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01.
arXiv (CS.CV) 2026-06-15

WAM4D: Fast 4D World Action Model via Spatial Register Tokens

World action models (WAMs) have recently shown promise in jointly modeling future observations and executable robot actions. However, most existing WAMs still operate in 2D video or latent spaces, where visually plausible rollouts miss the 3D spatial constraints and occluded contact geometry required for precise manipulation. While geometric foundation models offer strong priors for recovering dense 3D structure and motion from visual observations, forcing WAMs to predict the dense 4D representation introduces costly geometric decoding and slows down causal action generation. To address the trade-off, we present WAM4D, a fast 4D world action model that uses lightweight spatial register tokens as training-time future-depth readouts to transfer pretrained geometric priors into a causal video-action transformer, then removes the register branch for lightweight action inference. To prevent non-causal shortcuts, we further design causal mixture attention for the Mixture-of-Transformers (MoT) WAM backbone, defining modality-specific visibility among video, action, and geometry tokens. Comprehensive experiments on RoboTwin 2.0 and challenging real-world manipulation tasks show that WAM4D improves spatial consistency and achieves competitive action prediction while maintaining efficient inference.

02.
arXiv (CS.CV) 2026-06-12

AudioX-Turbo: A Unified Framework for Efficient Anything-to-Audio Generation

Audio and music generation based on flexible multimodal control signals is a widely applicable topic, with the following key challenges: 1) a unified multimodal modeling framework, 2) large-scale, high-quality training data, and 3) the prohibitive inference cost of multi-step diffusion sampling. As such, we propose AudioX-Turbo, a unified and efficient framework for anything-to-audio generation that integrates varied multimodal conditions (i.e., text, video, and audio signals) in this work. AudioX-Turbo follows a teacher-student paradigm. The teacher AudioX-Base is built on a Multimodal Diffusion Transformer with a Multimodal Adaptive Fusion module that aligns diverse multimodal inputs for high-fidelity synthesis, and is then distilled into the few-step student AudioX-Turbo via Distribution Matching Distillation adapted to flow matching, complemented by a diffusion-based discriminator for high-quality few-step generation. To support the training of AudioX-Turbo, we construct a large-scale, high-quality dataset, IF-caps-Pro, comprising approximately 9.2M samples curated through a two-stage data collection and annotation pipeline. We benchmark AudioX-Turbo across a wide range of tasks, finding that our model achieves superior performance, especially on text-to-audio and text-to-music generation, while operating at only 4 sampling steps and requiring approximately 25x fewer function evaluations (NFE) than multi-step baselines. These results demonstrate that our method is capable of audio generation under flexible multimodal control, showing efficient and powerful instruction-following capabilities. The code and datasets will be available at https://zeyuet.github.io/AudioX-Turbo/.

03.
arXiv (CS.LG) 2026-06-12

Out-of-Distribution (OOD) Detectors for Open-Set RF Fingerprinting

arXiv:2606.12718v1 Announce Type: new Abstract: Radio-frequency (RF) fingerprinting systems must operate in open-world environments where signals from unknown transmitters and temporal drift introduce distribution shift at test time. Out-of-distribution (OOD) detection provides a natural framework for this problem, yet its application to RF fingerprinting (RFF) remains limited. A key barrier to their adoption is that most OOD detectors require auxiliary OOD data for parameter tuning, an assumption that is difficult to satisfy in RF environments where representative OOD data is impractical to collect. In this work, we introduce a promising set of OOD detection methods from the machine learning literature to open-set RFF domain. We present these methods within a unified mathematical framework based on information theory, which is a natural framework for communication systems. Our framework allows for the systematic analysis of methods and development of new methods. We further demonstrate the applicability of recent work on tuning OOD detectors without given OOD tuning data for open-set RFF. We evaluate on the POWDER RF fingerprinting dataset, showing that detectors tuned without any given OOD data achieve performance comparable to baselines with access to true OOD tuning data and greatly out-perform baseline approaches without access to true OOD tuning data, showcasing the practical viability for the RFF problem.

04.
arXiv (CS.AI) 2026-06-16

The Integrator Advantage: Controlled Agentic AI for Small and Medium-Sized Companies

arXiv:2606.16649v1 Announce Type: new Abstract: Agentic AI marks a new phase of enterprise automation. Unlike traditional automation or conversational AI, agentic systems can interpret goals, plan multi step tasks, access tools, interact with enterprise systems, and execute workflows with varying degrees of autonomy. For small and medium sized companies, this creates potential to reduce administrative burden, accelerate routine processes, and improve the use of organizational knowledge. This paper argues that the near term value of Agentic AI does not lie in full autonomy or workforce reduction, but in controlled partial autonomy for simple and medium complexity business processes. It proposes an integration framework covering use case suitability, autonomy levels, technical integration, governance, security, employee enablement, and measurable impact. The paper concludes that Agentic AI can become a productivity lever when implemented as a human centered capability with responsibility and accountability retained by people.

05.
arXiv (CS.LG) 2026-06-11

Calibrating Decision Robustness via Inverse Conformal Risk Control

arXiv:2510.07750v3 Announce Type: replace-cross Abstract: Robust optimization safeguards decisions against uncertainty by optimizing against worst-case scenarios, yet their effectiveness hinges on a prespecified robustness level that is often chosen ad hoc, leading to either insufficient protection or overly conservative and costly solutions. Recent approaches using conformal prediction construct data-driven uncertainty sets with finite-sample coverage guarantees, but they still fix coverage targets a priori and offer little guidance for selecting robustness levels. We propose a new framework that provides distribution-free, finite-sample guarantees on both miscoverage and regret for any family of robust predict-then-optimize policies. Our method constructs valid estimators that trace out the miscoverage–regret Pareto frontier, enabling decision-makers to reliably evaluate and calibrate robustness levels according to their cost–risk preferences. The framework is simple to implement, broadly applicable across classical optimization formulations, and achieves sharper finite-sample performance. This paper offers a principled data-driven methodology for guiding robustness selection and empowers practitioners to balance robustness and conservativeness in high-stakes decision-making.

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

Scaling Limits of Bivariate Nearly-Unstable Hawkes Processes and Applications to Rough Volatility

arXiv:2605.03703v3 Announce Type: replace Abstract: We study a pair of nearly-unstable Hawkes processes coupled through a one-directional, or triangular, cross-excitation: the first component evolves autonomously and excites the second, but not conversely. Each component is self-exciting through a heavy-tailed memory kernel, and the two kernels are allowed to have different tail indices, so that the limiting components exhibit genuinely different degrees of roughness. As the system approaches criticality, we prove that the suitably rescaled intensity vector converges weakly to the unique solution of a coupled system of stochastic Volterra equations of rough-volatility type. The first limiting component is autonomous, while the second is driven both by its own noise and by an inherited noise transmitted from the first component through an effective cross-kernel. This cross-kernel is the convolution of the two limiting Mittag-Leffler kernels and therefore combines the two memory structures. As a consequence, we obtain a short-time cross-decorrelation law: although the two components are coupled, their functional correlation vanishes at small time scales at an explicit polynomial rate. This time-dependent correlation distinguishes the limit from independent rough processes and from classical bivariate rough models with constant Brownian correlation.

07.
bioRxiv (Bioinfo) 2026-06-14

FENNEC: Fine-Tuned Ensemble Neural Networks Accelerate Chemically Modified siRNA Design and Screening

Small interfering RNAs (siRNAs) are a clinically validated therapeutic modality, yet designing potent chemically modified siRNAs remains a costly and iterative process, limited by scarce public data. Computational prediction of siRNA efficacy is therefore essential for rational design and accelerated preclinical development. However, despite the critical role of chemical modifications in therapeutic performance, current state-of-the-art machine learning methods either are not designed to model the chemical diversity of therapeutic siRNAs, or exhibit poor generalization performance. Here, we present FENNEC (Fine-Tuned Ensemble of Neural Networks for siRNA Efficiency Characterization), a machine-learning framework for predicting siRNA activity across chemically diverse design spaces. To support this effort, we curated the largest patent-derived dataset to date of chemically modified siRNAs from 42 patents using OCR-based table extraction and stringent filtering. FENNEC combines temporal convolutional networks with thermodynamic descriptors, experimental covariates, and embeddings from RNA foundation models to capture both local chemical determinants and broader target-context information. Importantly, we show that language-model-derived embeddings provide meaningful higher-order representations of target transcripts, particularly in data-scarce settings. FENNEC achieved robust predictive performance across both gene-level and scaffold-level validation settings, with additional experimental validation on a novel AHSA1-targeting dataset further supporting its generalizability across chemically modified siRNAs. In benchmarking, FENNEC outperformed classical machine-learning and state-of-the-art deep learning models, demonstrating generalization to unseen chemistry. Model interpretation recovered established design principles, including position-specific effects of glycol nucleic acid, 2'-fluoro modifications, and phosphorothioate backbones. Furthermore, in silico perturbation analyses suggest that FENNEC can serve not only as a predictive model, but also as an oracle for the design and optimization of chemically modified siRNAs. Together, our work addresses a key gap in the field by enabling chemically aware deep learning for siRNA design, supported by a large and diverse collection of chemically modified siRNA measurements.

08.
arXiv (CS.AI) 2026-06-17

AnchorKV: Safety-Aware KV Cache Compression via Soft Penalty with a Refusal Anchor

arXiv:2606.17872v1 Announce Type: cross Abstract: Large language models (LLMs) outperform earlier architectures on generative inference and long-context tasks, but their large size introduces significant challenges in memory usage, energy cost, and on-device deployment. Since scaling pre-trained language models improves downstream capability [zhao2023survey], the key-value (KV) cache becomes a dominant inference bottleneck. Recent KV cache compression methods [jo2025fastkv,li2024snapkv,zhou2024dynamickv] reduce this cost by retaining only a subset of attention-relevant tokens. However, while these approaches preserve accuracy on benign workloads, their compression policies either fail to defend against jailbreak attacks [jiang2024robustkv] or degrade safety alignment under aggressive eviction. We propose AnchorKV, a drop-in modification to KV cache compression that biases token retention scores away from directions in key space associated with harmful prompts. AnchorKV constructs an offline safety anchor by adapting a difference-of-means representation engineering approach [arditi2024refusal,zou2023representation] to the layer-specific key projection space used in KV caching. Based on this anchor, a soft penalty token selection rule trades a small amount of utility for substantially improved safety alignment, while reducing to the original compressor when the penalty is zero.

09.
Nature (Science) 2026-06-10

Mitochondria tethered to the nucleus secure its energy supply

Direct interactions between the cell’s powerhouses and nuclear pores might channel energy straight into the nucleus, fuelling cell division and differentiation. Direct interactions between the cell’s powerhouses and nuclear pores might channel energy straight into the nucleus, fuelling cell division and differentiation.

10.
arXiv (CS.CV) 2026-06-16

HSQ-VLM: A Novel Spatially-Constrained Quadrant Segmentation VLM Model for Explainability in Diabetic Retinopathy

Diabetic Retinopathy (DR) is an aggressive retinal disease and a leading cause of global blindness, yet its clinical management is currently hindered by the black-box nature of diagnostic AI. While deep learning models achieve high classification accuracy, there is a critical lack of explainability methods capable of detailing the exact anatomical landmarks and lesion distributions that lead to a clinical decision for DR. Therefore, we propose HSQ-VLM, a novel quadrant segmentation pipeline on fundus images that utilizes a Landmark-Anchored Cartesian Cross-Attention mechanism to unify visual feature extraction with structured clinical reasoning. Unlike traditional methods that rely on arbitrary image partitioning, our pipeline implements 4-quadrant Topological Latent Partitioning (TLP) to dynamically align retinal features with a fovea-centered coordinate system. This allows the Vision-Language Model to generate natural language reports that quantify pathology with anatomical precision. On a dataset of 3,500 high-resolution fundus images, this innovative methodology achieved a lesion detection sensitivity of 99.6% for hemorrhages and 96.4% for microaneurysms, while demonstrating a significant reduction in boundary-ambiguity errors compared to standard segmentation baselines.

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

Fast Non-Episodic Finite-Horizon RL with K-Step Lookahead Thresholding

arXiv:2602.00781v2 Announce Type: replace Abstract: Online reinforcement learning in non-episodic, finite-horizon MDPs remains underexplored and is challenged by the need to estimate returns to a fixed terminal time. Existing infinite-horizon methods, which often rely on discounted contraction, do not naturally account for this fixed-horizon structure. We introduce a modified Q-function: rather than targeting the full-horizon, we learn a K-step lookahead Q-function that truncates planning to the next K steps. To further improve sample efficiency, we introduce a thresholding mechanism: actions are selected only when their estimated K-step lookahead value exceeds a time-varying threshold. We provide an efficient tabular learning algorithm for this novel objective, proving it achieves fast finite-sample convergence: it achieves minimax optimal constant regret for $K=1$ and $\mathcal{O}(\max((K-1),C_{K-1})\sqrt{SAT\log(T)})$ regret for any $K \geq 2$. We numerically evaluate the performance of our algorithm under the objective of maximizing reward. Our implementation adaptively increases K over time, balancing lookahead depth against estimation variance. Empirical results demonstrate superior cumulative rewards over state-of-the-art tabular RL methods across synthetic MDPs and RL environments: JumpRiverswim, FrozenLake and AnyTrading. Code is provided on \href{https://github.com/jamie01713/K-Step-Lookahead}{github}.

12.
arXiv (CS.LG) 2026-06-19

CAGE: Curvature-Aware Gradient Estimation For Accurate Quantization-Aware Training

arXiv:2510.18784v3 Announce Type: replace Abstract: Despite significant work on low-bit quantization-aware training (QAT), there is still an accuracy gap between such techniques and native training. To address this, we introduce CAGE (Curvature-Aware Gradient Estimation), a new QAT method that augments the straight-through estimator (STE) gradient with a curvature-aware correction designed to counteract the loss increase induced by quantization. CAGE is derived from a multi-objective view of QAT that balances loss minimization with the quantization constraints, yielding a principled correction term that depends on local curvature information. On the theoretical side, we introduce the notion of Pareto-optimal solutions for quantized optimization, and establish that CAGE yields strong convergence guarantees in the smooth non-convex setting. In terms of implementation, our approach is optimizer-agnostic, but we provide a highly-efficient implementation that leverages Adam statistics. CAGE significantly improves upon the prior state-of-the-art methods in terms of accuracy, for similar computational cost: for QAT fine-tuning, it halves the compression accuracy loss relative to the prior best method, while for QAT pre-training of Llama models, its accuracy for 3-bit weights-and-activations (W3A3) matches the accuracy achieved at 4-bits (W4A4) with the prior best method. The official implementation can be found over https://github.com/IST-DASLab/CAGE .

13.
Nature (Science) 2026-06-10

‘Hidden hero’ peptides guard crops against sudden cold

作者: 未知作者

A protein signal remains silent under normal conditions but is activated under cold stress to protect developing pollen. This ‘on-demand’ resilience mechanism could enable the development of ‘climate smart’ crops that maintain high yields in good years and food security under climate stress. A peptide signal ensures that, in cold conditions, developing pollen receives nutrients at the right time.

14.
arXiv (CS.CV) 2026-06-12

DiskChunGS: Large-Scale 3D Gaussian SLAM Through Chunk-Based Memory Management

Recent advances in 3D Gaussian Splatting (3DGS) have demonstrated impressive results for novel view synthesis with real-time rendering capabilities. However, integrating 3DGS with SLAM systems faces a fundamental scalability limitation: methods are constrained by GPU memory capacity, restricting reconstruction to small-scale environments. We present DiskChunGS, a scalable 3DGS SLAM system that overcomes this bottleneck through an out-of-core approach that partitions scenes into spatial chunks and maintains only active regions in GPU memory while storing inactive areas on disk. Our architecture integrates seamlessly with existing SLAM frameworks for pose estimation and loop closure, enabling globally consistent reconstruction at scale. We validate DiskChunGS on indoor scenes (Replica, TUM-RGBD), urban driving scenarios (KITTI), and resource-constrained Nvidia Jetson platforms. Our method uniquely completes all 11 KITTI sequences without memory failures while achieving superior visual quality, demonstrating that algorithmic innovation can overcome the memory constraints that have limited previous 3DGS SLAM methods.

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

Toward Vibe Medicine: A Self-Evolving Multi-Agent Framework for Clinical Decision Support

arXiv:2606.15504v1 Announce Type: new Abstract: In recent years, the advances of large language models and autonomous agents have revolutionized the healthcare field, facilitating diagnosis and improving treatment results. However, most existing AI systems rely on pre-trained knowledge and predefined pipelines, which struggle to learn dynamically from the interactive chat session history that contains patient outcomes and past failures. To address this limitation, we propose VIBEMed, a multi-agent framework with a built-in self-evolution mechanism and architecture-level safety sandbox for robust clinical decision support. The system integrates three specialized agents, including a Clinical Diagnostic Agent (CDA) for hypothesis generation, a Therapeutic Execution Agent (TEA) for treatment planning, and a Clinical Evolution Manager Agent (CEMA) that distills longitudinal clinical feedback into reusable knowledge, transforming multimodal patient information into personalized medical decisions. Through self-evolution mechanism, the framework enables iterative updates across memory, model behavior, and decision strategies, allowing the system to improve over time. Experimental results show that VIBEMed demonstrates superior performance through its evolving mechanism in complex clinical cases, particularly in tasks that require integrated decision-making and longitudinal planning. The framework also supports reliable end-to-end decisions in challenging scenarios such as oncology treatment planning, highlighting its feasibility in real-world clinical contexts. Overall, VIBEMed provides a practical path beyond static AI systems toward adaptive, experience-driven clinical decision support, demonstrating the value of combining multi-agent collaboration with continuous evolution for advancing precision medicine.

16.
arXiv (CS.LG) 2026-06-17

Generalization Guarantees for Multi-Input Neural Operator Learning in Sobolev Spaces

arXiv:2606.17419v1 Announce Type: new Abstract: We develop approximation and generalization error estimates for multi-input neural operators, with the output error measured in Sobolev norms. In contrast to standard operator-learning settings with a single input function, our framework allows multiple input functions defined on possibly different domains, with different dimensions and Sobolev regularities. The derived rates explicitly quantify the contribution of each input space to the final error bound. In particular, in the balanced regime, the approximation and generalization rates are governed by the interaction between the input dimensions, regularities, and Sobolev orders, while the dependence on the model complexity retains a \(\log\log/\log\)-type structure. Our analysis provides a general theoretical framework for multi-input operator learning, including Sobolev training, and is applicable to operator learning problems arising from partial differential equations and scientific computing.

17.
medRxiv (Medicine) 2026-06-22

A Plasmodium vivax controlled human infection and transmission model to evaluate interventions across the life cycle

Background Plasmodium vivax is an underappreciated cause of malaria disease burden. No reproducible and standardized full life-cycle controlled human malaria infection (CHMI) model to accelerate development of novel interventions is available. Methods This transmission-CHMI trial was conducted in Nijmegen, Netherlands. Healthy, malaria-naive adults were sequentially enrolled into three cohorts of four and inoculated with the asexual blood-stage isolate PvW1. Primary endpoint was proportion of oocyst-positive laboratory-reared Anopheles stephensi mosquitoes. The sequential design allowed for adaptations between cohorts. At parasitemia >10 parasites/microL or symptom onset, participants received oral gametocyte-sparing treatment (GST): mepacrine (Cohort 1 and 3; 100 mg at 0, 8 16 hours, then once daily for 3 days) or piperaquine (Cohort 3; 480 mg single-dose). Transmission was assessed by direct skin feeding (DSF) and membrane feeding assay (DMFA) with and without enrichment of gametocytes. End-of-study treatment was atovaquone-proguanil (1000/400 mg once daily for 3 days). The trial was registered: NL-OMON57011. Findings Participants were enrolled between September 17, 2024 and March 25, 2025, all (12/12) developed parasitemia and transmitted PvW1 to mosquitoes. No serious adverse events occurred. Most adverse reactions were related to malaria. Mepacrine and piperaquine reduced asexual parasitemia while preserving gametocytemia and transmission. Peak transmission occurred within 3 days after GST and depended on the parasite developmental cycle, with highest gametocyte-infectivity ~48 h post ring-stage. In Cohort 3, mosquito infection reached 100% in all transmission assays. Median peak oocyst counts were 24 (IQR: 14-31) for DSF, 17 (12-19) for DMFA, and 150 (116-199) for enriched DMFA. A two-fold increase in pre-GST maximal parasitemia was associated with 20 additional oocysts (95% CI 8,6-32) in enriched DMFA. Sporozoites were viable in primary human hepatocytes. Interpretation A PvW1 transmission-CHMI is reproducible and safe, enabling P. vivax sporozoite production, relapse models and evaluation of transmission-blocking interventions.

18.
medRxiv (Medicine) 2026-06-11

Polygenic risk scores associate with asthma phenotypes and proteomic analyses implicate IL1R1 in two family-based studies

Despite its high prevalence and the discovery of hundreds of genetic associations, the genetic determinants and heterogeneous manifestations of asthma remain incompletely understood. Incorporating polygenic risk scores (PRS) into asthma research offers a powerful approach to quantify inherited susceptibility, refine risk profiles, and advance mechanistic understanding of disease development. For this study, we leveraged whole-genome sequencing (WGS) data from two family-based cohorts of childhood asthma - the Genetics of Asthma in Costa Rica Study (GACRS) and the Childhood Asthma Management Program (CAMP) - to examine the transmission profiles of externally derived asthma PRS and their associations with clinical phenotypes in children with asthma. To further elucidate molecular mechanisms, we integrated large-scale external genome-wide association study (GWAS) summary statistics and genetic prediction models of protein abundance in a two-step proteome-wide association study (PWAS) of asthma. Our findings provide robust evidence supporting the validity of externally derived asthma PRS (asthma PRS association p-value p={10}^{-24} [GACRS and CAMP trios combined] for the Global Biobank Meta-analysis Initiative [GBMI]) and reveal consistent associations with spirometry measures and atopy markers across both studies, as 13 of 21 traits (62%) were significantly associated with the GBMI-PRS in the meta-analysis after multiple-testing correction. Moreover, the results of the integrative proteomic analysis implicate IL-1 signaling in the etiology of asthma, reinforcing the candidacy of IL1R1 antagonists for drug repurposing.

19.
arXiv (CS.CL) 2026-06-15

Every Eval Ever: A Unifying Schema and Community Repository for AI Evaluation Results

AI evaluations are widely used for testing and understanding progress. However, the diverse evaluators bring with them inconsistencies that challenge analysis and comparison. First, results are saved in incompatible formats, scattered across leaderboards, papers, blog posts, evaluation harness logs, and custom repositories. Second, results are created by different evaluation frameworks, which produce divergent scores for nominally identical evaluations and record metadata inconsistently, hindering comparison, cross-community evaluation science, cost reduction, and reuse. We introduce Every Eval Ever, the first shared schema and community-crowdsourced repository for AI evaluation results. The schema standardizes how evaluations are represented in a unified, single JSON document. It is source-agnostic by design, ingesting results from evaluation harnesses and papers alike, and optionally stores per-instance outputs for fine-grained analysis. We contribute: (i) a community-governed metadata schema with a companion instance-level schema, the first standardization effort of its kind; (ii) automatic converters from popular formats, evaluation harnesses, and leaderboards to the unified schema; and (iii) a crowdsourced community database hosted on Hugging Face, currently spanning to date 22,235 models, 2,273 unique benchmarks, and 31 evaluation formats.

20.
arXiv (quant-ph) 2026-06-15

Spin disorder competing with positional symmetry breaking governs the metal-insulator behavior in oxide paramagnets

arXiv:2606.14624v1 Announce Type: cross Abstract: Numerous transition-metal oxides have low-temperature antiferromagnetic (AFM) states and high-temperature paramagnetic (PM) phases, where the AFM state is usually insulating while the PM phase can be either insulating or metallic. Without involving strong correlation, we use symmetry-broken density-functional theory (DFT) to obtain the PM phases of insulating NaFeO3 vs the recently discovered metallic NaOsO3. We develop the understanding of insulating and metallic behaviors in paramagnetic oxides by analyzing the interactions between magnetic and positional symmetry breaking: The insulating gap is governed by the competition between the spin disorder that induces a distribution of different magnitudes of local magnetic moments and the polymorphous distribution of off-center atomic displacements. NaFeO3, on the other hand, has large positional displacement with small spin-disorder-induced moments distribution, leading to insulating PM phase, whereas NaOsO3 has a pronounced spin-disorder-induced moments distribution that forces the PM phase to become metallic. Our work identifies this symmetry-breaking competition as a general framework to bridge seemingly disparate metal-insulator behaviors in transition-metal oxides paramagnets without invoking strong correlation.

21.
bioRxiv (Bioinfo) 2026-06-12

Deciphering cross-omics complexity of tissues via diagonal integration of unpaired spatial multi-omics data

Recent spatial multi-omics technologies enable the simultaneous in situ profiling of multiple omics modalities on the same tissue section; however, they face challenges in experimental complexity and high costs. This technical limitation can be circumvented by diagonal integration methods, which integrate omics data from different modalities. However, existing single-cell diagonal integration approaches overlook spatial information, causing unreliable anchoring across omics layers. Here, we introduce STAMO, a graph attention neural network model for spatially aware integration of unpaired spatial slices from different omics. Systematic benchmarking on spatial epigenome-transcriptome slices proves that STAMO outperforms the state-of-the-art methods in generating aligned embeddings and identifying consensus spatial domains across omics. We apply STAMO to integrate unpaired data from diverse spatial omics types (transcripts, epigenetics, DNA, and proteins), including slices from spatial RNA and four different epigenomic modalities, spatial ATAC and RNA slices across embryonic stages, spatial protein and RNA slices, and spatial DNA and RNA slices. In addition, the integration capability of STAMO can be further used to achieve cross-omics generation, offering a solution for exploring spatial region-specific gene regulatory mechanisms.

22.
arXiv (CS.AI) 2026-06-17

Cluster-Aware Dual-Level Test Specification Generation for Large-Scale Automotive Software Requirements

arXiv:2606.17197v1 Announce Type: cross Abstract: Generating test specifications that satisfy Automotive SPICE SWE.6 requirements becomes increasingly challenging and time-consuming as projects scale to thousands of requirements. Because this manual process often consumes weeks of engineering effort, automation becomes a critical necessity. However, standard Large Language Model (LLM) approaches struggle at scale: processing requirements individually discards vital inter-requirement dependencies, while feeding entire corpora at once exceeds context-window limits, leading to incomplete integration coverage and redundant test cases. This paper presents a novel "Cluster-then-Summarize" pipeline that addresses these limitations through three-stages. Requirements are embedded using sentence transformers and grouped using UMAP dimensionality reduction followed by HDBSCAN density-based clustering. This grouping utilizes an automatic minimum cluster size selection driven by a quality criterion combining normalized Silhouette and Calinski-Harabasz scores. A multi-level map-reduce summarization algorithm then distills each cluster into concise, domain-conformant descriptions while preserving quantitative thresholds and safety integrity levels. The pipeline exploits the derived cluster topology to generate test specifications at two levels: individual requirement verification and cluster-level integration tests that verify cross-requirement feature behavior. A nearby-cluster context mechanism provides bounded cross-feature awareness during each LLM call, and Retrieval-Augmented Generation grounds all outputs in ISO 26262 and ASPICE standards. Evaluation on automotive requirement datasets of varying scale demonstrates that the cluster-aware approach improves integration test coverage and maintains summarization fidelity compared to baseline methods while scaling efficiently to thousands of requirements.

23.
arXiv (CS.AI) 2026-06-11

Preregistration for Experiments with AI Agents

arXiv:2606.11217v1 Announce Type: cross Abstract: The proliferation of large language models (LLMs) and autonomous AI agents has given rise to a rapidly growing methodological paradigm: "in silico" behavioral experiments. Originally conceived as a way to use AI agents as proxies for human participants in studies of cognition, decision-making, and social dynamics, this approach has taken on new significance – as AI agents increasingly negotiate, transact, and make consequential decisions on behalf of people and organizations, understanding their behavior has become a research priority in its own right. While these experiments with AI agents offer unprecedented advantages in terms of scalability, cost efficiency, and experimental control, they also inherit, and in some cases amplify, methodological vulnerabilities that have long plagued human subjects research. To address these issues, this paper argues that preregistration practices – central to improving the credibility of human subjects experiments – should now be extended to experiments with AI agents. We systematically catalog the researcher degrees of freedom that experiments with AI agents introduce – model selection, prompt wording, settings, and outcome-contingent redesign, for example – and show how the low cost of iteration and lack of reporting norms make these choices both easy to exploit and difficult to detect. We propose a preregistration template tailored to experiments with AI agents and call on conferences, journals, and funding agencies to make preregistration standard practice for this emerging research paradigm.

24.
arXiv (CS.CL) 2026-06-15

Spatio-Temporal Audio Language Modeling for Dynamic Sound Sources

Sound events are entities with semantic identities, locations, and trajectories, but current audio-language models usually reason about clips as global event content. Conversely, sound event localization models track source directions over time but offer limited semantic coverage for language reasoning. To address this gap, we introduce ST-AudioQA, a spatio-temporal audio QA dataset and benchmark built from first-order ambisonic (FOA) renderings of static and moving sound sources. Each scene provides source identity, activity, direction, distance, and motion metadata, enabling dense trajectory supervision and questions about what is sounding, where it is, how it moves, and how sources relate. We further propose ST-Audio Encoder, a time-resolved FOA audio encoder that learns event semantics together with source trajectories, and ST-AudioLM, which connects the audio tokens from the encoder to an LLM for spatio-temporal audio QA. Experiments show that this representation improves the semantic-localization tradeoff and yields stronger reasoning performance than static spatial and localization-oriented baselines.

25.
Nature (Science) 2026-06-10

SIRT7 regulates dosage compensation and safeguards the female X chromosome

Sirtuins are deacetylases implicated in stress responses and longevity in mammals1,2. Although their differential impact on disease for the two sexes has been noted3–7, the underlying reasons are unclear. Here, using Sirt7 as a model in mice, we examine the mechanisms leading to sex differences and find that Sirt7−/− female mice have decreased fitness throughout their lifespan. Notably, SIRT7 preferentially localizes to the sex chromosomes. In female individuals, SIRT7 loss affects X-chromosome inactivation, the first arm of dosage compensation that equalizes X-linked gene expression between males and females8–10. Xist is overexpressed and gene silencing becomes more efficient. However, SIRT7 loss has greatest impact on the active X (Xa) chromosome. The Xa chromosome becomes hyperacetylated at Lys36 of histone H3, structurally disorganized, prone to DNA damage and overexpressed. Increased Xa-chromosome expression leads to genome imbalance and augmented X-chromosome upregulation—the second arm of dosage compensation that balances X-chromosome versus autosomal gene expression. These data reveal an essential crosstalk between sirtuins and the sex chromosomes, with SIRT7 safeguarding X-chromosome integrity and dosage balance with autosomes. We propose that the sex bias in SIRT7 biology can be explained in part by unequal effects on the sex chromosomes. SIRT7 safeguards X-chromosome integrity and dosage balance with autosomes.