arXiv:2609.12413v1 Announce Type: new Abstract: Large language models (LLMs) are rapidly evolving from conversational assistants into agentic AI systems that reason, plan, invoke tools, maintain persistent memory, communicate with other agents, and execute multi-step tasks. At the same time, modern models exhibit substantially stronger native safety alignment than earlier generations on which many jailbreak attacks and defenses were originally studied. This shift raises a fundamental question: \textit{which established jailbreak-security findings remain valid in the era of modern LLMs and agentic AI?} We address this question through a Systematization of Knowledge (SoK) that reframes jailbreak security around the full agentic execution pipeline. We develop unified taxonomies of attacks and defenses spanning user interaction, planning and reasoning, memory, tool use, and inter-agent communication, and introduce a security--utility--efficiency evaluation framework that separates native harmful-prompt safety, adversarial jailbreak robustness, and agent-level security outcomes. We further conduct a controlled empirical study of representative attacks and defenses within a common agentic framework. Our results reveal three important gaps. First, strong native alignment does not imply robustness to adversarial jailbreaks. Second, defense effectiveness is highly model-, attack-, and component-dependent and can come at substantial cost in over-refusal, utility, and latency. Third, low final-response attack success can mask severe intermediate compromise: planning, memory, and tool interactions may remain unsafe even when the final response is successfully filtered. These findings motivate a shift from response-centric jailbreak defense toward cross-layer, execution-aware security that protects agent state, component transitions, and external actions while preserving practical utility and efficiency.

Zhang and colleagues reveal that GPX4 serves as a critical regulator of NRF2-mediated otoprotection against aminoglycoside-induced hair cell injury. Their findings identify a GPX4-dependent antioxidant mechanism that enables therapeutic activation of NRF2 and provides new insights into strategies for preventing drug-induced hearing loss.

AAV-WM04, an AAV vector identified through in-vivo-directed screening in the adult cochlea, enables highly efficient and selective inner hair cell transduction. Dual-AAV delivery of OTOF using AAV-WM04 restores hearing in a DFNA9 deafness mouse model at low doses, highlighting its translational potential for gene therapy.

arXiv:2605.23992v1 Announce Type: cross Abstract: Radiologist eye-tracking data provide a rich record of how experts search, compare, and accumulate evidence during image reading; yet, existing methods exploit this signal only partially, either as a static spatial prior or as an auxiliary prediction target decoupled from diagnosis. We propose GazeWorld, a medical imaging world model that treats the image as the world and the radiologist's fixation sequence as a trajectory through it. GazeWorld autoregressively predicts the latent representation of the next fixated patch from all previously visited ones, while a spatial-completion branch covers unvisited regions. At inference, GazeWorld generates a sequence of patch representations from the image alone without requiring real gaze data. Frozen GazeWorld features achieve state-of-the-art diagnostic accuracy across all nine supervised settings on CheXpert, RSNA Pneumonia, and SIIM-ACR Pneumothorax, as well as the highest zero-shot accuracy on all three benchmarks. On the GazeSearch benchmark, a generic decoder trained on the same frozen features outperforms the purpose-built LogitGaze-Med by over 16\% in ScanMatch and 22\% in SED, despite not being explicitly trained to predict gaze. GazeWorld demonstrates that modeling how experts read, not just what they conclude, offers a promising pretraining paradigm for medical imaging AI.

arXiv:2605.25952v1 Announce Type: cross Abstract: Despite the remarkable progress achieved by recent efficient methods in accelerating multimodal understanding, they still suffer from noticeable performance degradation. Their emphasis on the high compression ratio of a single visual clue and reliance on the heuristic pruning strategy with coarse attention alignment incurs a bottleneck on the information capacity and density of visual tokens. Addressing this limitation, we propose VEN-VL, a visual ensemble MoE framework for effective and efficient perception following the enrich then compact principle. Specifically, we first enrich the information capacity by unifying the visual representations of different perspectives, and then progressively compact it with adaptive routers in specialized visual experts to enhance the information density. Furthermore, we incorporate the reconstruction ability of vanilla structure via explicit visual supervision, facilitating crucial information preservation. Experimental results demonstrate our superiority in complex visual tasks with few information-condensed tokens, which effectively bridges the gap between performance and efficiency.

arXiv:2605.26026v1 Announce Type: cross Abstract: Light sheet fluorescence microscopy (LSM) enables high-resolution, three-dimensional (3D) imaging of biological specimens, providing rich volumetric data for studying cellular organization, pathology, and vascular networks. However, the size, dimensionality, and annotation burden of LSM data make supervised deep learning approaches costly and difficult to scale. Additionally, despite the abundance of unannotated LSM volumes, foundation models for this modality remain underexplored due to computational challenges and the complexity of volumetric representation learning. In this work, we introduce a 3D foundation model for LSM data, pretrained on a large curated collection of 3D images spanning multiple organisms, stains, and imaging protocols. We learn transferable volumetric representations by jointly optimizing for masked reconstruction and image-text alignment. The pretrained backbone drastically reduces the annotation burden, enabling efficient, few-shot adaptation for varied downstream tasks. We evaluate this approach on downstream segmentation, classification, and deblurring. Our results demonstrate consistent improvements over baselines, (1) when measured using standard evaluation metrics and (2) when rigorously assessed by domain experts. This highlights the potential of foundation model pretraining to reduce annotation requirements while improving performance across diverse LSM analysis tasks. Pretrained model weights and code for pretraining and finetuning are publicly available: https://github.com/AdinaScheinfeld/lsm_fm_public_repo.git.

arXiv:2604.11557v2 Announce Type: replace Abstract: Tool-use capability is a fundamental component of LLM agents, enabling them to interact with external systems through structured function calls. However, existing research exhibits inconsistent interaction representations, largely overlooks the structural distribution of tool-use trajectories, and relies on incompatible evaluation benchmarks. We present UniToolCall, a unified framework for tool learning that standardizes the entire pipeline from toolset construction and dataset generation to evaluation. The framework curates a large tool pool of 22k+ tools and constructs a hybrid training corpus of 390k+ instances by combining 10 standardized public datasets with structurally controlled synthetic trajectories. It explicitly models diverse interaction patterns, including single-hop vs. multi-hop and single-turn vs. multi-turn, while capturing both serial and parallel execution structures. To support coherent multi-turn reasoning, we further introduce an Anchor Linkage mechanism that enforces cross-turn dependencies. Furthermore, we convert 7 public benchmarks into a unified Query--Action--Observation--Answer (QAOA) representation with fine-grained evaluation at the function-call, turn, and conversation levels. Experiments show that fine-tuning Qwen3-8B on our dataset substantially improves tool-use performance. Under the distractor-heavy Hybrid-20 setting, achieves 93.0% single-turn Strict Precision, outperforming commercial models including GPT, Gemini, and Claude.

Nature, Published online: 20 May 2026; doi:10.1038/s41586-026-10570-z

Using high-resolution satellite imagery combined with a deep-learning-based framework to build a national energy inventory enables a data-driven assessment of solar–wind complementarity strategies to reduce power variability and enhance renewable energy penetration across China.

Nature, Published online: 20 May 2026; doi:10.1038/s41586-026-10571-y

The buffer pool designed to compensate for unintended carbon losses from the largest forest climate mitigation programme in the United States is too small when considering the impact of future climate change scenarios.

A mitochondrial transplantation approach rescues mitochondrial deficiency and prevents mitochondrial DNA depletion syndrome, Leigh syndrome, and Parkinson’s disease in cellular and mouse models.

arXiv:2604.03315v1 Announce Type: cross Abstract: Storyboarding is a core skill in visual storytelling for film, animation, and games. However, automating this process requires a system to achieve two properties that current approaches rarely satisfy simultaneously: inter-shot consistency and explicit editability. While 2D diffusion-based generators produce vivid imagery, they often suffer from identity drift along with limited geometric control; conversely, traditional 3D animation workflows are consistent and editable but require expert-heavy, labor-intensive authoring. We present StoryBlender, a grounded 3D storyboard generation framework governed by a Story-centric Reflection Scheme. At its core, we propose the StoryBlender system, which is built on a three-stage pipeline: (1) Semantic-Spatial Grounding, to construct a continuity memory graph to decouple global assets from shot-specific variables for long-horizon consistency; (2) Canonical Asset Materialization, to instantiate entities in a unified coordinate space to maintain visual identity; and (3) Spatial-Temporal Dynamics, to achieve layout design and cinematic evolution through visual metrics. By orchestrating multiple agents in a hierarchical manner within a verification loop, StoryBlender iteratively self-corrects spatial hallucinations via engine-verified feedback. The resulting native 3D scenes support direct, precise editing of cameras and visual assets while preserving unwavering multi-shot continuity. Experiments demonstrate that StoryBlender significantly improves consistency and editability over both diffusion-based and 3D-grounded baselines. Code, data, and demonstration video will be available on https://engineeringai-lab.github.io/StoryBlender/

arXiv:2604.03622v1 Announce Type: cross Abstract: Large language models (LLMs) have achieved strong performance on code generation, but existing methods still struggle with repository-level code generation under executable validation. Under this evaluation setting, success is determined not by the plausibility of isolated code fragments, but by whether a generated multi-file repository can be successfully installed, have its dependencies and internal references resolved, be launched, and be validated in a real execution environment. To address this challenge, we propose EnvGraph, a framework for repository-level code generation that formulates repository executability as an environment alignment problem. EnvGraph jointly models two coupled conditions for successful repository execution, namely external dependency satisfaction and repository-internal reference resolution. It maintains a dual-layer environment representation, uses execution evidence to perform execution-evidence-based attribution, and guides repository generation through a unified targeted revision mechanism within an iterative alignment loop. We evaluate EnvGraph on repository-level code generation with three representative backbone LLMs and compare it against representative environment-aware and repository-level baselines. Experimental results show that EnvGraph consistently achieves the best performance on these repository-level benchmarks. In particular, it outperforms the strongest non-EnvGraph baseline by an absolute margin of 5.72--5.87 percentage points in Functional Correctness and 4.58--8.66 percentage points in Non-Functional Quality.

arXiv:2604.03632v1 Announce Type: cross Abstract: Large language models (LLMs) have achieved substantial progress in repository-level code generation. However, solving the same repository-level task often requires multiple attempts, while existing methods still optimize each attempt in isolation and do not preserve or reuse task-specific state across attempts. In this paper, we propose LiveCoder, a novel framework for repository-level code generation based on cross-attempt knowledge optimization. LiveCoder maintains persistent task-specific state from prior attempts to guide subsequent generation. This state includes success knowledge, which captures reusable signals from previously strong repositories, failure knowledge, which records unsuccessful outcomes and their diagnostic signals, and a historical-best repository, which preserves the strongest result found so far and prevents regression. These components collectively transform repeated repository generation into a persistent, knowledge-driven optimization process. We evaluate LiveCoder using four frontier LLMs on two representative repository-level code generation benchmarks. Extensive experimental results demonstrate the effectiveness and efficiency of LiveCoder, improving the functional score by up to 22.94 percentage points, increasing repository reuse to 81.58%, and reducing cost by up to 53.63% on RAL-Bench while maintaining broadly stable non-functional quality.

arXiv:2604.03789v1 Announce Type: cross Abstract: Recent advances in large language models have significantly improved their ability to perform mathematical reasoning, extending from elementary problem solving to increasingly capable performance on research-level problems. However, reliably solving and verifying such problems remains challenging due to the inherent ambiguity of natural language reasoning. In this paper, we propose an automated framework for tackling research-level mathematical problems that integrates natural language reasoning with formal verification, enabling end-to-end problem solving with minimal human intervention. Our framework consists of two components: an informal reasoning agent, Rethlas, and a formal verification agent, Archon. Rethlas mimics the workflow of human mathematicians by combining reasoning primitives with our theorem search engine, Matlas, to explore solution strategies and construct candidate proofs. Archon, equipped with our formal theorem search engine LeanSearch, translates informal arguments into formalized Lean 4 projects through structured task decomposition, iterative refinement, and automated proof synthesis, ensuring machine-checkable correctness. Using this framework, we automatically resolve an open problem in commutative algebra and formally verify the resulting proof in Lean 4 with essentially no human involvement. Our experiments demonstrate that strong theorem retrieval tools enable the discovery and application of cross-domain mathematical techniques, while the formal agent is capable of autonomously filling nontrivial gaps in informal arguments. More broadly, our work illustrates a promising paradigm for mathematical research in which informal and formal reasoning systems, equipped with theorem retrieval tools, operate in tandem to produce verifiable results, substantially reduce human effort, and offer a concrete instantiation of human-AI collaborative mathematical research.

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