfamiliarity with specialized scientific tasks. To develop an LLM specialized in scientific literature understanding, we propose a hybrid strategy that integrates continual pre-training (CPT) and supervised fine-tuning (SFT), to simultaneously infuse scientific domain knowledge and enhance instruction-following capabilities for domain-specific tasks.cIn this process, we identify two key challenges: (1) constructing high-quality CPT corpora, and (2) generating diverse SFT instructions. We address these challenges through a meticulous pipeline, including PDF text extraction, parsing content error correction, quality filtering, and synthetic instruction creation. Applying this strategy, we present a suite of LLMs: SciLitLLM, specialized in scientific literature understanding. These models demonstrate promising performance on scientific literature understanding benchmarks. Our contributions are threefold: (1) We present an effective framework that integrates CPT and SFT to adapt LLMs to scientific literature understanding, which can also be easily adapted to other domains. (2) We propose an LLM-based synthesis method to generate diverse and high-quality scientific instructions, resulting in a new instruction set -- SciLitIns -- for supervised fine-tuning in less-represented scientific domains. (3) SciLitLLM achieves promising performance improvements on scientific literature understanding benchmarks.

cs.LG↗
arXiv2024

ReactXT: Understanding Molecular "Reaction-ship" via Reaction-Contextualized Molecule-Text Pretraining

Molecule-text modeling, which aims to facilitate molecule-relevant tasks with a textual interface and textual knowledge, is an emerging research direction. Beyond single molecules, studying reaction-text modeling holds promise for helping the synthesis of new materials and drugs. However, previous works mostly neglect reaction-text modeling: they primarily focus on modeling individual molecule-text pairs or learning chemical reactions without texts in context. Additionally, one key task of reaction-text modeling -- experimental procedure prediction -- is less explored due to the absence of an open-source dataset. The task is to predict step-by-step actions of conducting chemical experiments and is crucial to automating chemical synthesis. To resolve the challenges above, we propose a new pretraining method, ReactXT, for reaction-text modeling, and a new dataset, OpenExp, for experimental procedure prediction. Specifically, ReactXT features three types of input contexts to incrementally pretrain LMs. Each of the three input contexts corresponds to a pretraining task to improve the text-based understanding of either reactions or single molecules. ReactXT demonstrates consistent improvements in experimental procedure prediction and molecule captioning and offers competitive results in retrosynthesis. Our code is available at https://github.com/syr-cn/ReactXT.

q-bio.QM↗