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01.
arXiv (CS.CL) 2026-06-16

XAI-Grounded Explanation Generation for Speech Deepfake Detection with Training-Free Multimodal Large Language Models

Speech deepfake detection (SDD) systems require trustworthy explanations for reliable decision-making. Existing explanation ways mainly fall into two categories. Traditional explainable AI (XAI), such as gradient-based attribution, produces low-level attribution signals tightly coupled with model decisions, and harder to be understood by human than natural language explanations. Meanwhile, large language model (LLM)-based explanation generation often produces generic and ungrounded descriptions due to the lack of heuristic evidence and task-specific supervision, stemming from limited grounded explanation datasets for SDD. We therefore propose a training-free explanation framework that integrates XAI evidence with multimodal LLMs to generate grounded and specific explanations. Using the PartialSpoof dataset, we construct a grounded explanation dataset and show that methods with XAI increase inside accuracy by over 45\%, verified through human evaluation and faithfulness checks.

02.
arXiv (math.PR) 2026-06-18

Denoising Distances in Metric Measure Spaces

arXiv:2606.18301v1 Announce Type: cross Abstract: Recent work studied the problem of finding clusters and denoising pairwise distances from noisy distances of points sampled on a manifold. We study the same problems in more general metric measure spaces under \lowerphiregularity{}. We give an algorithm that extracts large localized clusters around every sampled point and uses them to denoise distances to any fixed accuracy, with near-linear running time in the dense fixed-accuracy regime. We also show how to achieve much higher accuracy with a non-efficient algorithm. This suggests that unlike the Riemannian case, denoising to higher accuracy in more general metric spaces has a statistical-computational gap.

03.
arXiv (CS.AI) 2026-06-19

Execution-bound advisory automation for agentic AI: a reproducible AIBOM-driven CSAF-VEX framework

arXiv:2606.19390v1 Announce Type: cross Abstract: A protocol driven framework is presented that binds SBOM and AIBOM artefacts to deterministic environment capture and structured runtime telemetry. Exploitability is computed from declared artefacts, observed activation conditions, and enforced execution policies. CSAF VEX advisories are generated from combined static and runtime evidence, cryptographically signed, and validated through deterministic replay. Evaluation uses approximately 10000 component entries across synthetic Agentic AI workloads 50 to 5000 components, incorporating OSV, GitHub Advisory, KEV, and EPSS datasets.

04.
arXiv (CS.AI) 2026-06-15

Learning Coordinated Preference for Multi-Objective Multi-Agent Reinforcement Learning

arXiv:2606.14693v1 Announce Type: cross Abstract: Cooperative multi-objective multi-agent reinforcement learning (MOMARL) models team decision making under multiple, potentially conflicting objectives. In this setting, conflicts arise not only across objectives but also across agents with different observations, roles, and contributions. We propose Preference Coordinated Multi-agent Policy Optimization (PCMA), which learns coordinated agent-specific preferences to enable complementary trade-offs among agents. Theoretically, we formulate cooperative MOMARL as a team-optimal game and show that, under suitable conditions, preference diversity can induce team improvement through a first-order improvement decomposition. Experiments on multiple cooperative MOMA environments and a practical traffic-control scenario show that PCMA improves both performance and trade-off coordination.

05.
arXiv (CS.CV) 2026-06-16

R2RDreamer: 3D-aware Data Augmentation for Spatially-generalized 2D Manipulation Policies

Spatial generalization is critical for imitation-learned manipulation policies, but achieving it typically requires scaling demonstrations across diverse object poses, robot configurations, and camera viewpoints. Data augmentation from a few source demonstrations offers a practical alternative to costly real-world collection. Simulation-based augmentation can create controllable variation, but requires complex environment and object setup and may introduce a sim-to-real gap. Recent real-to-real methods avoid these issues by jointly editing 3D observations and action trajectories from real demonstrations, yet they still rely on strong 3D scene parsing and geometry completion, and often produce observations tailored to 3D pointcloud policies rather than RGB-based 2D policies. We propose R2RDreamer, a real-to-real demonstration augmentation framework that preserves the geometric consistency of 3D action-observation editing while moving visual completion to 2D video space. Specifically, R2RDreamer first performs lightweight 3D augmentation by editing incomplete object pointclouds and end-effector trajectories in a shared 3D frame; it then projects the edited scene into masked image-space control videos with occlusion-aware reasoning and uses a dense-control image-to-video model to complete temporally coherent RGB observations. Experiments on spatially shifted manipulation tasks with both 2D diffusion-style policies and vision-language-action policies show that R2RDreamer improves spatial generalization from limited source demonstrations, with analyses validating the contributions of 3D editing, occlusion-aware projection, and video completion.

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

Online Convex Optimization with Sublinear Noisy Probes

arXiv:2606.14640v1 Announce Type: new Abstract: We study Online Convex Optimization (OCO) over a convex set $K\subseteq \mathbb R^d$, where in each round $t$ the learner selects $x_t\in K$ and then observes a convex loss $f_t:K\to[0,1]$, with the goal of minimizing regret to the best fixed decision in hindsight. We introduce a unified probing model that generalizes two recent lines of work: sublinear best-expert queries in the experts setting, and pairwise (comparison-based) feedback available every round in OCO. In our framework, the learner has a budget of $k\le T$ pairwise probes; on a probed round it may query two points and learn which one has smaller loss. Our main result shows that even a sublinear and noisy probe budget can provably improve worst-case regret in the full feedback OCO regime. With $k$ $\delta$-noisy pairwise probes, we obtain: $ Reg_T \le O\left(\min\left\{\sqrt{dT\ln T},\; \frac{dT\ln T}{k|1-2\delta|}\right\}\right) $, which is tight (up to logarithmic factors in $T$) across $T$, $k$ and $\delta$. Specifically regarding the noise parameter $\delta \in [0,1]$, the regret guarantee smoothly degrades as the oracle response approaches a coin flip, i.e., $\delta$ is close to $\frac{1}{2}$. When applying the same techniques to a finite $K$ for the prediction with $d$ experts setting, the resulting rates are instead completely tight in all parameters, including $d$. Our analysis gives a streamlined treatment of pairwise probing in OCO by quantifying the benefit of probing via a variance reduction effect, combined with a second-order (variance-based) analysis of Continuous Exponential Weights.

07.
arXiv (CS.CV) 2026-06-17

Recover Semantics First, Generate Better: Improved Latent Modeling for 3D MRI Reconstruction and Cross-Contrast Synthesis

Multi-contrast magnetic resonance imaging (MRI) provides complementary information for clinical diagnosis. However, acquiring all MRI sequences is often time-consuming and costly. Recent generative models perform cross-contrast synthesis to address this issue by inferring absent contrasts from the available ones. Nevertheless, synthesizing 3D MRI presents significant challenges. Due to the massive volume sizes, operating directly in the pixel space is computationally prohibitive; therefore, a common approach is to first compress the 3D volumes into a latent space and subsequently train generative models in that space. We observe that existing compression architectures face several critical issues: they under-preserve long-range anatomical coherence, discard clinically meaningful semantics, and rely on optimization objectives that lead to over-smoothed reconstructions. Ultimately, these shortcomings compromise the performance of subsequent generative models. In this work, we propose a semantics-first latent modeling framework for 3D MRI reconstruction and cross-contrast synthesis. Specifically, we introduce a Latent Harmonization Encoder (LHE) to capture global anatomical dependencies, ensuring coherent volumetric representations. To mitigate semantic degradation during latent compression, we further design a Semantic Recovery Block (SRB) that injects high-level priors from a self-supervised semantic teacher, enhancing contrast-aware separability in the latent space. Additionally, we propose an Anatomy-aware Frequency Loss (AFL) to adaptively preserve diagnostically relevant high-frequency structures. Extensive experiments on two public multi-contrast MRI datasets demonstrate consistent improvements in reconstruction fidelity and cross-contrast synthesis quality. Our code is available at https://github.com/script-Yang/RSF.

08.
bioRxiv (Bioinfo) 2026-06-10

ECMME: an atlas of selection pressures on the mammalian extracellular matrix reveals contrasting evolutionary dynamics

The extracellular matrix (ECM) is a fundamental metazoan innovation that provides structural support and regulatory cues essential for multicellular life. While core matrisome components are subject to strong functional constraints, their evolutionary dynamics at the molecular level remain incompletely characterized. Here, we present a comprehensive per-residue analysis of selection pressures across 272 human core matrisome proteins using high-quality orthologous sequences from up to 228 placental mammal species. We developed an automated pipeline integrating ortholog identification, codon-aware alignments, and site-specific selection analyses with the MEME and FUBAR methods from the HyPhy suite. Results reveal pervasive strong purifying selection across the matrisome, consistent with its structural and functional indispensability. This is accompanied by episodic positive selection and rarer pervasive positive selection, with collagens exhibiting significantly elevated episodic positive selection compared to glycoproteins and proteoglycans. To facilitate community access, we developed ECMME (ECM Molecular Evolution) browser, an intuitive open-access web resource that visualizes selection metrics plotted directly onto protein topologies. ECMME allows researchers to seamlessly browse and investigate the data, providing a powerful framework for interpreting functional sites. It is available online and requires no local installation or set-up (https://izzilab-ecmme.share.connect.posit.cloud/).

09.
arXiv (quant-ph) 2026-06-11

Dissociative recombination and ion-pair formation in $\mathrm{HeH^+}$ isotopologues: A time-dependent wave-packet study including rotational coupling

arXiv:2606.11352v1 Announce Type: cross Abstract: We present a comprehensive theoretical investigation of dissociative recombination (DR) and resonant ion-pair (RIP) formation in $\mathrm{HeH^+}$ isotopologues using time-dependent wave-packet propagation methods. Nuclear dynamics are treated on a set of 23 coupled electronic states, including $^2\Sigma$, $^2\Pi$, and $^2\Delta$ symmetries, in both adiabatic and strictly diabatic representations, with rotational couplings explicitly included. Reaction cross sections are computed over collision energies ranging from 0 to 50 eV. The results reveal that inclusion of a large manifold of resonant states and rotational couplings significantly enhances the DR cross section relative to earlier theoretical studies. In the diabatic representation, $^2\Sigma$ states dominate the recombination dynamics, while in the adiabatic representation, $^2\Pi$ and $^2\Delta$ states contribute significantly at low collision energies. For RIP formation, two different diabatization schemes yield systematically larger cross sections than previous models, highlighting the sensitivity of ion-pair production to electronic coupling structure. Isotopic effects are examined, showing a clear inverse dependence of cross section magnitude on reduced mass. The present results underscore the importance of multi-state coupling and nonadiabatic effects in accurately describing electron-molecule collision processes in primordial and astrophysical plasmas.

10.
PLOS Computational Biology 2026-06-10

Interpreting higher-order dependence in multimorbidity using cohort data: A partial information decomposition approach

by Cillian Hourican, Geeske Peeters, René J. F. Melis, Almar Kok, Natasja M. van Schoor, Sandra Wezeman, Mike Lees, Marcel G. M. Olde Rikkert, Rick Quax In the context of multimorbidity, clinical features seldom act in isolation: symptoms, signs and behaviours form interdependent systems in which joint effects on function can be demonstrated only when features are considered together. We introduce an open, reusable workflow that detects and interprets these “together-only” interactions using bivariate Partial Information Decomposition (PID; two sources to one target), linking synergy-based dependence to the broader network of clinical variables rather than to a single target. The workflow estimates synergy with small-sample bias correction and summarises each pair in a Breadth–Uniformity–Synergy–Total (BUST) map: breadth of synergy across target variables (broad “generalist” vs narrow “specialist” patterns), cross-stratum uniformity across age, sex and multimorbidity (uniform vs subgroup-specific), synergy strength, and total shared information. Simple diagnostics contrast observed targets with additive expectations, revealing the specific joint configurations through which non-additive effects arise. Applied to data from the Longitudinal Ageing Study Amsterdam, we treated all health-related variables—covering symptoms, clinical signs, behaviours, lifestyle factors, and self-rated health indicators—as both sources and targets in the PID framework. This symmetric design permits synergy to be quantified for every pair of variables with respect to every other variable. The workflow identifies synergistic constellations that additive models miss. Multidomain cliques involving subjective health, pain, cognition and grip strength showed multiple non-additive configurations, whereas pairs such as alcohol use with grip strength exhibited focused, narrow but uniform synergy. Notably, the pairs with the strongest synergistic contributions were largely distinct from those with the highest total mutual information, indicating that synergy captures dependency structure overlooked by conventional association measures. Rather than a new measure, this work provides a bias-aware workflow that makes higher-order dependence visible and transferable. Our results support synergy-aware mapping as a practical complement to conventional multimorbidity analyses: it highlights specific combinations of routinely assessed features whose joint states may be especially informative across multiple health targets and therefore candidates for prioritised joint assessment and future multi-domain intervention studies.

11.
arXiv (CS.AI) 2026-06-12

Select and Improve: Understanding the Mechanics of Post-Training for Reasoning

arXiv:2606.13125v1 Announce Type: cross Abstract: Reinforcement learning has rapidly emerged as a key component in the training of reasoning and coding models, yet it remains poorly understood from a mechanistic perspective. We study how and through what underlying processes capabilities are acquired or enhanced via reinforcement learning post-training. Our analysis, based on controlled math reasoning experiments with Qwen-2.5-1.5B, reveals two core mechanisms: strategy selection and strategy improvement. Our results highlight the role of SFT data and reinforcement learning data in activating these mechanisms, in particular showing how supervising the model on diverse reasoning strategies can enable strategy selection and how increasing difficulty in reinforcement learning data can enable strategy improvement. Taken together, our results provide mechanistic insight into RL training and suggest practical interventions to continue scaling reasoning capabilities.

12.
arXiv (CS.CL) 2026-06-17

Continuous Language Diffusion as a Decoder-Interface Problem

Gaussian-corrupted sentence embeddings have no direct linguistic interpretation, yet continuous diffusion language models can generate fluent text from them. We study this puzzle through Embedded Language Flows (ELF) and identify a decoder-basin mechanism: our evidence suggests that denoising becomes reliable when trajectories reach regions where the native decoder can read stable tokens. We introduce a diagnostic protocol for denoisability, semantic recoverability, order sensitivity, decoder compatibility, and trajectory reliability. It exposes failures hidden by scalar metrics: low mean-squared error can discard linguistic content, low perplexity can reflect low-entropy collapse, and clean latent reconstruction can coexist with a narrow decoder basin. A decoder-margin bound explains why token recovery depends on margin and local decoder sensitivity, not latent error alone. Auditing public ELF checkpoints reveals an interface phase diagram: early predictions are weakly readable, mid-trajectory disagreement marks a competition region, and late predictions enter a high-margin decoder basin. Once inside, token realization is surprisingly simple on generated ELF states: frozen T5 (Text-to-Text Transfer Transformer) token-embedding lookup recovers $93$–$96\%$ of native decoder decisions, and a single linear readout reaches $97.9\%$ agreement at 32k samples, leaving an $\approx1.1$–$1.2$ perplexity gap in a structured residual tail. Under conservative held-out gates, a margin rule exits roughly $17$–$28\%$ earlier in denoising steps under an explicit diagnostic monitor. Boundary checks on LangFlow, BitstreamDiffusion, and the Continuous Latent Diffusion Language Model (Cola-DLM) show that the same interface questions remain meaningful when the state object and decoder change. Continuous and latent diffusion language models should therefore be evaluated as representation-decoder systems.

13.
arXiv (CS.CV) 2026-06-12

UniDexTok: A Unified Dexterous Hand Tokenizer from Real Data

Dexterous hands are essential for fine-grained manipulation, but their hardware designs vary substantially across embodiments. Differences in kinematics, joint definitions, and degrees of freedom make it difficult to define a shared state representation compared with parallel grippers. As a result, dexterous-hand data remains fragmented and difficult to use for joint training. In this work, we propose the Unified Dexterous Hand Model (UDHM), which maps human and robot hand states into a shared 22-DoF semantic interface. Based on UDHM, we introduce UniDexTok, a retargeting-free state tokenizer that learns embodiment-conditioned discrete tokens from standardized real joint states. UniDexTok provides a unified representation for heterogeneous dexterous hands without relying on retargeting or simulation data. Compared with the recent baseline UniHM, UniDexTok reduces MPJAE from 15.63 degrees to 0.16 degrees and MPJPE from 18.51 mm to 0.18 mm, corresponding to error reductions of 98.98% and 99.03%, respectively. These results improve reconstruction from centimeter-scale to sub-millimeter accuracy. Experiments further show that data from other embodiments improves target-embodiment reconstruction accuracy, demonstrating the benefit of cross-embodiment tokenization. UniDexTok also shows strong zero-shot and few-shot reconstruction ability when new dexterous hands are introduced.

14.
arXiv (CS.LG) 2026-06-16

PHINN: Persistent Homology Inspired Neural Network for Rare-Event Time Series Generation

arXiv:2606.15452v1 Announce Type: new Abstract: Rare events in time series are critical to model but hard to learn due to data scarcity. Current generative models struggle with extreme values. We observe that rare events leave distinct topological fingerprints - transitions in Betti numbers from point-cloud embeddings - that are more stable and discriminative than statistical moments. We introduce PHINN, a flow-matching framework using dynamic Betti curves as conditioning signals and a persistence landscape loss for homology consistency. It scales to multivariate data, includes a natural-language interface to set Betti targets, supports cross-domain meta-learning and few-shot generation, and provides certified adversarial robustness. On financial, epidemiological, and multi-modal benchmarks, PHINN outperforms statistical and diffusion baselines in topological fidelity (beta-RMSE down 41-63%, transition accuracy up 84%) and matches jump-diffusion models in tail coverage while exceeding them in shape fidelity. All results have 95% confidence intervals.

15.
arXiv (CS.AI) 2026-06-12

Algorithmic Constitutionalism

arXiv:2606.12437v1 Announce Type: cross Abstract: The increasing encroachment of artificial intelligence (AI) on social life raises significant risks for society, particularly within the infospheres created and controlled by companies such as Google, Facebook, Apple, and Amazon. This article examines these risks through an in-depth analysis of Facebook's content moderation regime, which is already partially governed by algorithms. We argue that the idea of ethical engineering, often proposed in the literature as a solution to the governance challenges posed by AI, is inadequate for several reasons. In response, we develop an alternative framework, which we term "algorithmic constitutionalism." Our approach rests on three pillars: (a) a layered architecture consisting of two levels of code: (i) an operative or object level and (ii) a meta level designed to protect the system's core principles from algorithmically initiated change; (b) algorithmic meta-reasoning, which enables the system to operate simultaneously at both levels so that it can monitor, verify, and potentially correct in real time operations at the object level that depart from principles protected at the meta-code level; and (c) correction through deliberation. The article elaborates the concept of algorithmic constitutionalism and demonstrates how it may be applied to Facebook's content moderation regime. As part of this analysis, we examine the tension between societal constitutionalism and algorithmic constitutionalism. Paradoxically, attempts to subject AI systems to external deliberative control may also enable AI agents to intervene in that process, potentially undermining its purpose. The article concludes by considering the implications of this argument for the European Digital Services Act, which entered into force in October 2022.

16.
arXiv (CS.CL) 2026-06-12

EvoArena: Tracking Memory Evolution for Robust LLM Agents in Dynamic Environments

Large language model (LLM) agents have achieved strong performance on a wide range of benchmarks, yet most evaluations assume static environments. In contrast, real-world deployment is inherently dynamic, requiring agents to continually align their knowledge, skills, and behavior with changing environments and updated task conditions. To address this gap, we introduce EvoArena, a benchmark suite that models environment changes as sequences of progressive updates across terminal, software, and social domains. We further propose EvoMem, a patch-based memory paradigm that records memory evolution as structured update histories, enabling agents to reason about environmental evolution through changes in their memory. Experiments show that current agents struggle on EvoArena, achieving an average accuracy of 39.6% across evolving terminal, software, and social-preference domains. EvoMem consistently improves performance, yielding an average gain of 1.5% on EvoArena and also improving standard benchmarks such as GAIA and LoCoMo by 6.1% and 4.8%. Beyond individual tasks, EvoMem further improves chain-level accuracy by 3.7% on EvoArena, where success requires completing a consecutive sequence of related evolutionary subtasks. Mechanistic analysis shows that EvoMem improves evidence capture in the memory, indicating better preservation of complete evolving environment states. Our results highlight the importance of modeling evolution in both evaluation and memory for reliable agent deployment.

17.
arXiv (CS.CL) 2026-06-11

An Ontology-Guided Multi-Anchor Graph Retrieval Framework for Traffic Legal Liability Determination

Traffic law liability determination is critical for assigning legal penalties, requiring the simultaneous identification of interdependent statutory provisions across multiple legal dimensions. However, existing retrieval-augmented generation methods suffer from a multi-dimensional retrieval bottleneck: single axis architectures compress complex legal queries into a single pathway, causing interdependent statutory dimensions to be overlooked. To address this, we propose OMAGR, an ontology-guided framework that decomposes queries into ontology-aligned anchors and executes parallel graph retrieval across each dimension, ensuring independent retrieval across dimensions before fusion. To evaluate the proposed method, we created the TrafficLaw-QA dataset, an expert-validated benchmark dataset containing 200 questions and 527 legal provisions. Results show that TrafficOmni-RAG outperforms baselines on Context Precision and Faithfulness metrics. The findings demonstrate that parallel multi-anchor retrieval effectively resolves the multi-dimensional retrieval bottleneck, offering a promising direction for traffic law liability determination research.

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

LLM-Evolved Domain-Independent Heuristics for Symbolic AI Planning

arXiv:2605.29649v2 Announce Type: replace Abstract: Heuristic search is the dominant paradigm in symbolic AI planning, and the strongest heuristics are the result of decades of work by planning researchers. Recent work has shown that large language models (LLMs) can design heuristics for individual planning domains, but no LLM-generated heuristic has so far worked on arbitrary planning tasks. In this paper, we use evolutionary search to produce the first LLM-generated domain-independent heuristics that exceed the hand-engineered state of the art. We let an LLM mutate parent heuristics written in C++, store candidates in a MAP-Elites archive keyed on informedness and speed and calculate fitness scores by blending coverage with solving time. To place the evolved programs in context, we additionally benchmark a broad set of hand-engineered heuristics on their informedness-speed tradeoff, which to our knowledge has not been done before. On unseen testing domains, our best evolved heuristic solves more tasks than even the strongest baseline, with our full heuristic suite spanning the Pareto frontier of said tradeoff. We also find that seeding evolution from the trivial blind heuristic outperforms seeding from the strong FF heuristic, even when the resulting program is itself an FF variant, and that LLM reasoning effort affects how often candidates compile much more than the quality of those that do. Because the evolved programs are plain C++, they slot into existing planners as drop-in replacements and inherit the soundness and completeness guarantees of the underlying search.

19.
bioRxiv (Bioinfo) 2026-06-18

A Two-Stage Interpretable Framework for Predicting Plant-Derived Small RNA Targets on Human 3'UTRs

Authors:

Can plant-derived small RNAs target human mRNA 3'UTRs via complementary base pairing and produce experimentally detectable regulatory effects? This question concerns not only the fundamental feasibility of cross-kingdom RNA regulation but also the technological pathway for screening plant-derived active small nucleic acids. Existing miRNA target prediction tools are predominantly designed for endogenous miRNA-mRNA systems, exhibiting notable limitations when applied to cross-species small RNA inputs and small-sample wet-lab experimental adaptation. In this study, we developed a two-layer prediction framework, MetaLulu-AI. The first layer builds upon publicly available human miRNA-mRNA 3'UTR interaction data, utilizing XGBoost to learn foundational binding rules on human 3'UTRs based on 41 interpretable computational features, including seed region pairing types, local context sequence composition, site positioning, and RNA secondary structures. The second layer is tailored to the experimental system of plant-derived small RNAs and human target genes. It introduces 40 experimental samples using significant changes in endogenous protein expression as the regulatory standard (determined by Western blot or ELISA 48 hours post-transfection of small RNAs via Lipo3000). Using 52-dimensional computational features and the optimal transcript scores from the first layer as inputs, this layer employs TabPFN for experimental label adaptation. The first-layer dataset consists of 38,752 training samples, 5,536 validation samples, and 11,073 testing samples (totaling 55,361), with a positive-to-negative sample ratio of approximately 1:5.4. On the randomly split test set, the model achieved an AUC of 0.9686, a recall of 0.8523, a precision of 0.8080, and an accuracy of 0.9452 (at a decision threshold of 0.4797). Group-based splitting revealed that the model maintains high discriminative power for unseen genes (AUC = 0.9541), though its generalization ability for completely unseen miRNAs decreases (AUC = 0.7390). For the 40 experimental samples in the second layer, the TabPFN model achieved an average AUC of 0.7406 {+/-} 0.092 across ten repeated 70/30 random splits, outperforming the baseline of directly using the first-layer scores (0.3563 {+/-} 0.149); the average AUC in a 5-fold cross-validation was 0.770 {+/-} 0.177. SHAP analysis demonstrated a clear divergence in the discriminative basis of the two models: the first layer relies more heavily on the thermodynamics of the small RNA itself and the quality of canonical seed sites, whereas the second layer focuses more on the local UTR environment and statistical site features. Although the current second-layer results are constrained by sample size and gene coverage, this framework serves as a preliminary observation of the adaptation mechanism for cross-kingdom regulation experiments, and motivating future large-scale validation. Under stricter leave-one-gene-out and leave-one-small-RNA-out evaluation, the adapter exceeded the first-layer score baseline but only matched the majority-class baseline, underscoring that entity-level generalization is not yet established.

20.
medRxiv (Medicine) 2026-06-11

Global population frequencies of NAT2 star alleles observed in three large biobanks

NAT2 is an important pharmacogene which encodes the N-acetyltransferase 2 enzyme that is involved in the metabolism of multiple medications, and variants in this gene can affect patient response to these medications. CPIC has published a clinical guideline for prescribing hydralazine using NAT2 genotypes. Just prior to the guideline, updated NAT2 star allele numbering and definitions were released, differing somewhat from the historical nomenclature. Clinical pharmacogenomic testing panels often test for the most common star alleles, so knowledge of the most common updated NAT2 star alleles is critical for the implementation of the CPIC NAT2/hydralazine guideline. We first determine NAT2 diplotype frequencies from UK Biobank (UKBB) 200k phased genomes, then analyzed allele, diplotype, and phenotype population frequencies from the All of Us Research program, PennMedicine BioBank (PMBB) and UKBB 500k datasets. We found that analyzing NAT2 diplotypes from phased data provides critical information for algorithms designed to predict diplotypes from unphased data. We observed that NAT2*5, *6, and *4 were the most common star alleles in that order, and the top 11 most frequent NAT2 star alleles were the same across all biobanks. However, differences in star allele frequencies across biogeographical populations were observed. The largest difference led to a higher frequency of NAT2 poor metabolizer phenotypes as compared to rapid and intermediate metabolizer phenotypes in all global populations except in the EAS population, where NAT2 poor metabolizers were in the minority.

21.
bioRxiv (Bioinfo) 2026-06-11

TifBERT: a self-supervised foundation model for normalization-robust bulk RNA-seq representation learning

Bulk RNA sequencing remains central to translational genomics, yet foundation-model development has largely focused on single-cell data. Existing transformer approaches for bulk RNA-seq often rely on expression discretization, numerical reconstruction, external gene embeddings, or restricted gene sets, limiting robustness across normalization schemes and cohorts. Here, we introduce TifBERT, a self-supervised framework for full-transcriptome bulk RNA-seq representation learning. TifBERT converts each unordered expression profile into a sample-specific gene sequence using term frequency-inverse document frequency (TF-IDF) ordering, prioritizing genes that are both highly expressed within a sample and selectively expressed across the cohort. It is then pretrained using masked gene modeling, predicting gene identities from transcriptomic context rather than reconstructing expression values. Pretrained on harmonized TCGA Pan-Cancer data spanning five RNA-seq normalization schemes, TifBERT learns contextual representations across approximately 10,000 genes without expression binning, landmark-gene restriction, or external biological embeddings. Across 33 TCGA cancer types, TifBERT achieved 90.83% accuracy, 0.996 macro AUC-ROC, and 0.903 MCC. It also captured pathway-level biology, achieving mean sample-wise and pathway-wise Pearson correlations of 0.754 and 0.762 across 1,387 PARADIGM pathway activities. Independent evaluation on GTEx healthy tissues showed preservation of tissue-level transcriptomic structure without retraining. In comparison with existing models, TifBERT achieves competitive subtype discrimination with substantially greater stability and produces markedly richer embedding geometry (effective rank 95.6 versus 6.3), without requiring expression discretization or in-distribution pretraining exposure. Together, TifBERT provides a scalable, normalization-independent foundation model for reusable bulk transcriptomic representation learning

22.
arXiv (CS.LG) 2026-06-11

Discovery and inference beyond linearity for epidemiological data by integrating Bayesian regression, tree ensembles and Shapley values

arXiv:2505.00571v3 Announce Type: replace-cross Abstract: Machine Learning (ML) is gaining popularity in epidemiology and healthcare studies for hypothesis-free discovery of risk and protective factors. ML is strong at discovering nonlinearities and interactions, but this power is compromised by a lack of reliable inference. Although Shapley values provide local measures of features' effects, valid uncertainty quantification for these effects is typically lacking, thus precluding statistical inference. We propose RuleSHAP, a framework that addresses this limitation by combining a dedicated Bayesian sparse regression model with an improved tree-based rule generator and Shapley value attribution. RuleSHAP provides detection of nonlinear and interaction effects, with uncertainty quantification at the individual level as a key contribution. We derive an efficient formula for computing marginal Shapley values within this framework. We apply RuleSHAP to data from an epidemiological cohort to detect and infer several effects for high cholesterol and blood pressure, such as nonlinear interaction effects between features like age, sex, ethnicity, BMI and glucose level. To conclude, we demonstrate the validity of our framework on simulated data.

23.
arXiv (quant-ph) 2026-06-12

Squeezing Enhancement in Lossy Multi-Path Atom Interferometers

arXiv:2409.04091v3 Announce Type: replace Abstract: This paper explores the sensitivity gains afforded by spin-squeezed states in atom interferometry, in particular using Bragg diffraction. We introduce a generalised input-output formalism that accurately describes realistic, non-unitary interferometers, including losses due to velocity selectivity and scattering into undesired momentum states. This formalism is applied to evaluate the performance of one-axis twisted spin-squeezed states in improving phase sensitivity. Our results show that by carefully optimising the parameters of the Bragg beam splitters and controlling the degree of squeezing, it is possible to improve the sensitivity of the interferometer by several dB with respect to the standard quantum limit despite realistic levels of losses in light pulse operations. However, the analysis also highlights the challenges associated with achieving these improvements in practice, most notably the impact of finite temperature on the benefits of entanglement. The results suggest ways of optimising interferometric setups to exploit quantum entanglement under realistic conditions, thereby contributing to advances in precision metrology with atom interferometers.

24.
medRxiv (Medicine) 2026-06-16

Prevalence and Correlates of Ideal Cardiovascular Health among Ugandan Adolescents: A Cross-Sectional Study

Introduction: Cardiovascular disease (CVD) risk factors often emerge during adolescence and track into adulthood, yet data on cardiovascular health (CVH) in sub-Saharan Africa remain limited. We assessed the prevalence and correlates of ideal CVH among Ugandan adolescents. Methods: We analysed baseline data of adolescents enrolled in a cluster-randomised controlled trial being conducted in urban (Kampala) and rural (Jinja) districts of Uganda. In this study, Ideal CVH was defined as meeting "ideal" status of 5-7 of the American Heart Association's Life's Simple 7 metrics. Random-effects logistic regression was used to identify factors associated with ideal CVH, accounting for village-level clustering. Results: We recruited 1316 participants with a mean age of 13.2 years, of whom 58.1% were female. Overall, the prevalence of ideal CVH was 66.8% (95% CI: 64.2% - 69.3%). The prevalence was higher in Jinja (74.4%, 95%CI: 70.9% - 77.7%) than Kampala (59.6%, 95%CI: 55.8%-63.2%) and the difference was evident (p

25.
arXiv (CS.CV) 2026-06-17

EmbodiTTA: Resource-Efficient Test-Time Adaptation for Embodied Visual Systems

Continual Test-time adaptation (CTTA) continuously adapts the deployed model on every incoming batch of data. While achieving optimal accuracy, existing CTTA approaches present poor real-world applicability on resource-constrained edge devices, due to the substantial memory overhead and energy consumption. In this work, we first introduce a novel paradigm – on-demand TTA – which triggers adaptation only when a significant domain shift is detected. Then, we present OD-TTA, an on-demand TTA framework for accurate and efficient adaptation on edge devices. OD-TTA comprises three innovative techniques: 1) a lightweight domain shift detection mechanism to activate TTA only when it is needed, drastically reducing the overall computation overhead, 2) a source domain selection module that chooses an appropriate source model for adaptation, ensuring high and robust accuracy, 3) a decoupled Batch Normalization (BN) update scheme to enable memory-efficient adaptation with small batch sizes. Extensive experiments show that OD-TTA achieves comparable and even better performance while reducing the energy and computation overhead remarkably, making TTA a practical reality.