A vasoactive intestinal peptide (VIP)-based protein carrier self-assembles with respiratory syncytial virus circular RNA vaccines for intranasal delivery, inducing systemic antibodies, mucosal IgA, and Th1-biased protection in mice. This platform offers a protein-guided strategy for respiratory mucosal RNA vaccination and broadens the application of VIP in vaccine delivery.

arXiv:2609.09395v1 Announce Type: new Abstract: Language models act through tools, yet practical agents face libraries containing thousands of interfaces. We introduce the tool menu as the short, ordered subset of available tools shown to an agent before execution. The agent can call only tools in this menu. Multi-step tasks require the final action and the prerequisite tools that create its inputs in a usable order. Current constructors rank tools by request relevance, which can surface the final action while omitting or delaying less obvious producers. We introduce the state path, a pre-execution route from the observable request state to the desired outcome, and propose State-Path Tool Menu to learn it. Our framework treats the menu as an execution prior over these routes. Its encoder represents which tools can run from the current state, how their outputs satisfy later inputs, and which orders recur in training paths. A retriever covers an executable entry, the missing-input producers, and the final action. A reranker then places producers before consumers. On ToolBench, our menu raises online success from 0.737 to 0.898 and outperforms retrieval, reranking, generation, and routing baselines without changing the agent. The State-Path menu also covers more complete chains with 32 tools than the official list covers with 128, and its success gain persists across executor families with different model capacities. Our code is at https://github.com/Met2348/State-Path.

arXiv:2609.10177v1 Announce Type: new Abstract: In-context learning (ICL) is widely used in multimodal large language models (MLLMs) and achieves strong performance across a wide range of multimodal tasks. However, existing multimodal ICL methods often rely on surface level imitation of in-context demonstrations, making it difficult for MLLMs to align their responses with the reasoning path required by the given multimodal input. This limitation becomes more pronounced in complex multimodal tasks, thereby restricting further improvements in MLLM performance. To address this issue, we propose a new multimodal ICL framework that combines contrastive demonstration modeling with the self-refinement capability of MLLMs. Specifically, our framework reformulates each demonstration by explicitly contrasting a suboptimal response with a better response under the same input, together with a reasoning path that reveals how the response should be refined. This contrastive formulation makes the reasoning path toward the desired response more explicit and guides the MLLM beyond superficial imitation. Furthermore, because effective refinement depends on the current response, we introduce a response-conditioned retrieval mechanism to select demonstrations whose reasoning paths are more relevant to the current response. In addition, we use a lightweight alignment controller to predict response quality and determine whether further refinement is needed. Experiments on three types of multimodal tasks show that the proposed framework consistently improves MLLM performance, with particularly notable gains on visual question answering (VQA).

arXiv:2609.10108v1 Announce Type: cross Abstract: Aging clocks quantify biological aging and help characterize individual health status. What protein interactions are important for accurate aging clocks, and are they zeroth-order or higher-order? Addressing these questions requires learning from large molecular datasets distributed across medical centers, where privacy constraints prevent centralized data sharing. Federated learning offers a natural solution but faces four challenges in this setting: limited local sample sizes, sparse and directional inter-center trust, the need to retain discriminative age prediction while supporting interpretation, and model drift and forgetting under heterogeneous cross-center data. We propose TNFL, a trust-network-based federated learning framework that progressively propagates models along directed pairwise trust relations without centralized aggregation. TNFL combines an age-aware mixture-of-experts model with generative replay to preserve previously learned information and reduce forgetting and drift. Experiments across multiple molecular datasets show that TNFL enables effective aging-clock prediction with limited local data, provides interpretable age-dependent prediction patterns, and maintains stable performance across interaction orders. To investigate the biological questions, we analyze TNFL-identified pairwise protein interactions and their higher-order organization through functional and network analyses. The identified interactions repeatedly form coordinated higher-order subnetworks spanning multiple aging-related biological systems, with several proteins recurring across subnetworks. These findings suggest that TNFL captures molecular relationships beyond isolated pairwise associations and reveals coherent higher-order biological organization associated with aging.

arXiv:2606.08653v2 Announce Type: replace-cross Abstract: Action-supervised fine-tuning of vision-language-action (VLA) policies fits demonstrations effectively but constrains only the directions that change predicted actions, leaving visual structure consistent across action-equivalent states free to collapse. We formalize this as residual visual collapse along local action fibers and propose FiberTune, a training-time objective that preserves teacher-structured visual residuals without adding inference-time overhead. FiberTune uses an online action probe to estimate action-predictive feature directions, filters them from intermediate visual-token representations, and aligns the resulting probe-filtered residuals to a frozen visual teacher while regularizing their effective rank. Under identical training conditions, FiberTune improves over task-loss-only fine-tuning in every one of six controlled simulation settings spanning two benchmarks and two architectures (pi_0.5 and OpenVLA-OFT), as well as on physical SO-101 pick-place; representative gains include +10.7 percentage points SR(5) on long-horizon CALVIN ABC-to-D and physical SO-101 task success rising from 72.7% to 78.1%. Residual diagnostics show that these gains coincide with increased probe-filtered residual teacher alignment and effective rank, consistent with the action-fiber motivation.

arXiv:2605.25796v1 Announce Type: cross Abstract: Semantic-level watermarking (SWM) improves robustness against text modifications by treating sentences as the basic unit. However, robustness to paragraph-level paraphrasing remains difficult because such attacks globally disrupt watermark signals by changing sentence order. In this work, we propose SAMark, a self-anchored watermarking framework that removes the dependency on sentence order by establishing a step-independent green region in semantic space. To improve detectability, we introduce a multi-channel hyperbolic scoring mechanism that amplifies watermark signals while suppressing noise from weakly aligned candidates. We further propose a diversity-aware filtering strategy that combines hard filtering with soft regularization, extending beyond simple n-gram repetition filters to address semantic redundancy. Experimental results show that SAMark achieves up to 90.2% TP@FP1% under typical paragraph-level paraphrasing attacks, outperforming the strongest prior baseline by more than 30% on average, while maintaining generation quality competitive with unwatermarked text and breaking the robustness-quality trade-off that limits prior methods.

arXiv:2604.03592v1 Announce Type: cross Abstract: Mixture-of-Experts (MoE) models exhibit striking performance disparities across languages, yet the internal mechanisms driving these gaps remain poorly understood. In this work, we conduct a systematic analysis of expert routing patterns in MoE models, revealing a phenomenon we term Language Routing Isolation, in which high- and low-resource languages tend to activate largely disjoint expert sets. Through layer-stratified analysis, we further show that routing patterns exhibit a layer-wise convergence-divergence pattern across model depth. Building on these findings, we propose RISE (Routing Isolation-guided Subnetwork Enhancement), a framework that exploits routing isolation to identify and adapt language-specific expert subnetworks. RISE applies a tripartite selection strategy, using specificity scores to identify language-specific experts in shallow and deep layers and overlap scores to select universal experts in middle layers. By training only the selected subnetwork while freezing all other parameters, RISE substantially improves low-resource language performance while preserving capabilities in other languages. Experiments on 10 languages demonstrate that RISE achieves target-language F1 gains of up to 10.85% with minimal cross-lingual degradation.

Oncogene, Published online: 04 April 2026; doi:10.1038/s41388-026-03766-0

S100A6 promotes liver metastasis by activating FGFR3 signaling in BAP1-deficient uveal melanoma

npj Digital Medicine, Published online: 03 April 2026; doi:10.1038/s41746-026-02544-2

User-preference alignment with uncertainty-aware interactive rectification for liver organ and tumor segmentation and analysis from CT images

arXiv:2603.22655v1 Announce Type: cross Abstract: Learning system dynamics from observations is a critical problem in many applications over various real-world complex systems, e.g., climate, ecology, and fluid systems. Recently, neural dynamics modeling method have become a prevalent solution that embeds the object's observations into a latent space before learning dynamics using neural methods such as neural Ordinary Differential Equations (ODE). Existing dynamics modeling methods induce a specific model for each observation of different complex systems, resulting in poor generalization across systems. Inspired by the great success of pre-trained models, we conduct a generalized Pre-trained Dynamics EncoDER (PDEDER) which can embed the original state observations into a latent space where the dynamics can be captured more easily. To conduct the generalized PDEDER, we pre-train any Pre-trained Language Model (PLM) by minimizing the Lyapunov exponent objective, which constrains the chaotic behavior of governing dynamics learned in the latent space. By penalizing the divergence of embedded observations, our PDEDER promotes locally stable and well-structured latent dynamics, thereby facilitating more effective dynamics modeling than in the original observation space. In addition, we incorporate reconstruction and forecasting objectives to mitigate the risk of obtaining an over-smoothed latent space. Specifically, we collect 152 sets of real-world and synthetic observations from 23 complex systems as pre-training corpora and employ them to pre-train PDEDER. Given any future dynamic observation, we can fine-tune PDEDER with any specific dynamics modeling method. We evaluate PDEDER on 12 dynamic systems by short/long-term forecasting under both in-domain and cross-domain settings, and the empirical results indicate the effectiveness and generalizability of PDEDER.

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:2603.07915v1 Announce Type: new Abstract: Modern agents powered by thinking LLMs achieve high accuracy through long chain-of-thought reasoning but incur substantial inference costs. While many LLMs now support configurable reasoning levels (e.g., high/medium/low), static strategies are often ineffective: using low-effort modes at every step leads to significant performance degradation, while random selection fails to preserve accuracy or provide meaningful cost reduction. However, agents should reserve high reasoning effort for difficult steps like navigating complex website structures, while using lower-effort modes for simpler steps like opening a target URL. In this paper, we propose Ares, a framework for per-step dynamic reasoning effort selection tailored for multi-step agent tasks. Ares employs a lightweight router to predict the lowest appropriate reasoning level for each step based on the interaction history. To train this router, we develop a data generation pipeline that identifies the minimum reasoning effort required for successful step completion. We then fine-tune the router to predict these levels, enabling plug-and-play integration for any LLM agents. We evaluate Ares on a diverse set of agent tasks, including TAU-Bench for tool use agents, BrowseComp-Plus for deep-research agents, and WebArena for web agents. Experimental results show that Ares reduces reasoning token usage by up to 52.7% compared to fixed high-effort reasoning, while introducing minimal degradation in task success rates.

arXiv:2603.03825v1 Announce Type: cross Abstract: The cold-start initialization stage plays a pivotal role in training Multimodal Large Reasoning Models (MLRMs), yet its mechanisms remain insufficiently understood. To analyze this stage, we introduce the Visual Attention Score (VAS), an attention-based metric that quantifies how much a model attends to visual tokens. We find that reasoning performance is strongly correlated with VAS (r=0.9616): models with higher VAS achieve substantially stronger multimodal reasoning. Surprisingly, multimodal cold-start fails to elevate VAS, resulting in attention distributions close to the base model, whereas text-only cold-start leads to a clear increase. We term this counter-intuitive phenomenon Lazy Attention Localization. To validate its causal role, we design training-free interventions that directly modulate attention allocation during inference, performance gains of 1$-$2% without any retraining. Building on these insights, we further propose Attention-Guided Visual Anchoring and Reflection (AVAR), a comprehensive cold-start framework that integrates visual-anchored data synthesis, attention-guided objectives, and visual-anchored reward shaping. Applied to Qwen2.5-VL-7B, AVAR achieves an average gain of 7.0% across 7 multimodal reasoning benchmarks. Ablation studies further confirm that each component of AVAR contributes step-wise to the overall gains. The code, data, and models are available at https://github.com/lrlbbzl/Qwen-AVAR.