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Autonomous Agents for Scientific Discovery: Orchestrating Scientists, Language, Code, and Physics

arXiv:2510.09901v2 Announce Type: replace Abstract: Computing has long served as a cornerstone of scientific discovery. Recently, a paradigm shift has emerged with the rise of large language models (LLMs), introducing autonomous systems, referred to as agents, that accelerate discovery across varying levels of autonomy. These language agents provide a flexible and versatile framework that orchestrates interactions with human scientists, natural language, computer language and code, and physics. This paper presents our view and vision of LLM-based scientific agents and their growing role in transforming the scientific discovery lifecycle, from hypothesis discovery, experimental design and execution, to result analysis and refinement. We critically examine current methodologies, emphasizing key innovations, practical achievements, and outstanding limitations. Additionally, we identify open research challenges and outline promising directions for building more robust, generalizable, and adaptive scientific agents. Our analysis highlights the transformative potential of autonomous agents to accelerate scientific discovery across diverse domains.
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Efficient and Scalable Granular-ball Graph Coarsening Method for Large-scale Graph Node Classification

arXiv:2603.29148v1 Announce Type: cross Abstract: Graph Convolutional Network (GCN) is a model that can effectively handle graph data tasks and has been successfully applied. However, for large-scale graph datasets, GCN still faces the challenge of high computational overhead, especially when the number of convolutional layers in the graph is large. Currently, there are many advanced methods that use various sampling techniques or graph coarsening techniques to alleviate the inconvenience caused during training. However, among these methods, some ignore the multi-granularity information in the graph structure, and the time complexity of some coarsening methods is still relatively high. In response to these issues, based on our previous work, in this paper, we propose a new framework called Efficient and Scalable Granular-ball Graph Coarsening Method for Large-scale Graph Node Classification. Specifically, this method first uses a multi-granularity granular-ball graph coarsening algorithm to coarsen the original graph to obtain many subgraphs. The time complexity of this stage is linear and much lower than that of the exiting graph coarsening methods. Then, subgraphs composed of these granular-balls are randomly sampled to form minibatches for training GCN. Our algorithm can adaptively and significantly reduce the scale of the original graph, thereby enhancing the training efficiency and scalability of GCN. Ultimately, the experimental results of node classification on multiple datasets demonstrate that the method proposed in this paper exhibits superior performance. The code is available at https://anonymous.4open.science/r/1-141D/.
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Generative AI in Action: Field Experimental Evidence from Alibaba's Customer Service Operations

arXiv:2603.29888v1 Announce Type: cross Abstract: In collaboration with Alibaba, this study leverages a large-scale field experiment to assess the impact of a generative AI assistant on worker performance in e-commerce after-sales service. Human agents providing digital chat support were randomly assigned with access to a gen AI assistant that offered two core functions: diagnosis of customer issues and solution proposals, presented as text messages. Agents retained discretion to adopt, modify, or disregard AI-generated messages. To evaluate gen AI's impact, we estimate both the intention-to-treat (ITT) effect of gen AI access and the local average treatment effect (LATE) of gen AI usage. Results show that gen AI significantly improved service speed, measured by issue identification time and chat duration. Gen AI also improved subjective service quality reflected in customer ratings and dissatisfaction rates, but it had no significant effect on objective service quality indicated by customer retrial rates. The performance improvements stemmed not only from automation but also from changes in the dynamics of agent-customer interactions: agent communication became more informative and efficient, while customers experienced reduced communication burdens. Low performers achieved the greatest improvements in both service speed and quality, narrowing the performance gap. In contrast, top-performing agents showed little improvement in service speed but experienced declines in both subjective and objective service quality. Evidence suggests that this decline results from increased multitasking tendency, proxied by longer shift-away times across concurrent chats, which slowed customer responses and raised abandonment and retrial rates. These findings suggest that gen AI reshapes work, demanding tailored deployment strategies.
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Understanding vs. Generation: Navigating Optimization Dilemma in Multimodal Models

arXiv:2602.15772v2 Announce Type: replace-cross Abstract: Current research in multimodal models faces a key challenge where enhancing generative capabilities often comes at the expense of understanding, and vice versa. We analyzed this trade-off and identify the primary cause might be the potential conflict between generation and understanding, which creates a competitive dynamic within the model. To address this, we propose the Reason-Reflect-Refine (R3) framework. This innovative algorithm re-frames the single-step generation task into a multi-step process of "generate-understand-regenerate". By explicitly leveraging the model's understanding capability during generation, we successfully mitigate the optimization dilemma, achieved stronger generation results and improved understanding ability which are related to the generation process. This offers valuable insights for designing next-generation unified multimodal models. Code is available at https://github.com/sen-ye/R3.
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FedRG: Unleashing the Representation Geometry for Federated Learning with Noisy Clients

arXiv:2603.19722v2 Announce Type: replace-cross Abstract: Federated learning (FL) suffers from performance degradation due to the inevitable presence of noisy annotations in distributed scenarios. Existing approaches have advanced in distinguishing noisy samples from the dataset for label correction by leveraging loss values. However, noisy samples recognition relying on scalar loss lacks reliability for FL under heterogeneous scenarios. In this paper, we rethink this paradigm from a representation perspective and propose \method~(\textbf{Fed}erated under \textbf{R}epresentation \textbf{G}emometry), which follows \textbf{the principle of ``representation geometry priority''} to recognize noisy labels. Firstly, \method~creates label-agnostic spherical representations by using self-supervision. It then iteratively fits a spherical von Mises-Fisher (vMF) mixture model to this geometry using previously identified clean samples to capture semantic clusters. This geometric evidence is integrated with a semantic-label soft mapping mechanism to derive a distribution divergence between the label-free and annotated label-conditioned feature space, which robustly identifies noisy samples and updates the vMF mixture model with the newly separated clean dataset. Lastly, we employ an additional personalized noise absorption matrix on noisy labels to achieve robust optimization. Extensive experimental results demonstrate that \method~significantly outperforms state-of-the-art methods for FL with data heterogeneity under diverse noisy clients scenarios.
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Modeling Spatiotemporal Neural Frames for High Resolution Brain Dynamic

arXiv:2603.24176v2 Announce Type: replace-cross Abstract: Capturing dynamic spatiotemporal neural activity is essential for understanding large-scale brain mechanisms. Functional magnetic resonance imaging (fMRI) provides high-resolution cortical representations that form a strong basis for characterizing fine-grained brain activity patterns. The high acquisition cost of fMRI limits large-scale applications, therefore making high-quality fMRI reconstruction a crucial task. Electroencephalography (EEG) offers millisecond-level temporal cues that complement fMRI. Leveraging this complementarity, we present an EEG-conditioned framework for reconstructing dynamic fMRI as continuous neural sequences with high spatial fidelity and strong temporal coherence at the cortical-vertex level. To address sampling irregularities common in real fMRI acquisitions, we incorporate a null-space intermediate-frame reconstruction, enabling measurement-consistent completion of arbitrary intermediate frames and improving sequence continuity and practical applicability. Experiments on the CineBrain dataset demonstrate superior voxel-wise reconstruction quality and robust temporal consistency across whole-brain and functionally specific regions. The reconstructed fMRI also preserves essential functional information, supporting downstream visual decoding tasks. This work provides a new pathway for estimating high-resolution fMRI dynamics from EEG and advances multimodal neuroimaging toward more dynamic brain activity modeling.
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A multicenter randomized clinical trial of portable transcranial alternating current stimulation for major depressive disorder

npj Digital Medicine, Published online: 28 March 2026; doi:10.1038/s41746-026-02575-9

A multicenter randomized clinical trial of portable transcranial alternating current stimulation for major depressive disorder
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Inactivating <i>SnRK1β1A</i> promotes broad-spectrum disease resistance in rice

Nature, Published online: 25 March 2026; doi:10.1038/s41586-026-10273-5

SnRK1β1A in rice promotes susceptibility to multiple fungal diseases, and disrupting this infection-inducible gene confers broad-spectrum resistance without compromising growth or yield under normal field conditions.
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Single-cell multiomics uncovers an endothelial mechanosensitive PIEZO1-IL-33 axis driving pulmonary fibrosis

Nat Commun. 2026 Mar 20;17(1):2655. doi: 10.1038/s41467-026-70193-w.

ABSTRACT

Pulmonary fibrosis represents a progressive interstitial lung disease marked by excessive extracellular matrix deposition and architectural distortion. Vascular endothelial cells critically contribute to fibrogenesis through paracrine secretion of pro-fibrotic mediators, yet their mechanobiological regulation remains elusive. Using integrated single-cell multi-omics profiling of human pulmonary fibrosis specimens and experimental fibrosis models induced by bleomycin or silica, we identify mechanosensitive Piezo1 upregulation in Endothelial cells as a hallmark of fibrotic progression. Endothelial-specific Piezo1 knockout significantly attenuates Bleomycin-induced fibrotic remodeling in male mice, establishing its pathogenic necessity. Mechanistically, PIEZO1 activation promotes pulmonary fibrosis development via CAPN2-mediated STAT3 phosphorylation, which may regulate the secretion of the pro-fibrotic molecule interleukin-33. These findings suggest that the endothelial PIEZO1-CAPN2-STAT3-IL33 axis is a potential therapeutic target for PF intervention.

PMID:41862476 | PMC:PMC13004862 | DOI:10.1038/s41467-026-70193-w

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Hijacking ERAD for targeted degradation of transmembrane proteins

Development of an ERAD-hijacking technology overcomes the challenges of current targeted protein degradation approaches to achieve degradation of transmembrane proteins.
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Synthetic Data Generation for Brain-Computer Interfaces: Overview, Benchmarking, and Future Directions

arXiv:2603.12296v1 Announce Type: cross Abstract: Deep learning has achieved transformative performance across diverse domains, largely driven by the large-scale, high-quality training data. In contrast, the development of brain-computer interfaces (BCIs) is fundamentally constrained by the limited, heterogeneous, and privacy-sensitive neural recordings. Generating synthetic yet physiologically plausible brain signals has therefore emerged as a compelling way to mitigate data scarcity and enhance model capacity. This survey provides a comprehensive review of brain signal generation for BCIs, covering methodological taxonomies, benchmark experiments, evaluation metrics, and key applications. We systematically categorize existing generative algorithms into four types: knowledge-based, feature-based, model-based, and translation-based approaches. Furthermore, we benchmark existing brain signal generation approaches across four representative BCI paradigms to provide an objective performance comparison. Finally, we discuss the potentials and challenges of current generation approaches and prospect future research on accurate, data-efficient, and privacy-aware BCI systems. The benchmark codebase is publicized at https://github.com/wzwvv/DG4BCI.
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TaoBench: Do Automated Theorem Prover LLMs Generalize Beyond MathLib?

arXiv:2603.12744v1 Announce Type: cross Abstract: Automated theorem proving (ATP) benchmarks largely consist of problems formalized in MathLib, so current ATP training and evaluation are heavily biased toward MathLib's definitional framework. However, frontier mathematics is often exploratory and prototype-heavy, relying on bespoke constructions that deviate from standard libraries. In this work, we evaluate the robustness of current ATP systems when applied to a novel definitional framework, specifically examining the performance gap between standard library problems and bespoke mathematical constructions. We introduce TaoBench, an undergraduate-level benchmark derived from Terence Tao's Analysis I, which formalizes analysis by constructing core mathematical concepts from scratch, without relying on standard Mathlib definitions, as well as by mixing from-scratch and MathLib constructions. For fair evaluation, we build an agentic pipeline that automatically extracts a compilable, self-contained local environment for each problem. To isolate the effect of definitional frameworks, we additionally translate every problem into a mathematically equivalent Mathlib formulation, yielding paired TaoBench-Mathlib statements for direct comparison. While state-of-the-art ATP models perform capably within the MathLib framework, performance drops by an average of roughly 26% on the definitionally equivalent Tao formulation. This indicates that the main bottleneck is limited generalization across definitional frameworks rather than task difficulty. TaoBench thus highlights a gap between benchmark performance and applicability, and provides a concrete foundation for developing and testing provers better aligned with research mathematics.
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SkillsBench: Benchmarking How Well Agent Skills Work Across Diverse Tasks

arXiv:2602.12670v3 Announce Type: replace Abstract: Agent Skills are structured packages of procedural knowledge that augment LLM agents at inference time. Despite rapid adoption, there is no standard way to measure whether they actually help. We present SkillsBench, a benchmark of 86 tasks across 11 domains paired with curated Skills and deterministic verifiers. Each task is evaluated under three conditions: no Skills, curated Skills, and self-generated Skills. We test 7 agent-model configurations over 7,308 trajectories. Curated Skills raise average pass rate by 16.2 percentage points(pp), but effects vary widely by domain (+4.5pp for Software Engineering to +51.9pp for Healthcare) and 16 of 84 tasks show negative deltas. Self-generated Skills provide no benefit on average, showing that models cannot reliably author the procedural knowledge they benefit from consuming. Focused Skills with 2--3 modules outperform comprehensive documentation, and smaller models with Skills can match larger models without them.
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First-line zolbetuximab plus mFOLFOX6 and nivolumab in unresectable CLDN18.2-positive gastric or gastroesophageal junction adenocarcinoma: a phase 2 trial

Nature Medicine, Published online: 16 March 2026; doi:10.1038/s41591-026-04306-9

In cohort 4 of the ILUSTRO trial, combination of anti-CLDN18.2 zolbetuximab plus mFOLFOX6 and nivolumab in patients with CLDN18.2-positive, HER2-negative metastatic gastric or gastroesophageal junction adenocarcinoma led to encouraging clinical efficacy, supporting the testing of this combination in a phase 3 trial.
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MAPK14/SLC7A11/GPX4 axis dysregulation drives podocyte ferroptosis via mediating glycerophospholipid metabolism

Cell Death Discovery, Published online: 11 March 2026; doi:10.1038/s41420-026-02990-7

MAPK14/SLC7A11/GPX4 axis dysregulation drives podocyte ferroptosis via mediating glycerophospholipid metabolism
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HEARTS: Benchmarking LLM Reasoning on Health Time Series

arXiv:2603.06638v1 Announce Type: cross Abstract: The rise of large language models (LLMs) has shifted time series analysis from narrow analytics to general-purpose reasoning. Yet, existing benchmarks cover only a small set of health time series modalities and tasks, failing to reflect the diverse domains and extensive temporal dependencies inherent in real-world physiological modeling. To bridge these gaps, we introduce HEARTS (Health Reasoning over Time Series), a unified benchmark for evaluating hierarchical reasoning capabilities of LLMs over general health time series. HEARTS integrates 16 real-world datasets across 12 health domains and 20 signal modalities, and defines a comprehensive taxonomy of 110 tasks grouped into four core capabilities: Perception, Inference, Generation, and Deduction. Evaluating 14 state-of-the-art LLMs on more than 20K test samples reveals intriguing findings. First, LLMs substantially underperform specialized models, and their performance is only weakly related to general reasoning scores. Moreover, LLMs often rely on simple heuristics and struggle with multi-step temporal reasoning. Finally, performance declines with increasing temporal complexity, with similar failure modes within model families, indicating that scaling alone is insufficient. By making these gaps measurable, HEARTS provides a standardized testbed and living benchmark for developing next-generation LLM agents capable of reasoning over diverse health signals.
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ELLMob: Event-Driven Human Mobility Generation with Self-Aligned LLM Framework

arXiv:2603.07946v1 Announce Type: cross Abstract: Human mobility generation aims to synthesize plausible trajectory data, which is widely used in urban system research. While Large Language Model-based methods excel at generating routine trajectories, they struggle to capture deviated mobility during large-scale societal events. This limitation stems from two critical gaps: (1) the absence of event-annotated mobility datasets for design and evaluation, and (2) the inability of current frameworks to reconcile competitions between users' habitual patterns and event-imposed constraints when making trajectory decisions. This work addresses these gaps with a twofold contribution. First, we construct the first event-annotated mobility dataset covering three major events: Typhoon Hagibis, COVID-19, and the Tokyo 2021 Olympics. Second, we propose ELLMob, a self-aligned LLM framework that first extracts competing rationales between habitual patterns and event constraints, based on Fuzzy-Trace Theory, and then iteratively aligns them to generate trajectories that are both habitually grounded and event-responsive. Extensive experiments show that ELLMob wins state-of-the-art baselines across all events, demonstrating its effectiveness. Our codes and datasets are available at https://github.com/deepkashiwa20/ELLMob.
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SkillsBench: Benchmarking How Well Agent Skills Work Across Diverse Tasks

arXiv:2602.12670v2 Announce Type: replace Abstract: Agent Skills are structured packages of procedural knowledge that augment LLM agents at inference time. Despite rapid adoption, there is no standard way to measure whether they actually help. We present SkillsBench, a benchmark of 86 tasks across 11 domains paired with curated Skills and deterministic verifiers. Each task is evaluated under three conditions: no Skills, curated Skills, and self-generated Skills. We test 7 agent-model configurations over 7,308 trajectories. Curated Skills raise average pass rate by 16.2 percentage points(pp), but effects vary widely by domain (+4.5pp for Software Engineering to +51.9pp for Healthcare) and 16 of 84 tasks show negative deltas. Self-generated Skills provide no benefit on average, showing that models cannot reliably author the procedural knowledge they benefit from consuming. Focused Skills with 2--3 modules outperform comprehensive documentation, and smaller models with Skills can match larger models without them.
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ARLArena: A Unified Framework for Stable Agentic Reinforcement Learning

arXiv:2602.21534v2 Announce Type: replace Abstract: Agentic reinforcement learning (ARL) has rapidly gained attention as a promising paradigm for training agents to solve complex, multi-step interactive tasks. Despite encouraging early results, ARL remains highly unstable, often leading to training collapse. This instability limits scalability to larger environments and longer interaction horizons, and constrains systematic exploration of algorithmic design choices. In this paper, we first propose ARLArena, a stable training recipe and systematic analysis framework that examines training stability in a controlled and reproducible setting. ARLArena first constructs a clean and standardized testbed. Then, we decompose policy gradient into four core design dimensions and assess the performance and stability of each dimension. Through this fine-grained analysis, we distill a unified perspective on ARL and propose SAMPO, a stable agentic policy optimization method designed to mitigate the dominant sources of instability in ARL. Empirically, SAMPO achieves consistently stable training and strong performance across diverse agentic tasks. Overall, this study provides a unifying policy gradient perspective for ARL and offers practical guidance for building stable and reproducible LLM-based agent training pipelines.
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