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01.
arXiv (CS.CL) 2026-06-11

One Jailbreak, Many Tongues: Learning Language-Insensitive Intention Representations for Multilingual Jailbreak Detection

Large language models (LLMs) are increasingly deployed in applications for global multilingual users, yet safety training remains concentrated in dominant languages and has not progressed in parallel with multilingual capability, creating exploitable gaps for jailbreak attacks. Current jailbreak defenses are largely developed and evaluated in dominant languages, and their effectiveness is limited by the scarcity of aligned multilingual supervision and representations dispersion caused by language variation. To address this issue, we propose MLJailDe, a multilingual jailbreak detection framework designed to improve both multilingual robustness and cross-lingual generalization. MLJailDe first introduces a multilingual back-translation data augmentation algorithm to construct a semantically consistent and functionally effective dataset spanning 11 languages, consisting of 2,232 benign and 1,239 jailbreak samples. On this basis, MLJailDe employs relative-distance constraints to reduce cross-lingual representation dispersion and encourage jailbreak prompts with similar intent to form consistent clusters across languages, while an imbalance-aware classification objective is further used to alleviate class imbalance and learn more reliable multilingual decision boundaries. Experimental results show that MLJailDe outperforms state-of-the-art baselines across multiple languages, achieving an F1 score of 98.5\%, and obtains an average F1 score of 97.1\% on unseen languages, demonstrating strong effectiveness and cross-lingual generalization.

02.
medRxiv (Medicine) 2026-06-16

MRMU: A New Paradigm for Mendelian Randomization by Accounting for Measured Covariates and Unmeasured Confounders

Mendelian randomization (MR) is a powerful approach for causal inference, however, its reliability is frequently compromised by unadjusted covariates and unmeasured confounders, such as unmeasured pleiotropy and sample structure. To address these challenges, we introduce MRMU, a novel paradigm for the MR framework. Unlike traditional single-variable or multivariable MR methods, MRMU selects instrumental variables only from the exposure of interest and estimates one exposure effect at a time, while jointly accounting for measured covariates and unmeasured confounders. This design improves the reliability of MR analyses. In simulations and real data, MRMU achieved better type I error control, higher statistical power, and more accurate effect estimation than existing MR methods. Applying to coronary artery disease (CAD), MRMU identified robust cardiometabolic risk factors, including LDL-C, APOB, systolic blood pressure, body mass index, and smoking initiation, with consistent evidence across multiple CAD datasets. In contrast, traits such as HDL-C, height, and educational attainment, which were found to be significant by existing MR methods, were no longer supported by MRMU. MRMU further supported blood pressure-related traits, rather than lipid traits, as the more relevant pathway linking urate to CAD. Finally, by integrating large-scale plasma proteomics data, MRMU identified candidate CAD drug targets beyond established HMGCR- and PCSK9-related pathways, highlighting its utility for therapeutic target prioritization.

03.
arXiv (CS.LG) 2026-06-15

AcceRL: A Distributed Asynchronous Reinforcement Learning and World Model Framework for Vision-Language-Action Models

arXiv:2603.18464v3 Announce Type: replace Abstract: Reinforcement learning (RL) for large-scale Vision-Language-Action (VLA) models is severely bottlenecked by synchronization barriers and the high cost of environment data acquisition. To overcome these challenges, we propose AcceRL, a distributed asynchronous RL framework that physically isolates environment rollouts, model inference, and gradient updates. By eliminating the cascading long-tail idle bubbles inherent in synchronous systems, AcceRL maximizes hardware utilization and ensures scalable throughput. Furthermore, AcceRL features a modular design that supports the integration of diverse, plug-and-play world models into its distributed pipeline. Extensive experiments demonstrate that the base framework achieves highly competitive performance across all four LIBERO[liu2023libero] task suites. Systematically, the asynchronous architecture delivers a $2.4\times$ throughput speedup over leading synchronous baselines. Algorithmically, by leveraging a world model pre-trained on 1,000 offline trajectories, AcceRL achieves up to a $200\times$ improvement in online sample efficiency on LIBERO-Spatial, establishing a robust framework that is both sample-efficient and time-efficient for embodied AI. Code is included in the supplementary material. Code is available at https://github.com/distanceLu/AcceRL.

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

From Chatbot to Digital Colleague: The Paradigm Shift Toward Persistent Autonomous AI

arXiv:2606.14502v1 Announce Type: new Abstract: Large Language Models (LLMs) are undergoing a fundamental transformation from conversational generators into integrated AI systems capable of reasoning, action, memory, and self-improvement. We conceptualize this transition as a shift from Chatbot to Digital Colleague: from conversational answers to persistent work. We organize this transition along two tightly coupled dimensions. First, at the cognitive core level, LLMs are advancing from Chatbot-era "fast thinking" systems driven by next-token prediction toward Thinking LLMs that leverage inference-time computation, Chain-of-Thought reasoning, reflection, process supervision, and reinforcement learning to support more deliberate and reliable cognition. Second, at the tool-augmented task execution level, LLMs are progressing from tool-calling Agents that invoke external resources in an ad hoc manner toward OpenClaw-style workstation systems (OpenClaw) equipped with persistent Workspaces, skills, verification loops, and governance. The "Workspace + Skill" paradigm makes episodic tool use colleague-like via state persistence, reusable procedures, task closure, and experience reuse. We examine data construction shifts from instruction-response pairs to State-Action-Observation trajectories and evaluation from static benchmarks to sandboxed, auditable, self-evolving AI ecosystems.

05.
arXiv (CS.CV) 2026-06-15

Clay-CNN Hybrids: Leveraging Geo-Foundational Models as Auxiliary Context for Landslide Detection

Rapid post-event landslide mapping is essential for disaster response but remains difficult to automate due to extreme class imbalance. This study evaluates whether Clay v1.5, a Geo-Foundational Model (GFM), can improve pixel-level landslide segmentation on the Landslide4Sense (L4S) benchmark, which contains 3,799 training chips with 14 Sentinel-2 and terrain bands and approximately 2% positive pixels. We compare three strategies: Clay as the primary encoder with multi-scale residual terrain fusion, a U-Net backbone augmented with Clay semantic context at the bottleneck, and a standard U-Net baseline. The hybrid U-Net + Clay model with two-stage Low-Rank Adaptation (LoRA) achieved the best test F1 of 64.5 +/- 1.8% over three seeds, surpassing the Clay-only backbone (55.2 +/- 3.6%) and the U-Net baseline (59.9%). Clay as a standalone encoder underperformed the U-Net due to the absence of multi-scale skip connections, but its pretrained representations consistently improved performance when injected as auxiliary context. These findings suggest that GFMs are most effective for landslide detection when they complement spatially detailed convolutional architectures rather than replace them.

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

ScholaWrite: A Dataset of End-to-End Scholarly Writing Process

Writing is a cognitively demanding activity that requires constant decision-making, heavy reliance on working memory, and frequent shifts between tasks of different goals. To build writing assistants that truly align with writers' cognition, we must capture and decode the complete thought process behind how writers transform ideas into final texts. We present ScholaWrite, the first dataset of end-to-end scholarly writing, tracing the multi-month journey from initial drafts to final manuscripts. We contribute three key advances: (1) a Chrome extension that unobtrusively records keystrokes on Overleaf, enabling the collection of realistic, in-situ writing data; (2) a novel corpus of full scholarly manuscripts, enriched with fine-grained annotations of cognitive writing intentions. The dataset includes \LaTeX-based edits from five computer science preprints, capturing nearly 62K text changes over four months; and (3) analyses and insights into the micro-dynamics of scholarly writing, highlighting gaps between human writing processes and the current capabilities of large language models (LLMs) in providing meaningful assistance. ScholaWrite underscores the value of capturing end-to-end writing data to develop future writing assistants that support, not replace, the cognitive work of scientists.

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

Camera and LiDAR BEV Fusion for Cooperative 3D Object Detection on TUMTraf V2X

We describe a Camera and LiDAR fusion detector developed for the TUMTraf V2X cooperative 3D object detection track of the DriveX 2026 challenge. The detector fuses three roadside cameras with a fused infrastructure-plus-vehicle point cloud in a shared bird's-eye-view space and predicts boxes through a CenterPoint-style head with a generalized IoU regression loss and an IoU quality re-ranking head. Trained on the provided train and validation splits, the model reaches a 3D mAP of 0.85 on the public Codabench test split. While iterating on the system, we observed that 44 of the 50 test frames are also present in the released train (40) and validation (4) splits with their labels. We therefore conducted two additional studies to quantify how this overlap affects the final score: (1) a finetuning run that oversamples the 44 overlapping frames, reaching 0.89 mAP, and (2) a post-processing run that replaces predictions on those frames with the released ground truth, reaching 0.99 mAP (uploaded to our Codabench account for testing but not published on the leaderboard). All three configurations and their per-class results are reported.

08.
arXiv (CS.CL) 2026-06-11

Beyond Fully Random Masking: Attention-Guided Denoising and Optimization for Diffusion Language Models

Diffusion large language models (dLLMs) offer an efficient alternative to autoregressive models through parallel decoding, yet existing post-training methods largely rely on random masking strategies that overlook intrinsic token dependencies. In this work, we present an empirical analysis of attention in dLLMs and show that tokens attending more strongly to unmasked context exhibit greater generation stability and play a critical role in reasoning. Motivated by these findings, we propose AGDO, an attention-guided denoising and optimization framework that aligns both training and optimization with attention-derived dependencies. AGDO determines the denoising order based on attention structure and emphasizes attention-critical tokens during supervised fine-tuning and reinforcement learning. Experiments on mathematical and coding benchmarks demonstrate that AGDO consistently improves reasoning performance, outperforming state-of-the-art post-training methods for dLLMs.

09.
arXiv (CS.CL) 2026-06-16

The Dark Regulome: Disentangling Predictability from Regulation in Genomic Foundation Models

High-grade gliomas integrate into neural circuits through functional synapses with neurons, raising the question of which noncoding elements shape synaptogenic gene expression in tumor cells. The regulatory program written across the dark genome, what we call the $dark regulome$, is the natural substrate to probe, and sequence foundation models offer a zero-shot route through in-silico mutagenesis (ISM); yet likelihood-based scoring is tautologically coupled to local sequence predictability, leaving the regulatory interpretation underdetermined. Across three architecturally distinct foundation models (Caduceus-Ph, HyenaDNA, Enformer) and 30,448 dark genome elements at 92 glioma-relevant loci, we introduce a residualization-and-permutation diagnostic that separates predictability-driven from regulation-driven RIS variance. A sharp 10kb proximal-regulatory horizon survives every control we apply, but the LM-derived element-class hierarchy does not: a six-feature linear baseline matches Caduceus top-decile membership at AUC $= 0.985$. Cross-architecture decomposition cleanly separates a sequence-predictability layer (the two language models co-rank long well-predicted transposable elements) from a regulatory-output layer (Enformer alone retains residual cCRE-discriminative signal), with literally zero overlap between the two top-100 lists. Conservation, brain cis-eQTL, and STRING-PPI cross-checks then anchor what biology survives: top-100 elements across all three models are $3.3\times$ enriched per model for matching brain eQTLs ($p_\mathrm{emp} < 5\times 10^{-3}$), while a tempting transposable-element regulatory layer and a striking NRXN1+NLGN1 protein-pair convergence both fail proper permutation tests once those tests are constructed. We deliver the diagnostic as a general methodological tool for any ISM-based regulatory study.

10.
arXiv (CS.AI) 2026-06-12

CloudCons: A Comprehensive End-to-End Benchmark for Cloud Resource Consolidation

arXiv:2606.13513v1 Announce Type: new Abstract: Driven by conservative over-provisioning to guarantee service reliability, resource utilization in cloud data centers remains at low levels. To mitigate this, the forecast-then-optimize paradigm has emerged to optimize consolidation by anticipating future demands. While emerging time series foundation models promise to enhance this paradigm through zero-shot generalization, existing benchmarks focus solely on prediction error metrics. The actual decision utility of these advanced models remains unverified, rendering their practical value for downstream tasks uncertain. To bridge this gap, we propose CloudCons, a comprehensive end-to-end benchmark designed to evaluate forecasting models within the specific context of cloud resource consolidation. We build high-quality datasets that cover diverse workloads from Huawei Cloud, Microsoft Azure, and Google Borg, capturing distinct service characteristics ranging from synchronized diurnal rhythms to stochastic, pulse-like bursts and high-frequency noise. We conduct an extensive evaluation of statistical, deep learning, and foundation models. Our experiments reveal a pivotal finding: while foundation models demonstrate superior zero-shot forecasting accuracy, this advantage does not inherently translate into better decision utility. Of practical significance, we systematically analyze how the selection of predictive quantiles acts as a critical lever. We provide actionable guidelines for calibrating these selections to balance the trade-off between resource efficiency and service reliability, offering vital insights for real-world deployment decisions.

11.
medRxiv (Medicine) 2026-06-10

A risk-of-contagion index using a Bayesian based model for the COVID-19 epidemic in Mexico

During the COVID-19 pandemic, limited testing capacity and reporting delays complicated epidemic surveillance and decision-making in Mexico. We calibrated textit{covidestim}, a Bayesian nowcasting model, to estimate the total SARS-CoV-2 infections from reported cases and deaths using Mexican surveillance data. Disease-progression distribution priors were calibrated using Mexico City records and validated through comparisons with national seroprevalence surveys, hospitalization data, and annual reported severe-case rates across all states. Using the reconstructed estimates of active infections, we implemented an event-based risk framework that quantifies the probability of encountering at least one infectious individual in gatherings of different sizes. This probability was subsequently translated into a four-level epidemiological traffic-light indicator and computed at both state and municipality levels. The resulting estimates revealed substantial spatial heterogeneity that is obscured by state-level aggregation, particularly in states with marked differences between urban and rural municipalities. To evaluate consistency with public-health indicators, we compared the proposed risk classification with the official Mexican epidemiological traffic-light system, considering interpretable gathering sizes relevant to public-health decision making. Weekly reports derived from this framework were delivered to policymakers in the State of Queretaro in Mexico, as an anticipation tool for school reopening and public-space management. This demonstrates that this Bayesian reconstruction of infections combined with event-based risk metrics can provide an interpretable and generalizable municipality-level complement to routine surveillance systems, particularly in regions with limited testing capacity and heterogeneous local transmission dynamics.

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

Extracting Semantics: LLM-Guided Automatic Population of Robot Ontology from URDF

arXiv:2606.17073v1 Announce Type: cross Abstract: While commonsense knowledge may suffice for virtual agents, embodied robots interacting with humans require grounded and semantically rich representations of both their environment and their own physical embodiment. In cognitive robotics, ontologies are effective for integrating such heterogeneous knowledge to enable explainable reasoning, even during continuous knowledge updates. Yet, their manual construction remains a bottleneck. We present a preliminary approach for the automatic generation of robot semantic abstractions by transforming Unified Robot Description Format (URDF) models into populated ontologies. Although URDF files provide structural and kinematic descriptions, their identifiers often require commonsense interpretation to recover meaningful semantics, a task at which Large Language Models (LLMs) excel. Our pipeline leverages LLMs to infer semantic relationships by prompting them with concepts from an existing ontology, ensuring the final classification remains aligned with the formal model. To improve reliability, the pipeline combines majority voting across multiple LLM queries along with syntactic and schema-level validation to ensure that generated outputs conform to the expected representation format and ontology constraints. We evaluate the approach on multiple robot descriptions and discuss the generated abstractions. Initial results indicate that the proposed method can effectively bridge the gap between low-level robot descriptions and the structured, grounded knowledge representations required for human-robot interaction.

13.
arXiv (math.PR) 2026-06-19

Maximal rigidity of random measure and uniqueness pairs: stealthy processes, quasicrystals and periodicity

arXiv:2512.10686v2 Announce Type: replace Abstract: This article investigates the phenomenon of maximal rigidity in spatial processes, where perfect interpolation of the process is possible from partial information, specifically, from its restriction to a strict subdomain, often resulting in a trivial tail $\sigma$algebra. A classical example known since the 1930's is that a time series is fully determined by its values on the negative integers if its spectrum has a gap, or at least a sufficiently deep zero. We extend such results to higher dimensions and continuous settings by establishing a connection with the concept of uniqueness pairs, rooted in the uncertainty principle of harmonic analysis. We present several other manifestations of this principle, unify and strengthen seemingly unrelated results across different models: quasicrystals and stealthy processes are shown to be maximally rigid on cones, and discrete integer-valued processes are necessarily periodic when they have a simply connected spectrum. Finally, we identify a surprising class of continuous fields with seemingly standard behavior, such as linear variance and finite dependency range, that undergo a phase transition: they are perfectly interpolable on B(0, $\rho$) for $\rho$ ___ 2 $\pi$ but exhibit no rigidity for $\rho$ > 2.

14.
arXiv (quant-ph) 2026-06-12

Schrödinger Symmetry in Spherically-symmetric Static Mini-superspaces with Matter Fields

arXiv:2512.13651v3 Announce Type: replace-cross Abstract: Schr\"{o}dinger symmetry has been shown to emerge in a ``fluid limit" from the full superspace to several mini-superspace models. To investigate one aspect of the robustness of this emergent symmetry, we consider two spherically-symmetric static mini-superspace models with matter fields at the classical level: (i) a Maxwell field with a cosmological constant and (ii) $n$ massless scalar fields. By developing a method based on canonical transformations, we demonstrate that for model (i), 3D Schrödinger symmetry emerges, and the solution is the (anti-)de Sitter Reissner-Nordström spacetime, and for model (ii), $(2+n)$D Schrödinger symmetry appears, and the solution is a generalized Janis-Newman-Winicour spacetime and its ``interior", a Kantowski-Sachs type closed universe. Furthermore, for the vacuum model, we find that 2D Schrödinger symmetry holds with different lapse functions and mini-superspace coordinates, suggesting the potential, yet unconfirmed, covariance of the symmetry. Finally, we propose a physical interpretation of the symmetry under the Hamiltonian constraint $H$: symmetry generators commuting with $H$ map a solution to another one, while those non-commuting with $H$ generate a new theory with the Schrödinger symmetry and the transformed configuration is a solution to the new theory. These results reinforce the robustness of the emergent Schrödinger symmetry and open new frontiers for exploring dynamics of matter and gravity.

15.
arXiv (math.PR) 2026-06-17

Cutoff for asymmetric shelf shuffle

arXiv:2606.18039v1 Announce Type: new Abstract: A mechanical shuffler consists of $m$ shelves. A deck of $n$ cards, arranged in increasing order, is dealt from the bottom sequentially. Each card is assigned a shelf uniformly at random and placed on the top (bottom) of the existing pile with probability $p$ ($1-p$) independently. We refer to this as asymmetric shelf-shuffle. We find the law $\nu_{n, m}^{(p)}$ of the permutation induced by the asymmetric shelf-shuffle and show that the pair consisting of the number of descents and the number of valleys is a sufficient statistic. This generalizes a result of Diaconis, Fulman, and Holmes (Ann. Appl. Prob., 2013) corresponding to the case $p=1/2$. For $p=1/2$, Chen and Ottolini (ECP, 2025) established the cutoff in the total variation distance near $\lfloor n^{5/4}\rfloor$. We establish the cutoff for the asymmetric shelf shuffle. Let $\nu_n$ be the uniform measure on the set of all permutations $S_n$ of $\{1, \ldots, n\}$. For a fixed $p\neq 1/2$ and $c>0$, we show that \[\operatorname{TV}\left(\nu_{n, \lfloor cn^{3/2}\rfloor }^{(p)}, \nu_n\right)=1-2\Phi\left(-\frac{|2p-1|}{4\sqrt{3}c}\right)+O_{c, p}(n^{-1/2})\;.\] We also establish the cutoff in the separation distance near $m\approx n^{2}$ and in the relative entropy near $m=n^{3/2}$. In both cases, we also obtain the cutoff profile explicitly.

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

JoyAI-VL-Interaction: Real-Time Vision-Language Interaction Intelligence

Many moments in the real world do not wait for a user to ask. A fire starts on a security monitor, an expression flickers across a video call, or a product a viewer wants flashes by in a livestream. Yet today's large models remain mostly turn-based by design: they answer only when addressed, and even video-call apps that appear interactive still operate as question-answer systems, reacting only when polled or prompted. We argue for a different paradigm: a model that is present in the world like a person. It continuously watches what is happening now, decides on its own whether to speak or stay silent, interacts in real time, and delegates to a background model when the problem is hard. To advance interaction models and their adoption across domains, we make two fully open-sourced contributions. First, we release JoyAI-VL-Interaction, an 8B-scale, vision-first VL-interaction model. The model makes the response decision internally, choosing each second to stay silent, respond, or delegate to a background model, and it excels at vision-triggered responsiveness and time awareness. We pair it with a transferable training recipe, from which capabilities we never trained for emerge, such as guiding a shopper through changing app screens or improvising a lecture from a slide deck. Second, we release a complete, deployable system built around that model. The system streams any ongoing video into the model, making it genuinely present in the world. All other components are pluggable, including ASR/TTS modules, memory, visualization UI, and a background brain that can connect to any API or agent. Across six real-world scenarios, human raters prefer JoyAI-VL-Interaction over the in-app video-call assistants of Doubao and Gemini by a wide margin. To our knowledge, this is the first open, vision-driven interaction model released together with its training recipe, data, and complete deployable system.

17.
arXiv (CS.AI) 2026-06-15

Communication Policy Evolution for Proactive LLM Agents

arXiv:2606.14314v1 Announce Type: new Abstract: LLM agents have rapidly evolved into autonomous systems, yet a persistent information gap remains between users and agents: communication is costly, while users' identical preferences further limit information exchange. To investigate how agents should communicate across modalities, this paper formalizes Communication Policy, establishes textual and UI-based policies, and then evaluates communication policies across diverse environments, personas, and model combinations. Building information asymmetry for proactive agents, we set up two complementary settings, User-Agent and Planner-Executor. Experimental results reveal complementary strengths between interaction channels: text-based interaction often facilitates task performance, while structured UI improves agents' response quality and persona compliance. Motivated by that, a hybrid method combines these advantages. We further propose Communication Policy Evolution (CPE), a self-evolution framework for refining communication policies through rollout and prompt-level evolving. Without model modification, CPE achieves the best task success across multiple settings using prompt refinement alone. Our findings identify communication behavior as a critical yet underexplored design dimension for LLM agents.

18.
medRxiv (Medicine) 2026-06-10

Impact of Early Treatment on Symptom Improvement and Procedural Events among Men with BPH and Bothersome Lower Urinary Tract Symptoms: A Contemporary Analysis of the American Urological Association Quality (AQUA) Registry

PURPOSE: As the armamentarium of BPH therapies continues to expand, it remains imperative to maximize patient satisfaction and minimize decisional regret. We sought to determine the impact of time from BPH diagnosis to index treatment on symptom improvement and subsequent procedural events. MATERIALS AND METHODS: We queried the American Urological Association Quality Registry for men [&ge;] 40 years old with BPH, available IPSS data, and no receipt of prior BPH treatment. Index treatment included medication, surgery, or minimally invasive surgical therapy (MIST). Outcomes included IPSS over 3 years of follow-up, change in percentage of mild lower urinary tract symptoms (LUTS) by 3 months, and time to procedural event. Patients were stratified by time from index diagnosis to treatment by 3 years. Outcomes were compared across time-to-treatment cohorts with appropriate statistical tests with p < 0.05 as significant. RESULTS: 43,919 patients met criteria with 19,642 pursuing treatments. Patients pursued treatment at comparably lower baseline IPSS compared to prior prospective series. Patients undergoing surgery and MIST had significantly higher baseline IPSS, while medical comorbidities were significantly more common among men initiating pharmacotherapy. Early surgery and MIST were associated with significant improvement in IPSS within 6-12 months and an increase in mild LUTS by 3 months. All forms of early treatment were associated with delayed time to procedural events, including catheterization and fulguration. CONCLUSIONS: Early procedural intervention for BPH is associated with early symptom improvement and delayed time to procedural events among real-world, contemporary practice.

19.
bioRxiv (Bioinfo) 2026-06-19

Accurate detection of tumor clonality and ongoing expansion mode from genomic data

Recent evidence shows that despite considerable effort, currently available algorithms for estimating intra-tumor heterogeneity (ITH) remain limited. We developed DECODE (Deciphering Cancer Origin from DNA Evolution), a novel mutation clustering method that incorporates the impact of sample-specific sequencing coverage and mutation calling biases. On synthetic data, DECODE outperformed existing methods across multiple clonality metrics and accurately detected and characterized the neutral tail in the site frequency spectrum (SFS), which encodes the tumor's ongoing expansion mode. In acute myeloid leukemia, accounting for the neutral tail enabled DECODE to yield more parsimonious clonal decompositions that align more closely with known subclonal dynamics that drive relapse. Applied to data from The Cancer Genome Atlas, DECODE not only detected a neutral SFS tail in most samples across tumor types but also uncovered a clinically meaningful link between ITH and survival in low-grade glioma. By jointly inferring clonality and expansion mode, DECODE provides two complementary and prognostically relevant readouts of tumor evolution from single tumor genomic samples.

20.
bioRxiv (Bioinfo) 2026-06-11

STITCH links cellular morphology and gene expression in spatial transcriptomics

In situ spatial (ISS) sequencing can uncover co-variation between cellular morphology and gene expression in vivo. However, a principled and interpretable mathematical representation of morphology has not yet been applied in this context. In particular, current deep learning-based representations of cell images confound a cell's shape with its size. We present an interpretable representation of cellular boundary contours, based on tangent principal component analysis (TPCA) in a Kendall shape manifold, that captures size-independent contour shape features. This approach successfully recovers shape-perturbing genes in an RNAi screen than a previous metric geometry-based approach. We build on TPCA to develop STITCH (Shape-TranscriptomIc Correlation and Harmonization), an approach to reveal covariation between cell morphology with gene expression in ISS datasets. In a Xenium dataset, STITCH outperforms a deep learning-based approach in both recovering the layered organization of keratinocytes and a spatial gradient in nuclear eccentricity. Across samples in a melanoma CosMx dataset, STITCH reproducibly associates elongated and triangular fibroblasts with proximity to malignant cells and myofibroblast-like transcriptional program. Finally, STITCH independently recovers a known link between mesenchymal-like malignant cell states and increased cell area in two melanoma cohorts. STITCH can thus yield interpretable morphology-transcriptome relationships across cell types, patients, and spatial transcriptomics platforms.

21.
arXiv (CS.AI) 2026-06-19

Global Ease of Living Index: a machine learning framework for longitudinal analysis of major economies

arXiv:2502.06866v3 Announce Type: replace-cross Abstract: The drastic changes in the global economy, geopolitical conditions, and disruptions such as the COVID-19 pandemic have impacted the cost of living and quality of life. It is essential to comprehend the long-term implications of the cost of living and quality of life in major economies. A transparent and comprehensive living index must include multiple dimensions of living conditions. In this study, we present an approach to quantifying the quality of life through the Global Ease of Living Index that combines various socio-economic and infrastructural factors into a single composite score. Our index utilises economic indicators that define living standards, which could help in targeted interventions to improve specific areas. We present a machine learning framework to address missing data for certain economic indicators in specific countries. We then curate and update the data and use a dimensionality reduction approach (Principal Component Analysis and Factor Analysis) to create the Ease of Living Index for major economies since 1970. Our work significantly adds to the literature by offering a practical tool for policymakers to identify areas needing improvement, such as healthcare systems, employment opportunities, and public safety. Our approach with open data and code can be easily reproduced and applied to various contexts, providing transparency and accessibility for ongoing research and policy development in quality-of-life assessment.

22.
arXiv (CS.CL) 2026-06-18

Mitigating Scoring Errors and Compensating for Nonverbal Subtests in Speech-Based Dementia Assessment

Early detection of cognitive impairment relies on neuropsychological tests to minimize subjectivity by assessing multiple cognitive domains. Speech-based evaluation can support diagnostics and improve accessibility, but transcription errors and the omission of nonverbal subtests (e.g., motor skills) limit accuracy. Beyond conventional test scores, speech-derived features can provide additional insights into cognitive status. This study investigates the speech-based evaluation of the German "Syndrom-Kurz-Test," a standardized dementia screening test comprising verbal and motor subtests. We train models that integrate transcript-derived scores and Whisper embeddings per verbal subtest to reduce scoring errors. To compensate for missing motor subtests, we then leverage these fused representations to approximate expert overall ratings. Despite omitting subtests, our models strongly correlate with expert ratings and efficiently and accurately discriminate between cognitive status groups.

23.
arXiv (math.PR) 2026-06-16

Logarithmic Large Deviations for Heavy-Tailed Sums

arXiv:2606.16487v1 Announce Type: new Abstract: We establish logarithmic large-deviation bounds for sums of independent nonnegative random variables with regularly varying tails. The normalization is chosen at the extreme-value scale and the speed is $\log n$. In contrast with Cramér's theorem, the resulting rate function is determined only by the tail index. The proof transfers a maximum large-deviation principle to sums in the one-big-jump region.

24.
arXiv (CS.AI) 2026-06-19

One Probe Won't Catch Them All: Towards Targeted Deception Detection

arXiv:2602.01425v2 Announce Type: replace Abstract: Linear probes are a promising approach for monitoring AI systems for deceptive behaviour. Previous work has shown that a linear classifier trained on a contrastive instruction pair and a simple dataset can achieve good performance. However, these probes exhibit notable failures even in straightforward scenarios, including spurious correlations and false positives on non-deceptive responses. In this paper, we demonstrate that deception detection is inherently heterogeneous: while a single universal probe achieves modest improvements (+0.032 AUC), post-hoc oracle analysis reveals substantially higher potential (+0.108 AUC) when probes are matched to specific deception types, and synthetic validation experiments suggest this ceiling is achievable a priori when the deception type is known in advance. Our findings reveal that instruction pairs capture deceptive intent rather than content-specific patterns, explaining why prompt choice dominates probe performance (70.6% of variance). Given this heterogeneity, we conclude that organizations should define their specific threat models and deploy appropriately matched probes rather than seeking a universal deception detector.

25.
arXiv (CS.CL) 2026-06-11

Fanar-Sadiq: A Multi-Agent Architecture for Grounded Islamic QA

Large language models (LLMs) can answer religious knowledge queries fluently, yet they often hallucinate and misattribute sources, which is especially consequential in Islamic settings where users expect grounding in canonical texts (Qur'an and Hadith) and jurisprudential (fiqh) nuance. Retrieval-augmented generation (RAG) improves grounding, however, a single retrieve-then-generate pipeline is insufficient for diverse Islamic queries, including verbatim scripture, citation-grounded guidance, and rule-constrained computations such as zakat and inheritance. To address these challenges, we present Fanar-Sadiq, a bilingual Arabic-English Islamic QA system built on a multi-agent, tool-augmented architecture. It is a core component of the Fanar AI platform. Fanar-Sadiq routes Islamic queries to specialized modules within an agentic tool architecture. It supports intent-aware routing, retrieval-grounded fiqh answers with normalized citations and verification traces, exact verse lookup with quotation validation, and deterministic Sunni zakat and inheritance calculators with madhhab-sensitive branching. We evaluate the end-to-end system on public Islamic QA benchmarks and show strong effectiveness and efficiency. It is publicly accessible through an API and Web application and has received over 1.9M accesses in less than a year (https://api.fanar.qa/docs).