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01.
arXiv (CS.CL) 2026-06-18

Notation Matters: A Benchmark Study of Token-Optimized Formats in Agentic AI Systems

Large language models in Agentic AI systems consume tool schemas and execution results and emit tool invocations as structured data. The default language for that exchange, JSON, was designed for application-to-application interchange rather than token efficiency, so its structural elements impose substantial token overhead. Recent work proposes token-optimized alternatives such as TOON (Token-Oriented Object Notation) and TRON (Token Reduced Object Notation) as more compact replacements, but these formats have been evaluated only on isolated comprehension or generation tasks. Whether their token reductions hold inside end-to-end agentic loops therefore remains an open question. We evaluate TOON and TRON on four agentic benchmarks (BFCL, MCPToolBenchPP, MCP-Universe, StableToolBench) and five open-weight LLMs, decoupling input compression from output compression to measure comprehension and generation independently. TRON reduces tokens by up to 27% with accuracy within 14pp of the JSON baseline. TOON achieves up to 18% reduction at a similar 9pp accuracy cost, but additionally cascades on multi-turn parsing failures and collapses parallel tool-call output for most models. The code is available at: https://github.com/lkutschka/notation-matters

02.
arXiv (CS.CV) 2026-06-15

What Drives Test-Time Adaptation for CLIP? A Controlled Empirical Study from an Update Perspective

Vision-Language Models (VLMs) such as CLIP have become a standard backbone for open-vocabulary recognition, yet their zero-shot predictions remain vulnerable to distribution shifts encountered at deployment. Test-Time Adaptation (TTA) has recently been extended to CLIP as a lightweight solution, leading to a rapidly growing body of TTA4CLIP methods. However, empirical progress in this area has largely outpaced our understanding of what truly drives adaptation, where their gains originate, and under which shifts they remain reliable. In this paper, we take a step back from the pursuit of state-of-the-art accuracy and conduct a systematic controlled study of TTA4CLIP. We first organize existing methods into three unified paradigms according to what is updated at test time. We then introduce TTABC, an open-source TTA Benchmark for CLIP, which standardizes evaluation protocols and integrates more than 20 representative methods. Our controlled empirical analysis focuses on three key areas. First, we determine the driving factors in parameter-based methods, revealing that adaptation gains are primarily driven by test-time evidence and reliable proxies rather than heavy optimization. Second, we explore evidence utilization beyond heavy parameter tuning, showing that competitive and efficient performance can be achieved through cross- or current-sample evidence and lightweight prototype updates. Finally, we demonstrate that there is no silver bullet for TTA: no single adaptation paradigm is universally optimal, and the preferred paradigm depends on the nature of shift. We hope our benchmark and study provide a clearer understanding of the current TTA4CLIP landscape and establish a foundation for further research.

03.
arXiv (CS.AI) 2026-06-11

MoCA-Agent: A Market-of-Claims Code Agent for Financial and Numerical Reasoning

arXiv:2606.11537v1 Announce Type: new Abstract: Financial and tabular question answering requires more than fluent reasoning: answers must be grounded in the exact facts, formulas, units, signs, and scales that support them. A single misread cell or incorrect operation can silently produce a plausible but wrong result. We introduce \textsc{MOCA-Agent}, a market-of-claims code agent that replaces free-form multi-agent debate with claim-level verification. The system decomposes each question into typed atomic claims, asks specialist trader agents to buy or sell those claims, clears their orders into confidence-weighted accept/reject decisions, and synthesizes an executable Python program from market-supported evidence. A code-aware verifier then checks the program for execution, structural consistency, and common financial reasoning errors, with at most one market-aware repair round. Across ten public benchmarks spanning financial numerical reasoning, general tabular reasoning, ESG question answering, and multimodal chart reasoning, \textsc{MOCA-Agent} achieves strong performance using a fixed Qwen3.6-27B backbone, including $78.3\%$ on FinQA, $76.0\%$ on FinanceMath, $71.2\%$ on MultiHiertt, $86.9\%$ on ESGenius, and $85.6\%$ average on FinChart-Bench. These results show that aggregating evidence at the level of atomic claims, rather than whole answers, improves robustness in high-stakes numerical reasoning.\footnote{The code and data are available: https://github.com/UBC-NLP/MoCA-Agent.

04.
arXiv (CS.LG) 2026-06-19

Self-Adaptive Scale Handling for Forecasting Time Series with Scale Heterogeneity

arXiv:2606.20010v1 Announce Type: new Abstract: Current time series forecasting (TSF) research predominantly focuses on scale-homogeneous data, where different time series share similar numerical magnitude ranges. However, in real-world industrial scenarios such as financial product sales, different time series often differ by orders of magnitude (scale heterogeneity). Since these series share similar temporal patterns, joint modeling is desirable for better data utilization, yet existing scaling methods either compress low-scale signals (global normalization) or destroy semantic discriminability and amplify inverse-scaling errors (window-based scaling). This paper proposes a self-Adaptive Scale-handling (AS) module that learns adaptive scale factors tailored to each input, preserving semantic discriminability while reducing inverse-scaling errors. AS consists of Scale Calibrating (SC), which calibrates prior mean scaling factors through neural networks, and Scaling Selection (SS), which decides whether to apply calibration or retain the original factor, avoiding over-calibration. Experiments on real-world fund sales datasets from Ant Fortune and Alipay show that AS seamlessly integrates into popular TSF models and consistently improves their performance. The code and dataset are available at the link https://github.com/Meteor-Stars/ASTSF.

05.
arXiv (CS.CV) 2026-06-17

FATE: Pillar Encoding and Frequency-Aware Training for Event-Based Object Detection

Event cameras are bio-inspired sensors that asynchronously capture logarithmic intensity changes, offering inherent advantages in high-speed and high-dynamic-range scenarios. However, the sparse and asynchronous nature of event streams poses a fundamental challenge for modern deep learning architectures. To enable compatibility with standard models, most existing approaches partition the accumulation window into fixed temporal sub-bins. While effective for spatial processing, this internal discretization discards fine-grained temporal structure and constrains inference to the low temporal frequencies imposed by training supervision. To address this limitation, we propose FATE, a unified framework built upon a novel Pillar Encoding (PE). While operating over discrete macro-accumulation windows dictated by the target frequency, PE avoids internal temporal sub-binning. It organizes events into spatial pillars and approximates their intra-window evolution via projection onto a continuous-time orthogonal polynomial basis. This formulation yields an L2-optimal representation that retains rich temporal dynamics in a dense pseudo-image, mitigating information loss under sparse event conditions. To fully leverage this representation, we introduce Frequency-Aware Training (FAT), a soft mean-teacher curriculum that generates temporally dense pseudo-labels, effectively bridging the mismatch between low-frequency supervision and high-frequency inference. Extensive experiments demonstrate that FATE generalizes across architectural paradigms and consistently outperforms strong baselines. It enables robust object detection at high temporal resolutions up to 200 Hz, while incurring minimal overhead in parameter count and inference latency

06.
arXiv (CS.CV) 2026-06-16

MVM-IOD: An Industrial Object-Centric Benchmark Dataset for the Evaluation of 3D Reconstruction Methods

3D object reconstruction, and camera pose estimation in industrial applications are challenging tasks, as errors are costly while the computation time is often limited. The complexity of typical industrial objects further complicates these tasks. Most of the existing datasets in this context do not depict realistic industrial scenarios. Therefore, we introduce the Machine Vision Metrology Industrial Object Dataset (MVM-IOD). Images of typical industrial objects are captured systematically, by moving a camera, mounted at the end effector of an industrial robot arm, on a hemisphere around the objects. MVM-IOD contains reference camera poses and reference 3D point clouds, the acquired RGB images of 9 objects and 2 background choices resulting in 18 scenes, which allows evaluation of all image based methods that compute a 3D reconstruction, camera poses, or novel views of a scene. Based on MVM-IOD, we extensively evaluate current SOTA 3D reconstruction and camera pose estimation methods, such as Structure from Motion, Multi-View Stereo, recent feed forward methods (Visual Geometry Grounded Transformer, {\pi}3), and 2D Gaussian Splatting and report our findings as a baseline for future research. The experiments show that capture setups like ours generate out-of distribution images for feed forward methods, leading to suboptimal point clouds and camera poses. However, these out-of-distribution images can be shifted closer to the training distribution by applying simple preprocessing steps. Consequently, in certain industrial applications, feed forward methods should be used with caution.

07.
arXiv (CS.LG) 2026-06-12

The Geometry of Phase Transitions in Generative Dynamics via Projection Caustics

arXiv:2606.13191v1 Announce Type: new Abstract: Continuous-state generative samplers, including diffusion and flow-matching models, evolve through continuous reverse-time dynamics, yet their samples often undergo abrupt qualitative changes: trajectories commit to modes, semantic alternatives collapse, and small perturbations in narrow time windows can produce large downstream effects. This paper develops a geometric account of such phase-transition-like behaviour. We view denoising as gradient descent on a free energy landscape and show that sharp transitions arise near projection caustics, where the nearest-point projection onto the data support ceases to be unique. Motivated by this perspective, we introduce the Critical Boundary Detector (CBD), as practical diagnostics for score-direction instability. Across toy models, standard diffusion models, and latent text-to-image diffusion models, CBD localises mode commitment, predicts intervention-sensitive windows, and supports targeted control in geometrically sensitive regions. Our results connect geometry of data and dynamics of diffusion generation.

08.
arXiv (CS.AI) 2026-06-19

VCG: A Multimodal Retrieval Framework for E-Commerce Video Feeds under Extreme Cold-Start Conditions

arXiv:2606.19627v1 Announce Type: cross Abstract: The digital commerce landscape is shifting from static, search-driven catalogs to dynamic, immersive video feeds. This transition introduces an ``extreme cold-start'' problem: unlike traditional items, new short-form videos lack the dense interaction history required for collaborative filtering. Furthermore, immersive feeds introduce strong position and duration biases that distort standard engagement signals. In this paper, we demonstrate the Video Candidate Generation (VCG) system, a scalable multimodal retrieval engine designed to solve these challenges in a large-scale e-commerce environment. By leveraging a domain-adapted vision-language model (based on CLIP), we map users and videos into a shared semantic space, enabling zero-shot retrieval based on visual content rather than behavioral history. We detail the system's architecture and present a rigorous evaluation comparing generative (LLM) vs. discriminative (CLIP) embeddings. Our results show that while generative models excel at attribute prediction, they suffer from embedding space collapse in retrieval tasks. Online A/B testing demonstrates that VCG effectively mitigates engagement biases, yielding a 50\% uplift in deep video completion. To showcase the system's capabilities, we present an interactive demonstration featuring three bi-directional retrieval scenarios: Product-to-Video, Video-to-Product, and Zero-Shot Semantic Search.

09.
arXiv (CS.CV) 2026-06-12

Comparing Commercial Depth Sensor Accuracy for Medical Applications

Depth estimation has numerous medical and surgical applications. We benchmark four depth sensors on a porcine bone specimen, a porcine belly specimen, and a silicone kidney phantom using stylus-sampled references. These objects contain several real-world challenges, including homogeneous surfaces, specular surfaces, and subsurface scattering. The comparison includes stereo, structured-light, and time-of-flight sensors at a distance of approximately 50 cm. Specifically, the Intel RealSense D405 (Intel RealSense, United States), PMD Flexx2 (pmdtechnologies, Germany), Stereolabs ZED 2i (Stereolabs, France), and Zivid 2M+ 60 (Zivid, Norway) are compared. The Zivid 2M+ 60 performed best across all objects and metrics considered in this work. The ZED ranked second for real tissue, but last on the phantom.

10.
medRxiv (Medicine) 2026-06-12

Association of circulating endothelial progenitor cell count and functional outcome in patients with acute ischemic stroke due to intracranial large vessel occlusion

Background: Circulating endothelial progenitor cells (cEPCs) contribute to vascular repair following an ischemic stroke. The aim of the study was to evaluate the association between cEPCs and functional outcomes in patients with acute ischemic stroke (AIS) due to large vessel occlusion (LVO) who received endovascular therapy (EVT). Methods: Prospective study of patients with LVO-AIS who received EVT. Blood samples were obtained within 24 +- 12 hours and on day 7+-1 from stroke onset. cEPCs were detected using flow cytometry (CD34+/VEGFR2+/CD133+). The primary endpoint was a favourable functional outcome (modified Rankin Scale 0-2) at three months of follow-up. Secondary endpoints include baseline to 24 hours/day 7 changes in the National Institutes of Health Stroke Scale (NIHSS) score and collateral circulation (CC) status. Bivariate and multivariable logistic regression analyses were performed. Results: Included were 90 patients (73.2+-12.7 years, 41.1% women) in 42 of whom (46.7%) cEPCs were detected at 24 hours. On day 7, cEPCs were detected in 27 (43.6%) of 62 patients for which this information was available. Atrial fibrillation, prior anticoagulant treatment and stroke onset-to-door time

11.
arXiv (CS.CL) 2026-06-16

Utility-Diversity Aware Online Batch Selection for LLM Supervised Fine-tuning

Supervised fine-tuning (SFT) is a commonly used technique to adapt large language models (LLMs) to downstream tasks. In practice, SFT on a full dataset is computationally expensive and sometimes suffers from overfitting or bias amplification. This facilitates the rise of data curation in SFT, which prioritizes the most valuable data to optimze. This work studies the online batch selection family that dynamically scores and filters samples during the training process. However, existing popular methods often (i) rely merely on the utility of data to select a subset while neglecting other crucial factors like diversity, (ii) rely on external resources such as reference models or validation sets, and (iii) incur extra training time over full-dataset training. To address these limitations, this work develops UDS (Utility-Diversity Sampling), a framework for efficient online batch selection in SFT. UDS leverages the nuclear norm of the logits matrix to capture both data utility and intra-sample diversity, while estimating inter-sample diversity through efficient low-dimensional embedding comparisons with a lightweight memory buffer of historical samples. Such a design eliminates the need for external resources and unnecessary backpropagation, securing computational efficiency. Experiments on multiple benchmarks demonstrate that UDS consistently outperforms state-of-the-art online batch selection methods under varying data budgets, and significantly reduces training time compared to full-dataset fine-tuning. Code is available at https://github.com/gfyddha/UDS.

12.
arXiv (quant-ph) 2026-06-16

Entanglement as a Witness of Quantum Coherence: A Bipartite Monty-Hall Protocol

arXiv:2604.25953v3 Announce Type: replace Abstract: We present a bipartite protocol inspired by the Monty Hall puzzle that operationally distinguishes quantum coherence from classical ignorance. A principal qutrit is entangled with an ancillary qutrit via a controlled unitary, preparing $|\Psi\rangle = \frac{1}{\sqrt{3}}(|A,0\rangle + |B,1\rangle + |C,2\rangle)$. A rank-1 projective discard then eliminates one basis state, leaving a coherent superposition of the two remaining states. Finally, the ancilla and qutrit are measured, yielding joint probabilities that encode the interplay between superposition and measurement back-action. We show that the conditional probability $P(B|anc=0)$ takes the value $1/4$ in both quantum mechanics and the classical ignorant-host model, making it unsuitable as a witness. The true quantum-classical separation emerges in conditional joint probabilities that correlate ancilla outcomes with specific discard operations. We define witnesses $\mathcal{W}_{i,j} = P(anc=i, qutrit=j \mid discard k)$ where $j$ differs from the ancilla-implied state. Quantum mechanics predicts $\mathcal{W} = 1/4$, while any classical epistemic model with perfect initial correlations yields $\mathcal{W} = 0$. We provide the explicit $9 \times 9$ unitary matrix, a complete analysis of all measurement outcomes, and a detailed proof of the violation. The witness is fully immune to white noise and robust against moderate dephasing. The protocol requires only a single pair of entangled qutrits and sequential measurements – no spatial separation, no multiple copies, and no complex sets of incompatible observables. This makes it suitable for advanced undergraduate laboratories and provides a pedagogically accessible test of the ontic-epistemic distinction in quantum foundations.

13.
arXiv (CS.CL) 2026-06-17

Variable-Width Transformers

Scaling model size, specifically depth and width, has driven significant progress in transformer-based language models. However, most architectures maintain a constant width across all layers, allocating a fixed parameter and computation budget evenly despite different layers potentially playing distinct computational roles. In this work, we empirically investigate nonuniform capacity allocation across network depth by proposing a $\times$-shaped >

15.
arXiv (CS.LG) 2026-06-16

Machine learning enables roughness-driven inverse design of milling processes

arXiv:2606.16032v1 Announce Type: cross Abstract: Interest in applying data-driven approaches in manufacturing has grown significantly, particularly for mapping complex, high-dimensional relationships. The milling process is one area where predictive models can link influential parameters to surface roughness metrics prior to in situ operations. While this approach offers clear advantages, it faces challenges due to limited datasets and robustness issues in inverse design paradigms. To address these challenges, this paper proposes a machine learning (ML)-based framework for the inverse design of the surface milling process, with a focus on surface roughness as the design objective. The framework employs forward training of two ML models, a deep neural network (DNN) and a random forest (RF) ensemble, both developed using a high-fidelity synthetic dataset generated from a computational simulation framework. These trained models are integrated into a Bayesian optimization (BO) procedure to overcome the multiplicity problem arising from the many-to-one mapping inherent in the dataset. The approach identifies top-performing milling process configurations, considering both process and tool parameters, and presents them from the full solution space. The models achieve average relative errors below 5% when compared to reference results, thereby demonstrating the robustness and reliability of the proposed methodology.

17.
arXiv (CS.CL) 2026-06-18

Simulating Hate Speech Cascades with Multi-LLM Agents: Empirical Grounding, Modeling Fidelity, and Intervention Strategies

作者:

Faithful modeling of hateful content propagation on online platforms remains an open problem for moderation research. Classical cascade models that do not explicitly represent the profile, community, and content factors associated with hateful-content propagation may yield moderation strategies that behave less effectively when deployed in real-world scenarios. Multi-agent large language model (LLM) systems can, in principle, make each reshare decision depend on the user's profile, the surrounding community, and the post's content, but it remains unclear whether this added flexibility actually reproduces real hateful cascades more faithfully than classical baselines. We study three hateful Bluesky cascades and a size-matched benign control. In the empirical Bluesky data, we found that: 97.4–99.7\% of reposters take a hostile stance; toxicity-engagement homophily is higher on the diffusion tree than on the follower graph for hateful cascades; topology is star-like for the hateful cascades (most reposts come directly from the root) versus tree-like for the benign cascade (reposts propagate through multi-hop chains). In simulation, a multi-LLM-agent simulator reproduces the stance monoculture and the toxicity-delta direction. A structured ablation identifies agent heterogeneity as the leading fidelity factor, and amplifier targeting on dense networks yields 7.5–12.9\% reduction at 5.7\% benign collateral.

18.
arXiv (CS.AI) 2026-06-18

Learning from Own Solutions: Self-Conditioned Credit Assignment for Reinforcement Learning with Verifiable Rewards

arXiv:2606.18810v1 Announce Type: cross Abstract: Reinforcement learning with verifiable rewards (RLVR) has driven substantial progress in training LLMs for reasoning tasks, but representative methods such as GRPO assign uniform credit across all tokens, wasting gradient on routine tokens while under-crediting pivotal reasoning steps. Existing token-level credit assignment methods require resources beyond the model's own rollouts. GRPO variants rely on process reward models or ground-truth answers. Knowledge distillation assigns credit through per-token divergence but requires external teachers (On-Policy Distillation) or privileged information (On-Policy Self Distillation). However, these dependencies limit applicability in the pure RLVR setting. We observe that conditioning the model on its own verified trajectories induces a measurable per-token KL divergence between the original and conditioned distributions, and prove that distilling from a self-teacher constructed by verified trajectories leads to infeasible weighted-average solutions when multiple verified trajectories exist. We propose SC-GRPO (Self-Conditioned GRPO), which uses KL divergence mentioned before as a multiplicative weight on GRPO gradients. Across five benchmarks spanning math, code, and agentic tasks, SC-GRPO consistently outperforms 8.1% over GRPO and 5.9% over DAPO with stronger OOD performance. Moreover, SC-GRPO achieves higher performance than OPD.

19.
arXiv (math.PR) 2026-06-16

Malliavin Calculus for the stochastic Cahn-Hilliard equation driven by fractional noise

arXiv:2601.10490v2 Announce Type: replace Abstract: The stochastic partial differential equation analyzed in this work is the Cahn-Hilliard equation perturbed by an additive fractional white noise (fractional in time and white in space). We work in the case of one spatial dimension and apply Malliavin calculus to investigate the existence of a density for the stochastic solution $u$. In particular, we show that $u$ admits continuous paths almost surely and construct a localizing sequence through which we prove that its Malliavin derivative exists locally, and that its law is absolutely continuous with respect to the Lebesgue measure on $\bf R$, establishing thus that a density exists. A key contribution of this work is the analysis of the stochastic integral appearing in the mild formulation: we derive sharp estimates for the expectation of the $p$-th power ($p \geq 2$) of the $L^{\infty}(D)$-norm of this stochastic integral as well as for the integral involving the $L^{\infty}(D)$-norm of the operator associated with the kernel appearing in the integral representation of the fractional noise, all of which are essential for this study.

20.
arXiv (CS.LG) 2026-06-17

From Reasoning Traces to Reusable Modules: Understanding Compositional Generalization in Language Model Reasoning

arXiv:2606.18089v1 Announce Type: new Abstract: Post-training pipelines that combine supervised fine-tuning (SFT) with reinforcement learning (RL) have emerged as the key recipe for transforming large language models (LLMs) into robust reasoners. We argue that this combined success is driven by compositional generalization, which we formalize through a hierarchical latent selection model. In this framework, reasoning traces are generated by a cascade of discrete latent selection variables corresponding to reusable atomic modules, including both skills (local operations) and routing mechanisms (how intermediate information is selected, reused, and composed). Within this model, we theoretically show that SFT and RL play asymmetric, complementary roles: SFT supplies the raw module materials in compositional traces, and RL decomposes those traces to identify the latent atomic modules and enable compositional generalization. We design controlled experiments to validate this theory. Our results demonstrate that RL can extract atomic modules from compound traces supplied by SFT and recombine them to solve new configurations. Moreover, we find that training on compound traces yields stronger generalization than training on isolated atomic modules. Finally, we investigate the relationship between SFT and RL data and identify an effective protocol in which SFT ensures coverage of all atomic modules through compositional traces, while RL focuses on novel compositions outside the SFT support to drive exploration.

21.
arXiv (quant-ph) 2026-06-16

Noise-Adaptive Predictive Dynamical Decoupling

arXiv:2606.15769v1 Announce Type: new Abstract: Protecting quantum coherence against realistic environmental noise remains one of the fundamental obstacles to scalable quantum technologies. We develop a noise-adaptive dynamical decoupling framework that combines analytical open-quantum-system modeling with machine-learning-based forecasting for a qubit interacting with random telegraph noise. Unlike conventional dynamical decoupling protocols based on fixed pulse schedules, the proposed approach continuously forecasts short-time coherence evolution and adaptively applies control pulses according to the instantaneous noise dynamics. We investigate stationary and non-stationary environments spanning both Markovian and non-Markovian regimes. Numerical simulations demonstrate that the machine-learning-assisted adaptive control strategy substantially outperforms conventional periodic dynamical decoupling while using a comparable number of control pulses. The improvement becomes particularly pronounced in non-Markovian and non-stationary regimes, where memory effects, coherence revivals, and temporally evolving noise strongly limit the effectiveness of static pulse protocols. These results establish predictive machine-learning-assisted dynamical decoupling as a promising and scalable framework for adaptive quantum control in realistic noisy quantum devices.

22.
Nature (Science) 2026-06-17

<i>CHPO</i> coordinates chilling recovery and nitrogen use in rice

作者:

Global rice production faces mounting challenges from abnormal temperature fluctuations and nitrogen-fertilizer-driven environmental pollution1–7. Developing varieties that balance chilling resilience and nitrogen-use efficiency (NUE) offers a promising solution, but the molecular networks coordinating these traits remain poorly understood. Here we identify CHILLING PHOENIX (CHPO), a major gene underlying the quantitative trait locus shared by both chilling tolerance and resilience. It encodes a MYB transcription factor that acts as a key regulator coordinating post-chilling recovery with nitrogen use in rice. Natural variation in a GCG-repeat-encoded polyalanine tract alters CHPO DNA-binding preference and redirects regulatory outputs between the japonica-type (CHPOjap) and indica-type (CHPOind), causing opposing effects on chilling tolerance and resilience. This allelic variation is shaped by domestication selection, with the CHPOjap allele probably derived from Chinese wild rice. CHPOjap directly targets OsTCP19 and OsNRT2.4 to fine-tune NUE, thereby enhancing chilling tolerance and resilience. These findings provide a mechanistic framework for a chilling-induced high-nitrogen-utilization module that alleviates the damage caused by chilling stress, and a potential molecular design&nbsp;strategy for breeding rice varieties with both chilling resilience and high NUE at the&nbsp;recovery stage. A rice gene, CHPO, links chilling resilience with nitrogen-use efficiency, revealing a domestication-shaped regulatory mechanism that could guide breeding of climate-resilient, sustainable rice varieties.

23.
PLOS Computational Biology 2026-05-29

Structural and dynamic basis of NOD2 tandem CARD association and NOD1/2–RIP2 signaling complexes

by Jitendra Maharana, Aritra Bej, Debasish Biswal, Debashis Panda, Arjun Sharma NOD1 and NOD2, founding members of the NOD-like receptor (NLR) family, play a crucial role in host defense against bacterial infections. Recognition of peptidoglycan-derived ligands triggers ATP-dependent oligomerization of the NACHT domain, exposing the CARD domains that recruit the adaptor protein RIP2 via CARD–CARD interactions to activate the NF-κB signaling cascade. Although NOD1/2-RIP2 interactions and RIP2CARD filament assembly are established, the precise interfaces that stabilize hetero–CARD filaments remain poorly defined. Here, we integrate in silico structural modeling with molecular dynamics (MD) simulations to elucidate structurally compatible arrangements of NOD1–RIP2 and NOD2–RIP2 hetero–CARD filaments. Our results reveal that NOD1CARD subunits form a structurally compatible homomeric scaffold via canonical (type-I–III) interfaces, accommodating multiple tiers of RIP2CARD rings at both filament termini. Meanwhile, the NOD2 tandem CARDs adopt multiple discrete conformations, reflecting a more intricate structural mechanism. In stable filament conformations, tandem CARDs converge at the type-II interface, with RIP2CARD rings stacking onto CARDa (top-down) and CARDb (bottom-up) interfaces, highlighting the structural role of NOD2CARDb in RIP2-mediated CARD–CARD interaction. In silico mutagenesis, involving charge-reversal and alanine scanning of key interfacial residues, disrupts NOD1–RIP2 and NOD2–RIP2 interactions at both top-down and bottom-up interfaces, leading to rapid interface destabilization within 0.1–0.4 μs of simulation. Together, these results reveal conserved and receptor-specific mechanisms governing NOD1/2–RIP2 CARD–CARD interactions and provide deeper structural and dynamic insights into the complex structural mechanisms for NLR-mediated inflammatory signaling.

24.
arXiv (CS.LG) 2026-06-16

A Fully First-Order Layer for Differentiable Optimization

arXiv:2512.02494v2 Announce Type: replace Abstract: Differentiable optimization layers enable learning systems to make decisions by solving embedded optimization problems. However, computing gradients via implicit differentiation requires solving a linear system with Hessian terms, which is both compute- and memory-intensive. To address this challenge, we propose a novel algorithm that computes the gradient using only first-order information. The key insight is to rewrite the differentiable optimization as a bilevel optimization problem and leverage recent advances in bilevel methods. Specifically, we introduce an active-set Lagrangian hypergradient oracle that avoids Hessian evaluations and provides finite-time, non-asymptotic approximation guarantees. We show that an approximate hypergradient can be computed using only first-order information in $\tilde{O}(1)$ time, leading to an overall complexity of $\tilde{O}(\delta^{-1}\epsilon^{-3})$ for constrained bilevel optimization, which matches the best known rate for non-smooth non-convex optimization. Furthermore, we release an open-source Python library that can be easily adapted from existing solvers. The source code is available at https://github.com/guaguakai/FFOLayer.

25.
Nature Medicine 2026-06-09

Adjuvanted inactivated rabies virus-vectored Lassa virus vaccine in healthy adults: a phase 1 trial

Lassa fever causes substantial morbidity and mortality in West Africa, and no licensed vaccine is available. We evaluated LASSARAB, an inactivated rabies virus-vectored Lassa virus (Josiah strain) glycoprotein complex vaccine. We conducted a randomized, controlled, dose-escalation phase 1 trial. Participants (total n = 54) received two intramuscular doses of LASSARAB containing 700 (n = 15), 1,400 (n = 15) or 2,800 (n = 14) relative units of antigen formulated with the TLR-4 agonist 3D-6-acyl PHAD-SE adjuvant, or licensed rabies vaccine control (n = 10), administered 28 days apart. This protocol-defined interim analysis reports the primary safety evaluation and secondary immunogenicity assessments through day 61. There were no prespecified hypotheses or formal power calculations. All primary safety end points demonstrated an acceptable safety profile. After dose 1, local solicited adverse events occurred in 86.7–100.0% of LASSARAB groups and 80% of controls; systemic events in 33.3–71.4% and 60.0% of controls. After dose 2, local solicited adverse events occurred in 66.7–86.7% of LASSARAB groups and 55.6% of controls; systemic events in 53.3–71.4% of LASSARAB groups and 55.6% of controls. Events were predominantly mild and self-limited. Unsolicited adverse events occurred in 28.6–60.0% of LASSARAB groups and 20.0% of controls. No serious adverse event, immune-mediated condition or sensorineural hearing loss occurred. Safety laboratory abnormalities occurred in 13.3–66.7% of LASSARAB groups and 30.0% of controls (14 mild, 6 moderate and none severe). After two doses, Lassa virus GPC IgG ELISA seroconversion (≥fourfold rise) was achieved in 100.0% (44 of 44) of LASSARAB recipients and 0.0% (0 of 10) of controls. Rabies glycoprotein IgG ELISA seroconversion (≥fourfold rise) and neutralizing antibody by rapid fluorescent focus inhibition test (RFFIT) seroprotection (≥0.5 IU ml−1) were also 100% across all groups, including controls. LASSARAB + 3D-6-acyl phosphorylated hexaacyl disaccharide (PHAD)-SE demonstrated a favorable safety profile and immunogenicity against Lassa and rabies viruses. The per-protocol final study report will include safety and durability through day 394. ClinicalTrials.gov identifier NCT06546709 . An interim report of a first-in-human phase 1 trial found an adjuvanted, combination inactivated rabies-vectored, Lassa fever vaccine (LASSARAB + 3D-6-acyl PHAD-SE) to be safe and induced immunogenicity to both Lassa and rabies viruses in healthy participants.