Yaorui Shi

Zhiyuan Liu, Yaorui Shi, An Zhang et al.

Masked graph modeling excels in the self-supervised representation learning of molecular graphs. Scrutinizing previous studies, we can reveal a common scheme consisting of three key components: (1) graph tokenizer, which breaks a molecular graph into smaller fragments (i.e., subgraphs) and converts them into tokens; (2) graph masking, which corrupts the graph with masks; (3) graph autoencoder, which first applies an encoder on the masked graph to generate the representations, and then employs a decoder on the representations to recover the tokens of the original graph. However, the previous MGM studies focus extensively on graph masking and encoder, while there is limited understanding of tokenizer and decoder. To bridge the gap, we first summarize popular molecule tokenizers at the granularity of node, edge, motif, and Graph Neural Networks (GNNs), and then examine their roles as the MGM's reconstruction targets. Further, we explore the potential of adopting an expressive decoder in MGM. Our results show that a subgraph-level tokenizer and a sufficiently expressive decoder with remask decoding have a large impact on the encoder's representation learning. Finally, we propose a novel MGM method SimSGT, featuring a Simple GNN-based Tokenizer (SGT) and an effective decoding strategy. We empirically validate that our method outperforms the existing molecule self-supervised learning methods. Our codes and checkpoints are available at https://github.com/syr-cn/SimSGT.

Yaorui Shi, An Zhang, Enzhi Zhang et al.

Predicting chemical reactions, a fundamental challenge in chemistry, involves forecasting the resulting products from a given reaction process. Conventional techniques, notably those employing Graph Neural Networks (GNNs), are often limited by insufficient training data and their inability to utilize textual information, undermining their applicability in real-world applications. In this work, we propose ReLM, a novel framework that leverages the chemical knowledge encoded in language models (LMs) to assist GNNs, thereby enhancing the accuracy of real-world chemical reaction predictions. To further enhance the model's robustness and interpretability, we incorporate the confidence score strategy, enabling the LMs to self-assess the reliability of their predictions. Our experimental results demonstrate that ReLM improves the performance of state-of-the-art GNN-based methods across various chemical reaction datasets, especially in out-of-distribution settings. Codes are available at https://github.com/syr-cn/ReLM.

Yuxin Chen, Yi Zhang, Zhengzhou Cai et al.

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.

Meituan LongCat Team, Anchun Gui, Bei Li et al.

We introduce LongCat-Flash-Thinking-2601, a 560-billion-parameter open-source Mixture-of-Experts (MoE) reasoning model with superior agentic reasoning capability. LongCat-Flash-Thinking-2601 achieves state-of-the-art performance among open-source models on a wide range of agentic benchmarks, including agentic search, agentic tool use, and tool-integrated reasoning. Beyond benchmark performance, the model demonstrates strong generalization to complex tool interactions and robust behavior under noisy real-world environments. Its advanced capability stems from a unified training framework that combines domain-parallel expert training with subsequent fusion, together with an end-to-end co-design of data construction, environments, algorithms, and infrastructure spanning from pre-training to post-training. In particular, the model's strong generalization capability in complex tool-use are driven by our in-depth exploration of environment scaling and principled task construction. To optimize long-tailed, skewed generation and multi-turn agentic interactions, and to enable stable training across over 10,000 environments spanning more than 20 domains, we systematically extend our asynchronous reinforcement learning framework, DORA, for stable and efficient large-scale multi-environment training. Furthermore, recognizing that real-world tasks are inherently noisy, we conduct a systematic analysis and decomposition of real-world noise patterns, and design targeted training procedures to explicitly incorporate such imperfections into the training process, resulting in improved robustness for real-world applications. To further enhance performance on complex reasoning tasks, we introduce a Heavy Thinking mode that enables effective test-time scaling by jointly expanding reasoning depth and width through intensive parallel thinking.

Yuxin Chen, Xiaodong Cai, Junfeng Fang et al.

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.

Sihang Li, Jin Huang, Jiaxi Zhuang et al.

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.

Leheng Sheng, Yongtao Zhang, Wenchang Ma et al.

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.

Zhiyuan Liu, Yaorui Shi, An Zhang et al.

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.

Yuchun Miao, Sen Zhang, Yuqi Zhang et al.

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.

Zhiyuan Liu, Yanchen Luo, Han Huang et al.

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.

Yaorui Shi, Shugui Liu, Yu Yang et al.

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.

Ziang Ye, Wentao Shi, Yuxin Liu et al.

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.

Jiaxi Zhuang, Yaorui Shi, Jue Hou et al.

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.

Yaorui Shi, Yuxin Chen, Zhengxi Lu et al.

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.

Yaorui Shi, Sihang Li, Taiyan Zhang et al.

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.

Yaorui Shi, Jiaqi Yang, Changhao Nai et al.

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.

Wenyu Mao, Haoyang Liu, Zhao Liu et al.

Memory systems are crucial to personalized LLMs by mitigating the context window limitation in capturing long-term user-LLM conversations. Typically, such systems leverage multiple agents to handle multi-granular memory construction and personalized memory retrieval tasks. To optimize the system, existing methods focus on specializing agents on their local tasks independently via prompt engineering or fine-tuning. However, they overlook cross-agent collaboration, where independent optimization on local agents hardly guarantees the global system performance. To address this issue, we propose a Collaborative Reinforcement Learning Framework for Multi-Agent Memory Systems (CoMAM), jointly optimizing local agents to facilitate collaboration. Specifically, we regularize agents' execution as a sequential Markov decision process (MDP) to embed inter-agent dependencies into the state transition, yielding both local task rewards (e.g., information coverage for memory construction) and global rewards (i.e., query-answer accuracy). Then, we quantify each agent's contribution via group-level ranking consistency between local and global rewards, treating them as adaptive weights to assign global credit and integrate local-global rewards. Each agent is optimized by these integrated rewards, aligning local improvements with the global performance. Experiments show CoMAM outperforms leading memory systems, validating the efficacy of our proposed collaborative reinforcement learning for joint optimization.

Yaorui Shi, Yuxin Chen, Siyuan Wang et al.

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 corpus that is dynamically updated during a single-pass document scan, also known as the "memorize while reading" methods. While this approach scales efficiently, it suffers from irreversible forward-only processing, information loss through overwriting, and sparse reinforcement learning signals. To tackle these challenges, we present ReMemR1, a memory-augmented agent with callback-enhanced memory that allows selective retrieval from the entire memory history and allows non-linear reasoning and revisiting of early evidence. To further strengthen training, we propose Reinforcement Learning with Multi-Level Rewards (RLMLR), 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 multi-hop memory utilizing. Experiments on long-document QA show significant gains over existing memory-based approaches, which validates ReMemR1 as an effective solution for long-context reasoning agents.