Large Language Models (LLMs) have extended their impact beyond Natural Language Processing, substantially fostering the development of interdisciplinary research. Recently, various LLM-based agents have been developed to assist scientific discovery progress across multiple aspects and domains. Among these, computer-using agents, capable of interacting with operating systems as humans do, are paving the way to automated scientific problem-solving and addressing routines in researchers' workflows. Recognizing the transformative potential of these agents, we introduce ScienceBoard, which encompasses two complementary contributions: (i) a realistic, multi-domain environment featuring dynamic and visually rich scientific workflows with integrated professional software, where agents can autonomously interact via different interfaces to accelerate complex research tasks and experiments; and (ii) a challenging benchmark of 169 high-quality, rigorously validated real-world tasks curated by humans, spanning scientific-discovery workflows in domains such as biochemistry, astronomy, and geoinformatics. Extensive evaluations of agents with state-of-the-art backbones (e.g., GPT-4o, Claude 3.7, UI-TARS) show that, despite some promising results, they still fall short of reliably assisting scientists in complex workflows, achieving only a 15% overall success rate. In-depth analysis further provides valuable insights for addressing current agent limitations and more effective design principles, paving the way to build more capable agents for scientific discovery.

This survey addresses the crucial issue of factuality in Large Language Models (LLMs). As LLMs find applications across diverse domains, the reliability and accuracy of their outputs become vital. We define the “factuality issue” as the probability of LLMs to produce content inconsistent with established facts. We first delve into the implications of these inaccuracies. Subsequently, we analyze the mechanisms through which LLMs store and process facts, seeking the primary causes of factual errors. Our discussion then transitions to methodologies for evaluating LLM factuality, emphasizing key metrics, benchmarks, and studies. We further explore strategies for enhancing LLM factuality. Our survey offers a structured guide for researchers aiming to fortify the factual reliability of LLMs. We consistently maintain and update the related open-source materials at https://github.com/wangcunxiang/LLM-Factuality-Survey.

Diffusion models have achieved remarkable success across a wide range of generative tasks, yet their training paradigm largely treats injected noise as uniformly informative. In this work, we challenge this assumption and introduce NoiseRater, a meta-learning framework for instance-level noise valuation in diffusion model training. We propose a parametric noise rater that assigns importance scores to individual noise realizations conditioned on data and timestep, enabling adaptive reweighting of the training objective. The rater is trained via bilevel optimization to improve downstream validation performance after inner-loop diffusion updates. To enable efficient deployment, we further design a decoupled two-stage pipeline that transitions from soft weighting during meta-training to hard noise selection during standard training. Extensive experiments on FFHQ and ImageNet demonstrate that not all noise samples contribute equally, and that prioritizing informative noise improves both training efficiency and generation quality. Our results establish noise valuation as a complementary and previously underexplored axis for improving diffusion model training. Our code is available at: https://anonymous.4open.science/r/NoiseRater-DEB116.

Large language models (LLMs) have recently shown strong progress on scientific reasoning, yet two major bottlenecks remain. First, explicit retrieval fragments reasoning, imposing a hidden tool tax of extra tokens and steps. Second, multi-agent pipelines often dilute strong solutions by averaging across all candidates. We address these challenges with a unified framework that combines implicit retrieval and structured collaboration. At its foundation, a Monitor-based retrieval module operates at the token level, integrating external knowledge with minimal disruption to reasoning. On top of this substrate, Hierarchical Solution Refinement (HSR) iteratively designates each candidate as an anchor to be repaired by its peers, while Quality-Aware Iterative Reasoning (QAIR) adapts refinement to solution quality. On Humanity’s Last Exam (HLE) Bio/Chem Gold, our framework achieves 48.3% accuracy—the highest reported to date, surpassing the strongest agent baseline by 13.4 points and leading frontier LLMs by up to 18.1 points, while simultaneously reducing token usage by 53.5% and agent steps by 43.7%. Results on SuperGPQA and TRQA confirm robustness across domains. Error analysis shows that reasoning failures and knowledge gaps co-occur in over 85% of cases, while diversity analysis reveals a clear dichotomy: retrieval tasks benefit from solution variety, whereas reasoning tasks favor consensus. Together, these findings demonstrate how implicit augmentation and structured refinement overcome the inefficiencies of explicit tool use and uniform aggregation.

Current chemical large language models (LLMs) predominantly rely on explicit Chain-of-Thought (CoT) to solve complex reasoning problems. However, forcing nonverbal tacit chemical logic into discrete natural language imposes a fundamental “modality mismatch,” creating an artificial bottleneck for reasoning. We introduce LatentChem, a reasoning interface that decouples chemical logic from linguistic generation, enabling the model to process information via continuous thought vectors and dynamic perception. Our investigation reveals a pivotal emergent behavior: spontaneous internalization, defined here as self-selected under outcome-only optimization. When optimized for task success, the model abandons verbose textual derivations in favor of implicit latent computation, suggesting that it identifies the continuous manifold as a more native substrate for chemical logic. This paradigm shift also proves to be a superior computational strategy: LatentChem achieves a 59.88% non-tie win rate against the strong CoT baseline on the rigorous ChemCoTBench, while delivering a broad 10.84× average reduction in reasoning step overhead (5.96× wall-clock speedup) across all evaluated benchmarks. Our results provide empirical evidence that chemical reasoning is more naturally and effectively realized as continuous latent dynamics rather than discretized linguistic trajectories.

The performance of Large Language Models (LLMs) hinges on carefully engineered prompts. However, prevailing prompt optimization methods, ranging from heuristic edits and reinforcement learning to evolutionary search, primarily target point-wise accuracy. They seldom enforce paraphrase invariance or searching stability, and therefore cannot remedy this brittleness in practice. Automated prompt search remains brittle: small, semantically preserving paraphrases often cause large performance swings. We identify this brittleness as the **textual sharpness** of the **prompt landscape**. In this work, we provide the first formal treatment of textual sharpness in the discrete, semantic space of prompts, together with an operational robustness criterion over a semantic neighborhood; the design is black-box or API-only, requiring no gradients to update the model's parameters. Then we introduce **TARE** (Textual Sharpness-Aware Evolving), a derivative-free framework that alternates between an inner, sampling-based adversarial search that stresses a prompt with hard paraphrases and an outer, robust selection that prefers candidates whose neighborhoods remain strong. We further propose **ATARE**, which learns anisotropic weights to shape the semantic neighborhood and adapts its radius over time to balance exploration and fidelity. Diverse tasks evaluate our methods, whose design for minimizing textual sharpness gap leads to prompts that preserve accuracy under paraphrasing, outperforming accuracy-only prompt search while remaining computationally practical. The code is available for anonymous access at https://anonymous.4open.science/r/ATARE_TARE/.

Reasoning is a fundamental cognitive process underlying inference, problem-solving, and decision-making. While large language models (LLMs) demonstrate strong reasoning capabilities in closed-world settings, they struggle in open-ended and dynamic environments. Agentic reasoning marks a paradigm shift by reframing LLMs as autonomous agents that plan, act, and learn through continual interaction. In this survey, we organize agentic reasoning along three complementary dimensions. First, we characterize environmental dynamics through three layers: foundational agentic reasoning, which establishes core single-agent capabilities including planning, tool use, and search in stable environments; self-evolving agentic reasoning, which studies how agents refine these capabilities through feedback, memory, and adaptation; and collective multi-agent reasoning, which extends intelligence to collaborative settings involving coordination, knowledge sharing, and shared goals. Across these layers, we distinguish in-context reasoning, which scales test-time interaction through structured orchestration, from post-training reasoning, which optimizes behaviors via reinforcement learning and supervised fine-tuning. We further review representative agentic reasoning frameworks across real-world applications and benchmarks, including science, robotics, healthcare, autonomous research, and mathematics. This survey synthesizes agentic reasoning methods into a unified roadmap bridging thought and action, and outlines open challenges and future directions, including personalization, long-horizon interaction, world modeling, scalable multi-agent training, and governance for real-world deployment.

Complex medical reasoning requires integrating heterogeneous clinical evidence across multiple inference steps. Large language models (LLMs) now approach this through two routes: internalized reasoning and externalized agent scaffolding (frameworks that decompose problems collaboratively among multiple LLMs). To determine whether these routes are exclusive or complementary, we introduce MedicalAgentsBench, a filtered benchmark of 862 complex clinical questions drawn from the union of eight medical datasets via difficulty-aware curation and contamination screening. Evaluating three internalized reasoning models (DeepSeek-R1, o1-mini, and o3-mini), seven base models, and nine externalized agent-based methods, we find that internalized and externalized approaches each independently improve performance and that their benefits compound: the highest accuracy is achieved by layering agent workflows onto an internalized reasoning model (i.e., o3-mini + MDAgents with 35.1%). Pareto analysis shows this combination dominates the cost-performance frontier; moreover, lightweight optimization on inexpensive models offers an entry point for resource-constrained settings.

Deep learning in de novo protein design has achieved atomic-level fidelity. However, existing models remain largely non-deliberative: they directly synthesize molecular geometries without explicitly reasoning about which residues or interactions are functionally essential. As a result, design decisions are entangled with continuous sampling dynamics, limiting interpretability, controllability, and systematic reuse of biochemical knowledge. We introduce Proteo-R1, a reasoning-guided protein design framework that explicitly decouples molecular understanding from geometric generation. Proteo-R1 adopts a dual-expert architecture in which a multimodal large language model (MLLM) serves as an understanding expert, analyzing protein sequences, structures, and textual context to identify key functional residues that govern binding and specificity. These residue-level decisions are then passed as hard constraints to a separate diffusion-based generation expert, which performs conditional co-design while respecting the fixed interaction anchors. This factorization mirrors how human experts approach molecular engineering: first, reasoning about critical interactions, then optimizing geometry subject to those constraints. By operationalizing reasoning as explicit residue-level commitments rather than latent textual guidance, Proteo-R1 achieves stable, interpretable, and modular integration of LLM reasoning with state-of-the-art geometric generative models. Code, data, and demos are available at https://smiles724.github.io/r1/.

Proteins are crucial to biological processes, and therapeutic peptides are emerging as promising pharmaceutical agents. Among these, D-peptides are resistant to proteolysis, exhibit greater in vivo stability, and are easier to synthesize. Despite advances in deep learning for peptide discovery, the scarcity of natural D-protein data limits the transfer of existing generative models to the D-peptide chemical space. We propose D-Flow, a full-atom flow-based framework for de novo D-peptide design. Conditioned on receptor binding, D-Flow uses structural representations incorporating backbone frames, side-chain angles, and discrete amino acid types. A mirror-image algorithm is implemented to address the lack of training data for D-proteins by converting the chirality of L-receptors. Furthermore, we enhance D-Flow's capacity by integrating protein language models (PLMs) with structural awareness through a lightweight structural adapter that injects structural representations into PLM embeddings. This enables D-Flow to learn conformational priors in the D-peptide chemical space and to accommodate the chiral selectivity of binding sites, thereby mitigating the scarcity of D-peptide data. A two-stage training pipeline and a control toolkit enable D-Flow to transition from general protein design to targeted binder design while preserving pre-training knowledge. Results on the PepMerge benchmark show D-Flow's effectiveness. D-peptides generated by D-Flow align more closely with native sequences and structures, with sequence identity improving by 10.2% over the best baseline and the top affinity score reaching 24.31%. Overall, D-Flow shows potential for D-peptide design, facilitating the development of bioorthogonal and stable molecular tools and diagnostics. Code is available at https://github.com/smiles724/PeptideDesign.

LLM agent failures are difficult to debug because the step where an error surfaces is often not the one that caused it. Existing observability tools replay execution traces but provide little support for identifying the root cause or translating diagnosis into recovery. We present AgentDebugX, an open-source debugging framework that organizes debugging as a closed loop of Detect, Attribute, Recover, and Rerun. At its core, DeepDebug performs multi-turn root-cause diagnosis through global trajectory understanding, structure-guided investigation, and cross-examination. On the Who and When benchmark, DeepDebug achieves the best strict attribution accuracy among the evaluated methods on both tested open-weight backbones, reaching 28.8 percent exact agent-and-step accuracy on qwen3.5-9b versus 21.7 percent for the strongest single-pass baseline. On GAIA, DeepDebug repairs 13 of 73 failed tasks in a single rerun, compared with 4 to 6 for three decoupled self-correction baselines, improving overall accuracy from 55.8 percent to 63.6 percent. AgentDebugX exposes this workflow through a Python library, CLI, web console, and installable agentic skill, and provides an opt-in Error Hub for sharing scrubbed failure-diagnosis-repair bundles and reusing them as debugging memory.

Protein function is largely determined by molecular surface geometry and physicochemical complementarity, yet most protein design methods condition only on backbone structure. We introduce SurfDesign, a surface-conditioned protein design framework that models molecular surfaces as continuous geometric manifolds and integrates them with pretrained protein language models. SurfDesign employs surface-based equivariant message passing to capture surface normals, curvature, and directional geometry, together with a parameter-efficient fine-tuning strategy. Focusing on functional protein design, we show that SurfDesign consistently outperforms prior surface-conditioned and backbone-only methods on de novo binder and enzyme design benchmarks. We also report strong performance on inverse-folding benchmarks as a diagnostic of structural compatibility. Our results highlight manifold-aware surface representations as a principled foundation for functional protein and enzyme design. Code is available at https://github.com/smiles724/SurfDesign.

Computer-use agents (CUAs) operate real desktop and web interfaces through screenshots, mouse and keyboard actions, and stateful UI feedback, yet their failures remain difficult to diagnose and repair. Unlike text-only agents, CUA failures arise from coupled visual perception, spatial grounding, low-level interaction, task reasoning, and environment dynamics, making debugging a distinctive multimodal causal localization problem. We introduce CUADebug, a framework for diagnosing and repairing CUA failures. CUADebug includes a CUA-specific error taxonomy, CUAErrorBench, a human-annotated OSWorld failure benchmark, and CUADebugger, a tool-augmented debugger. Instead of prompting over the full trajectory once, CUADebugger actively inspects suspicious steps with paired before/after screenshots and action traces, then submits a structured diagnosis containing the root-cause step, error type, grounded evidence, and corrective strategy for re-execution. Human annotations over 204 failed trajectories show that task reasoning and control is the largest failure family (110/204), followed by perception (36), grounding/interaction (25), external/system (13), and an others category of 20 OSWorld infeasible-task cases. On the main Claude-agent split, CUADebugger improves joint subtype-and-step diagnosis from 11.2

Medical Large Vision-Language Models (Med-LVLMs) have shown strong potential in multimodal diagnostic tasks. However, existing single-agent models struggle to generalize across diverse medical specialties, limiting their performance. Recent efforts introduce multi-agent collaboration frameworks inspired by clinical workflows, where general practitioners (GPs) and specialists interact in a fixed sequence. Despite improvements, these static pipelines lack flexibility and adaptability in reasoning. To address this, we propose MMedAgent-RL, a reinforcement learning (RL)-based multi-agent framework that enables dynamic, optimized collaboration among medical agents. Specifically, we train two GP agents based on Qwen2.5-VL via RL: the triage doctor learns to assign patients to appropriate specialties, while the attending physician integrates the judgments from multi-specialists and its own knowledge to make final decisions. To address the inconsistency in specialist outputs, we introduce a curriculum learning (CL)-guided RL strategy with dynamic entropy regulation, progressively teaching the attending physician to balance between imitating specialists and correcting their mistakes. Experiments on five medical VQA benchmarks demonstrate that MMedAgent-RL outperforms both open-source and proprietary Med-LVLMs. Notably, it achieves an average performance gain of 23.6\% over strong baselines.

Language agents have demonstrated remarkable potential in web search and information retrieval. However, these search agents assume user queries are complete and unambiguous, an assumption that diverges from reality where users begin with incomplete queries requiring clarification through interaction. Yet most agents lack interactive mechanisms during the search process, and existing benchmarks cannot assess this capability. To address this gap, we introduce INTERACTCOMP, a benchmark designed to evaluate whether search agents can recognize query ambiguity and actively interact to resolve it during search. Following the principle of easy to verify, interact to disambiguate, we construct 210 expert-curated questions across 9 domains through a target-distractor methodology that creates genuine ambiguity resolvable only through interaction. Evaluation of 17 models reveals striking failure: the best model achieves only 13.73% accuracy despite 71.50% with complete context, exposing systematic overconfidence rather than reasoning deficits. Forced interaction produces dramatic gains, demonstrating latent capability current strategies fail to engage. Longitudinal analysis shows interaction capabilities stagnated over 15 months while search performance improved seven-fold, revealing a critical blind spot. This stagnation, coupled with the immediate feedback inherent to search tasks, makes INTERACTCOMP a valuable resource for both evaluating and training interaction capabilities in search agents.

While large language models (LLMs) with Chain-of-Thought (CoT) reasoning excel in mathematics and coding, their potential for systematic reasoning in chemistry, a domain demanding rigorous structural analysis for real-world tasks like drug design and reaction engineering, remains untapped. Current benchmarks focus on simple knowledge retrieval, neglecting step-by-step reasoning required for complex tasks such as molecular optimization and reaction prediction. To address this, we introduce ChemCoTBench, a reasoning framework that bridges molecular structure understanding with arithmetic-inspired operations, including addition, deletion, and substitution, to formalize chemical problem-solving into transparent, step-by-step workflows. By treating molecular transformations as modular "chemical operations", the framework enables slow-thinking reasoning, mirroring the logic of mathematical proofs while grounding solutions in real-world chemical constraints. We evaluate models on two high-impact tasks: Molecular Property Optimization and Chemical Reaction Prediction. These tasks mirror real-world challenges while providing structured evaluability. By providing annotated datasets, a reasoning taxonomy, and baseline evaluations, ChemCoTBench bridges the gap between abstract reasoning methods and practical chemical discovery, establishing a foundation for advancing LLMs as tools for AI-driven scientific innovation.

Reinforcement learning with verifiable rewards (RLVR) is a practical, scalable way to improve large language models on math, code, and other structured tasks. However, we argue that many headline RLVR gains are not yet well validated because reports often conflate policy improvement with three confounds: (i) budget mismatch between RLVR and baseline evaluations, (ii) attempt inflation and calibration drift that convert abstentions into confident answers, and (iii) benchmark data contamination. Using budget-matched reproductions and partial-prompt contamination probes, we find that several widely cited gaps shrink substantially or disappear once budgets, prompts, and dataset versions are matched and contaminated sets are treated as memorization probes rather than evidence of reasoning. This does not mean that RLVR is ineffective, but it implies that current measurements often overstate capability gains and obscure reliability costs. We therefore propose a compact, tax-aware minimum standard for RLVR training and evaluation: budget-matched saturation curves with variance, calibration, and abstention tracking, a judge-robustness stress test when LLM judges are used, and an explicit contamination screen. With these controls, RLVR remains effective and deployable in verifiable domains, but reasoning gains should be treated as provisional without them.

Large Language Model (LLM)-based agents have shown effectiveness across many applications. However, their use in data science scenarios requiring solving long-term interconnected tasks, dynamic data adjustments and domain expertise remains challenging. Previous approaches primarily focus on individual tasks, making it difficult to assess the complete data science workflow. Moreover, they struggle to handle real-time changes in intermediate data and fail to adapt dynamically to evolving task dependencies inherent to data science problems. In this paper, we present Data Interpreter, an LLM-based agent designed to automatically solve various data science problems end-to-end. Our Data Interpreter incorporates two key modules: 1) Hierarchical Graph Modeling, which breaks down complex problems into manageable subproblems, enabling dynamic node generation and graph optimization; and 2) Programmable Node Generation, a technique that refines and verifies each subproblem to iteratively improve code generation results and robustness. Extensive experiments consistently demonstrate the superiority of Data Interpreter. On InfiAgent-DABench, it achieves a 25 75.9 performance from 88 the MATH dataset, Data Interpreter achieves remarkable performance with a 26 improvement compared to state-of-the-art baselines. The code is available at https://github.com/geekan/MetaGPT.

We present SciArena, an open and collaborative platform for evaluating foundation models on scientific literature-grounded tasks. Unlike traditional benchmarks for scientific literature understanding and synthesis, SciArena engages the research community directly, following the Chatbot Arena evaluation approach of community voting on model comparisons. By leveraging collective intelligence, SciArena offers a community-driven evaluation of model performance on open-ended scientific tasks that demand literature-grounded, long-form responses. The platform currently supports 47 foundation models and has collected over 20,000 votes from human researchers across diverse scientific domains. Our analysis of the data collected so far confirms its high quality. We discuss the results and insights based on the model ranking leaderboard. To further promote research in building model-based automated evaluation systems for literature tasks, we release SciArena-Eval, a meta-evaluation benchmark based on collected preference data. It measures the accuracy of models in judging answer quality by comparing their pairwise assessments with human votes. Our experiments highlight the benchmark's challenges and emphasize the need for more reliable automated evaluation methods.