arXiv:2604.01520v1 Announce Type: new Abstract: Traditional social science research often requires designing complex experiments across vast methodological spaces and depends on real human participants, making it labor-intensive, costly, and difficult to scale. Here we present S-Researcher, an LLM-agent-based platform that assists researchers in conducting social science research more efficiently and at greater scale by "siliconizing" both the research process and the participant pool. To build S-Researcher, we first develop YuLan-OneSim, a large-scale social simulation system designed around three core requirements: generality via auto-programming from natural language to executable scenarios, scalability via a distributed architecture supporting up to 100,000 concurrent agents, and reliability via feedback-driven LLM fine-tuning. Leveraging this system, S-Researcher supports researchers in designing social experiments, simulating human behavior with LLM agents, analyzing results, and generating reports, forming a complete human-AI collaborative research loop in which researchers retain oversight and intervention at every stage. We operationalize LLM simulation research paradigms into three canonical reasoning modes (induction, deduction, and abduction) and validate S-Researcher through systematic case studies: inductive reproduction of cultural dynamics consistent with Axelrod's theory, deductive testing of competing hypotheses on teacher attention validated against survey data, and abductive identification of a cooperation mechanism in public goods games confirmed by human experiments. S-Researcher establishes a new human--AI collaborative paradigm for social science, in which computational simulation augments human researchers to accelerate discovery across the full spectrum of social inquiry.

arXiv:2604.01647v1 Announce Type: new Abstract: Embedding LLM-driven agents into environmental FAIR data management is compelling - they can externalize operational knowledge and scale curation across heterogeneous data and evolving conventions. However, replacing deterministic components with probabilistic workflows changes the failure mode: LLM pipelines may generate plausible but incorrect outputs that pass superficial checks and propagate into irreversible actions such as DOI minting and public release. We introduce EnviSmart, a production data management system deployed on campus-wide storage infrastructure for environmental research. EnviSmart treats reliability as an architectural property through two mechanisms: a three-track knowledge architecture that externalizes behaviors (governance constraints), domain knowledge (retrievable context), and skills (tool-using procedures) as persistent, interlocking artifacts; and a role-separated multi-agent design where deterministic validators and audited handoffs restore fail-stop semantics at trust boundaries before irreversible steps. We compare two production deployments. The University's GIS Center Ecological Archive (849 curated datasets) serves as a single-agent baseline. SF2Bench, a compound flooding benchmark comprising 2,452 monitoring stations and 8,557 published files spanning 39 years, validates the multi-agent workflow. The multi-agent approach improved both efficiency - completed by a single operator in two days with repeated artifact reuse across deployments - and reliability: audited handoffs detected and blocked a coordinate transformation error affecting all 2,452 stations before publication. A representative incident (ISS-004) demonstrated boundary-based containment with 10-minute detection latency, zero user exposure, and 80-minute resolution. This paper has been accepted at PEARC 2026.

A multi-omic single-cell atlas of the aging mouse brain reveals cell-type-specific transposon methylation changes, strengthening of 3D genome boundaries, and regionally heterogeneous aging signatures. These findings offer a resource to understand the molecular mechanisms of brain aging and guide future research on neurodegeneration.

arXiv:2603.28817v1 Announce Type: cross Abstract: Small Language Models (SLMs) are emerging as efficient and economically viable alternatives to Large Language Models (LLMs), offering competitive performance with significantly lower computational costs and latency. These advantages make SLMs suitable for resource-constrained and efficient deployment on edge devices. However, existing jailbreak defenses show limited robustness against heterogeneous attacks, largely due to an incomplete understanding of the internal representations across different layers of language models that facilitate jailbreak behaviors. In this paper, we conduct a comprehensive empirical study on 9 jailbreak attacks across 7 SLMs and 3 LLMs. Our analysis shows that SLMs remain highly vulnerable to malicious prompts that bypass safety alignment. We analyze hidden-layer activations across different layers and model architectures, revealing that different input types form distinguishable patterns in the internal representation space. Based on this observation, we propose GUARD-SLM, a lightweight token activation-based method that operates in the representation space to filter malicious prompts during inference while preserving benign ones. Our findings highlight robustness limitations across layers of language models and provide a practical direction for secure small language model deployment.

arXiv:2511.10788v3 Announce Type: replace Abstract: Recent advances in large language models (LLMs) have made reasoning a central benchmark for evaluating intelligence. While prior surveys focus on efficiency by examining how to shorten reasoning chains or reduce computation, this view overlooks a fundamental challenge: current LLMs apply uniform reasoning strategies regardless of task complexity, generating long traces for trivial problems while failing to extend reasoning for difficult tasks. This survey reframes reasoning through the lens of {adaptivity}: the capability to allocate reasoning effort based on input characteristics such as difficulty and uncertainty. We make three contributions. First, we formalize deductive, inductive, and abductive reasoning within the LLM context, connecting these classical cognitive paradigms with their algorithmic realizations. Second, we formalize adaptive reasoning as a control-augmented policy optimization problem balancing task performance with computational cost, distinguishing learned policies from inference-time control mechanisms. Third, we propose a systematic taxonomy organizing existing methods into training-based approaches that internalize adaptivity through reinforcement learning, supervised fine-tuning, and learned controllers, and training-free approaches that achieve adaptivity through prompt conditioning, feedback-driven halting, and modular composition. This framework clarifies how different mechanisms realize adaptive reasoning in practice and enables systematic comparison across diverse strategies. We conclude by identifying open challenges in self-evaluation, meta-reasoning, and human-aligned reasoning control.

Oncogene, Published online: 01 April 2026; doi:10.1038/s41388-026-03756-2

Correction: The multifunctional RNA helicase DDX39A drives glioblastoma progression by modulating WISP1 alternative splicing that induces an immunosuppressive macrophage polarization

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

arXiv:2603.23447v1 Announce Type: cross Abstract: While multi-modality large language models excel in object-centric or indoor scenarios, scaling them to 3D city-scale environments remains a formidable challenge. To bridge this gap, we propose 3DCity-LLM, a unified framework designed for 3D city-scale vision-language perception and understanding. 3DCity-LLM employs a coarse-to-fine feature encoding strategy comprising three parallel branches for target object, inter-object relationship, and global scene. To facilitate large-scale training, we introduce 3DCity-LLM-1.2M dataset that comprises approximately 1.2 million high-quality samples across seven representative task categories, ranging from fine-grained object analysis to multi-faceted scene planning. This strictly quality-controlled dataset integrates explicit 3D numerical information and diverse user-oriented simulations, enriching the question-answering diversity and realism of urban scenarios. Furthermore, we apply a multi-dimensional protocol based on text-similarity metrics and LLM-based semantic assessment to ensure faithful and comprehensive evaluations for all methods. Extensive experiments on two benchmarks demonstrate that 3DCity-LLM significantly outperforms existing state-of-the-art methods, offering a promising and meaningful direction for advancing spatial reasoning and urban intelligence. The source code and dataset are available at https://github.com/SYSU-3DSTAILab/3D-City-LLM.

arXiv:2603.03292v2 Announce Type: replace-cross Abstract: Large Language Models (LLMs) exhibit high reasoning capacity in medical question-answering, but their tendency to produce hallucinations and outdated knowledge poses critical risks in healthcare fields. While Retrieval-Augmented Generation (RAG) mitigates these issues, existing methods rely on noisy token-level signals and lack the multi-round refinement required for complex reasoning. In the paper, we propose MA-RAG (Multi-Round Agentic RAG), a framework that facilitates test-time scaling for complex medical reasoning by iteratively evolving both external evidence and internal reasoning history within an agentic refinement loop. At each round, the agent transforms semantic conflict among candidate responses into actionable queries to retrieve external evidence, while optimizing history reasoning traces to mitigate long-context degradation. MA-RAG extends the self-consistency principle by leveraging the lack of consistency as a proactive signal for multi-round agentic reasoning and retrieval, and mirrors a boosting mechanism that iteratively minimizes the residual error toward a stable, high-fidelity medical consensus. Extensive evaluations across 7 medical Q&A benchmarks show that MA-RAG consistently surpasses competitive inference-time scaling and RAG baselines, delivering substantial +6.8 points on average accuracy over the backbone model. Our code is available at https://github.com/NJU-RL/MA-RAG.

Nature, Published online: 25 March 2026; doi:10.1038/s41586-026-10264-6

Androgen activity in the male embryonic hindbrain prolongs hindbrain differentiation in male individuals and drives sex differences in the incidence and prognosis of posterior fossa type A (PFA) ependymoma, an aggressive childhood brain tumour.

Nature, Published online: 11 March 2026; doi:10.1038/s41586-026-10241-z

INSTALL overcomes fundamental challenges for DNA delivery and integration methods by synergizing immune-stealth nucleic acids with recombinases to enable kilobase-scale integration strategies without viral vectors.

arXiv:2603.06697v1 Announce Type: cross Abstract: Vision--language models (VLMs) process images as visual tokens, yet their intermediate reasoning is often carried out in text, which can be suboptimal for visually grounded radiology tasks. Radiologists instead diagnose via sequential visual search; eye-tracking captures this process as time-ordered gaze trajectories that reveal how evidence is acquired over time. We use eye-gaze as supervision to guide VLM reasoning by introducing a small set of dedicated gaze tokens. These tokens are trained to predict gaze-selected image patch indices in temporal order, encouraging the model to follow human-like evidence acquisition and integration. Experiments on MIMIC-EYE and multiple external zero-shot benchmarks show consistent gains over baselines, achieving state-of-the-art in-domain performance and improved out-of-domain robustness. These results highlight temporally ordered gaze as an effective supervision signal for learning visually grounded medical reasoning.

arXiv:2603.01396v2 Announce Type: replace Abstract: Single-cell perturbation studies face dual heterogeneity bottlenecks: (i) semantic heterogeneity--identical biological concepts encoded under incompatible metadata schemas across datasets; and (ii) statistical heterogeneity--distribution shifts from biological variation demanding dataset-specific inductive biases. We propose HarmonyCell, an end-to-end agent framework resolving each challenge through a dedicated mechanism: an LLM-driven Semantic Unifier autonomously maps disparate metadata into a canonical interface without manual intervention; and an adaptive Monte Carlo Tree Search engine operates over a hierarchical action space to synthesize architectures with optimal statistical inductive biases for distribution shifts. Evaluated across diverse perturbation tasks under both semantic and distribution shifts, HarmonyCell achieves a 95% valid execution rate on heterogeneous input datasets (versus 0% for general agents) while matching or even exceeding expert-designed baselines in rigorous out-of-distribution evaluations. This dual-track orchestration enables scalable automatic virtual cell modeling without dataset-specific engineering.

arXiv:2511.02872v4 Announce Type: replace-cross Abstract: Recent advances in large language models (LLMs) have demonstrated impressive capabilities in formal theorem proving, particularly on contest-based mathematical benchmarks like the IMO. However, these contests do not reflect the depth, breadth, and abstraction of modern mathematical research. To bridge this gap, we introduce FATE (Formal Algebra Theorem Evaluation), a new benchmark series in formal algebra designed to chart a course toward advanced mathematical reasoning. We present two new components, FATE-H and FATE-X, each with 100 problems in abstract and commutative algebra. The FATE series spans a difficulty spectrum from undergraduate exercises to problems exceeding PhD qualifying exams. Notably, FATE-X is the first formal benchmark to surpass both PhD-level exam difficulty and the coverage of the Mathlib library. Our evaluations of state-of-the-art LLM provers on this new benchmark reveal a stark performance gap compared to contest math: the best model achieves only 3% (pass@64) accuracy on FATE-H and 0% on FATE-X. Our two-stage evaluation reveals that models' natural-language reasoning is notably more accurate than their ability to formalize this reasoning. We systematically classify the common errors that arise during this formalization process. Furthermore, a comparative study shows that a specialized prover can exhibit less effective reflection than general-purpose models, reducing its accuracy at the natural-language stage. We believe FATE provides a robust and challenging benchmark that establishes essential checkpoints on the path toward research-level formal mathematical reasoning.

arXiv:2603.03292v1 Announce Type: cross Abstract: Large Language Models (LLMs) exhibit high reasoning capacity in medical question-answering, but their tendency to produce hallucinations and outdated knowledge poses critical risks in healthcare fields. While Retrieval-Augmented Generation (RAG) mitigates these issues, existing methods rely on noisy token-level signals and lack the multi-round refinement required for complex reasoning. In the paper, we propose **MA-RAG** (**M**ulti-Round **A**gentic RAG), a framework that facilitates test-time scaling for complex medical reasoning by iteratively evolving both external evidence and internal reasoning history within an agentic refinement loop. At each round, the agent transforms semantic **conflict** among candidate responses into actionable queries to retrieve external evidence, while optimizing history reasoning traces to mitigate long-context degradation. MA-RAG extends the *self-consistency* principle by leveraging the lack of consistency as a proactive signal for multi-round agentic reasoning and retrieval, and mirrors a *boosting* mechanism that iteratively minimizes the residual error toward a stable, high-fidelity medical **consensus**. Extensive evaluations across 7 medical Q&A benchmarks show that MA-RAG consistently surpasses competitive inference-time scaling and RAG baselines, delivering **substantial +6.8 points** on average accuracy over the backbone model. Our code is available at [this url](https://github.com/NJU-RL/MA-RAG).

arXiv:2603.04024v1 Announce Type: cross Abstract: Equivocal 3D lesion segmentation exhibits high inter-observer variability. Conventional deterministic models ignore this aleatoric uncertainty, producing over-confident masks that obscure clinical risks. Conversely, while generative methods (e.g., standard diffusion) capture sample diversity, recovering complex topology from pure noise frequently leads to severe structural fractures and out-of-distribution anatomical hallucinations. To resolve this fidelity-diversity trade-off, we propose Volumetric Directional Diffusion (VDD). Unlike standard diffusion models that denoise isotropic Gaussian noise, VDD mathematically anchors the generative trajectory to a deterministic consensus prior. By restricting the generative search space to iteratively predict a 3D boundary residual field, VDD accurately explores the fine-grained geometric variations inherent in expert disagreements without risking topological collapse. Extensive validation on three multi-rater datasets (LIDC-IDRI, KiTS21, and ISBI 2015) demonstrates that VDD achieves state-of-the-art uncertainty quantification (significantly improving GED and CI) while remaining highly competitive in segmentation accuracy against deterministic upper bounds. Ultimately, VDD provides clinicians with anatomically coherent uncertainty maps, enabling safer decision-making and mitigating risks in downstream tasks (e.g., radiotherapy planning or surgical margin assessment).

arXiv:2601.12349v2 Announce Type: replace-cross Abstract: Large multimodal model powered GUI agents are emerging as high-privilege operators on mobile platforms, entrusted with perceiving screen content and injecting inputs. However, their design operates under the implicit assumption of Visual Atomicity: that the UI state remains invariant between observation and action. We demonstrate that this assumption is fundamentally invalid in Android, creating a critical attack surface. We present Action Rebinding, a novel attack that allows a seemingly-benign app with zero dangerous permissions to rebind an agent's execution. By exploiting the inevitable observation-to-action gap inherent in the agent's reasoning pipeline, the attacker triggers foreground transitions to rebind the agent's planned action toward the target app. We weaponize the agent's task-recovery logic and Android's UI state preservation to orchestrate programmable, multi-step attack chains. Furthermore, we introduce an Intent Alignment Strategy (IAS) that manipulates the agent's reasoning process to rationalize UI states, enabling it to bypass verification gates (e.g., confirmation dialogs) that would otherwise be rejected. We evaluate Action Rebinding Attacks on six widely-used Android GUI agents across 15 tasks. Our results demonstrate a 100% success rate for atomic action rebinding and the ability to reliably orchestrate multi-step attack chains. With IAS, the success rate in bypassing verification gates increases (from 0% to up to 100%). Notably, the attacker application requires no sensitive permissions and contains no privileged API calls, achieving a 0% detection rate across malware scanners (e.g., VirusTotal). Our findings reveal a fundamental architectural flaw in current agent-OS integration and provide critical insights for the secure design of future agent systems. To access experimental logs and demonstration videos, please contact yi_qian@smail.nju.edu.cn.

arXiv:2602.07883v2 Announce Type: replace Abstract: Agentic systems powered by Large Language Models (LLMs) have demonstrated remarkable potential in tackling complex, long-horizon tasks. However, their efficacy is fundamentally constrained by static configurations governing agent behaviors, which are fixed prior to execution and fail to adapt to evolving task dynamics. Existing approaches, relying on manual orchestration or heuristic-based patches, often struggle with poor generalization and fragmented optimization. To transcend these limitations, we propose ToolSelf, a novel paradigm enabling tool-driven runtime self-reconfiguration. By abstracting configuration updates as a callable tool, ToolSelf unifies task execution and self-adjustment into a single action space, achieving a phase transition from external rules to intrinsic parameters. Agents can thereby autonomously update their sub-goals and context based on task progression, and correspondingly adapt their strategy and toolbox, transforming from passive executors into dual managers of both task and self. We further devise Configuration-Aware Two-stage Training (CAT), combining rejection sampling fine-tuning with trajectory-level reinforcement learning to internalize this meta-capability. Extensive experiments across diverse benchmarks demonstrate that ToolSelf rivals specialized workflows while generalizing to novel tasks, achieving a 24.1% average performance gain and illuminating a path toward truly self-adaptive agents.

arXiv:2512.00403v2 Announce Type: replace-cross Abstract: Scientific discovery increasingly entails long-horizon exploration of complex hypothesis spaces, yet most existing approaches emphasize final performance while offering limited insight into how scientific exploration unfolds over time, particularly balancing efficiency-diversity trade-offs and supporting reproducible, human-in-the-loop discovery workflows. We introduce SelfAI, a self-directed, multi-agent-enabled discovery system that automates scientific exploration as a strategic, trajectory-driven decision-making process. SelfAI translates high-level research intent into executable experiments, reasons over accumulated experimental trajectories to guide subsequent exploration, and applies adaptive stopping decisions to terminate unproductive search paths within a closed-loop workflow governed by explicit efficiency-diversity trade-offs. Evaluated using real-world experiments spanning domains from machine learning to drug discovery, SelfAI consistently discovers high-quality solutions with substantially fewer redundant trials than classical optimization and recent LLM-based baselines. The proposed methods establish a general framework for organizing long-horizon scientific discovery and adaptive decision-making in complex scientific and engineering systems.