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

The Linguistics Olympiads: Towards a New Corpus for Linguistics Research?

Linguistics olympiad problems (LOPs) are a category of self-sufficient puzzles consisting of a scaled-down corpus representative of certain linguistic phenomena, from which the solver must deduce a primitive set of rules of the language and then translate a new set of elements. The linguistics olympiads (LOs) have become a worldwide phenomenon with 43 different territories taking part in the International Linguistics Olympiad (IOL) 2025. While the typology and solving strategies of LOPs have been analysed, their scientific facet and connections to academic linguistics have yet to be explored. LOPs are directly connected to many linguistic fields, e.g., linguistic typology, linguistic relativity, and linguistics fieldwork. Recently, LOPs have become a research focus as benchmarks for large language models, thus highlighting their usefulness in computational linguistics. Nevertheless, they have not yet been integrated into mainstream linguistics research. This paper attempts to open new directions of including this particular type of puzzle in academic research by offering a structured evaluation of LOPs as linguistic data sources and proposes criteria for their responsible use in academic research. Starting from a set of over 1800 LOPs, this study critically examines the potential of LOPs as a novel corpus for linguistics research by discussing their strengths and limitations as tools, as well as the areas of linguistics into which these problems could fit. This work forms the foundation for a broader initiative aimed at bridging the gap between LOs and academic linguistics, by establishing a robust theoretical framework for LOPs.

02.
arXiv (quant-ph) 2026-06-25

Feasibility-driven QAOA with penalty scheduling

arXiv:2606.25117v1 Announce Type: new Abstract: Most available quantum algorithms address constrained optimization problems by treating constraints as soft penalty terms within a QUBO formulation. This approach requires careful adjustment of the penalty coefficients, which scales poorly with the number of constraints and lacks a proper strategy to balance feasibility and solution quality. In this work, we introduce two extensions of standard linear-ramp QAOA (lr-QAOA) tailored to problems with multiple heterogeneous constraints. We first construct $\Lambda$-lr-QAOA, in which each penalty term is assigned its own linear-ramp schedule, promoting penalty weights from external hyperparameters to internal variational parameters of QAOA, similarly to the objective and mixer parameters. By optimizing all schedules jointly in a single run, this approach eliminates nested penalty tuning and scales more efficiently to multiple constraints. The optimization is guided by a feasibility-driven loss function that pushes the quantum state towards high-quality feasible solutions. As a further refinement, we introduce piecewise-ramp QAOA, in which the linear ramps are replaced by two-segment piecewise schedules, enhancing the expressiveness of the Ansatz at the cost of a small parameter overhead independent of the circuit depth. We benchmark both methods on Earth-observation satellite mission planning tasks formulated as budget-constrained Maximum Weight Independent Set problems. Numerical results show that piecewise-ramp QAOA consistently outperforms lr-QAOA and $\Lambda$-lr-QAOA across circuit depths and system sizes. Furthermore, both $\Lambda$-lr-QAOA and piecewise-ramp QAOA exhibit a high feasibility rate, which is crucial in industrial applications. Our analysis highlights an intrinsic feasibility-optimality trade-off, which we address by introducing a filtered variant of the loss providing a single hyperparameter to tune this balance.

03.
arXiv (math.PR) 2026-06-25

Imprecise Transition Matrices for Markov Cohort Models: Lower and Upper Expectations with a Practical Health Economic Application

arXiv:2606.25716v1 Announce Type: cross Abstract: In applied health research, Markov cohort models are built on a precisely specified transition probability matrix. However, in many applications, the available evidence – transition counts, structural constraints, and treatment-effect data – identifies a set of admissible matrices rather than one uniquely justified matrix. This paper formulates an imprecise-probability extension in which inference yields lower and upper expectations over an evidence-compatible set of precise Markov cohort models. The contribution differs from existing imprecise Markov-chain work by focusing on finite-horizon cohort trajectories, additive accumulated outcomes, and transition matrices constructed from empirical transition counts. Under non-empty compact separately specified outgoing-row sets, the lower and upper accumulated outcomes are computed exactly by Bellman-style lower and upper transition operators. We prove the envelope theorem, reduction to the classical model, coherence properties of the lower transition operator, and algebraic conditions under which a single selected matrix yields a non-robust decision. We then show how multinomial transition counts induce admissible matrix sets through the Imprecise Dirichlet Model. A real-world cost-effectiveness example of patent foramen ovale closure after cryptogenic stroke illustrates the practical consequence: the empirical transition matrix slightly favors closure, whereas the imprecise analysis yields an incremental net monetary benefit interval crossing zero. The method provides both a rigorous lower-expectation formulation and a practical diagnostic for decisions that depend on transition probabilities not fully resolved by the evidence.

04.
arXiv (CS.CV) 2026-06-25

LinStereo: Linear-Complexity Global Attention for Multi-Scale Iterative Stereo Matching

Existing Vision Foundation Model (VFM)-based iterative stereo pipelines under-exploit three information pathways: multi-scale backbone features are collapsed into single-level correlations, geometric priors remain untapped at initialization, and context propagates only locally. These gaps widen under degraded photometric cues, making underwater scenes a stringent generalization test. To address this, we propose LinStereo, built upon Depth Anything V3, whose core is a Position-Aware Linear Attention (PALA) module that replaces local recurrence with global aggregation at linear cost, propagating reliable estimates from well-matched regions into degraded areas while preserving disparity structure. PALA is made effective by two enabling components: Hierarchical Semantic Cost Volumes (HSCV), which supply scale-aligned correlations from the VFM feature hierarchy, and a Depth Prior Initialization (DPI) that converts monocular depth into a metrically calibrated warm start. LinStereo achieves state-of-the-art-level accuracy on standard benchmarks and strong cross-domain generalization, particularly on underwater scene where severe photometric degradation makes stereo matching particularly challenging, attaining the best overall accuracy with consistent gains 28% lower AbsRel on TartanAir-UW, 26% on SQUID, a real-world underwater dataset).

05.
arXiv (math.PR) 2026-06-17

Non-asymptotic Tail Bounds for the Kostlan–Shub–Smale Field: Tensor PCA and Spherical $k$-Spin Complexity

arXiv:2606.17665v1 Announce Type: cross Abstract: This paper builds a hierarchy of explicit, non-asymptotic tail bounds for the supremum of the Kostlan–Shub–Smale (KSS) random field on the sphere, and applies it to two problems: Spiked Tensor PCA and the landscape of the spherical $k$-spin model. For Tensor PCA, we study the non-asymptotic statistical limits of estimating a rank-$R$ symmetric signal tensor of order~$k\ge 3$ and dimension~$d\ge 3$ from a single Gaussian observation at signal-to-noise ratio~$\lambda$, through the profile maximum likelihood estimator, the MLE restricted to normalized rank-$R$ tensors of coherence at least~$\kappa$. Our analysis uses a single reduction: a deterministic geometric inequality (the Tube Method) and a rank-reduction step bound the estimation error by the supremum of the canonical KSS field, which the Kac–Rice formula turns into a Gaussian integral against the expected absolute characteristic polynomial of a shifted Gaussian Orthogonal Ensemble, controlled in turn by the four explicit tail bounds of our hierarchy (three from a Mehta–Fyodorov representation, one from a Ben Arous–Dembo–Guionnet large deviation). The same reduction yields two results, each with explicit constants. For estimation, a finite-$(k,d)$ error bound recovers the asymptotically optimal rate~$\sqrt{d\log k}$ of Perry, Wein and Bandeira, with explicit dependence on the rank~$R$ and the coherence~$\kappa$. For the landscape, a two-sided non-asymptotic bracketing of the annealed complexity of the spherical $k$-spin Hamiltonian recovers the Auffinger–Ben Arous–\v{C}ern\'y complexity function in the high-dimensional limit.

06.
arXiv (CS.AI) 2026-06-25

RWGBench: Evaluating Scholarly Positioning in Related Work Generation

arXiv:2606.24894v1 Announce Type: cross Abstract: Large language models have shown strong fluency in scientific writing, yet the evaluation of related work generation (RWG) remains limited. Existing RWG evaluations largely inherit summarization-oriented metrics, using lexical or semantic similarity to reference sections as proxies for quality. However, related work writing is fundamentally a citation-level scholarly positioning task: it requires selecting, organizing, and framing prior work to clarify how a target paper relates to, differs from, and contributes beyond existing research.As a result, models may generate coherent and semantically-relevant text while exhibiting academically critical failures, such as inappropriate citation selection or misplaced references, that conventional metrics do not capture.To this end, we introduce RWGBench, a benchmark that evaluates RWG from the perspective of citation decision-making rather than text similarity. RWGBench is constructed from a large-scale collection of 40,108 computer science papers and a retrieval corpus of 1.09 million documents, with a carefully curated test set comprising 100 papers and their corresponding published related work sections.We propose a multi-dimensional evaluation framework that assesses citation selection, contextual appropriateness, organization, and discourse structure.Experiments reveal systematic limitations in current systems that are obscured by standard evaluations, while Oracle studies further disentangle retrieval-level and generation-level bottlenecks. Human evaluation further shows that our citation-centric metrics align substantially better with expert judgment than surface-level text metrics. RWGBench offers a citation-centric testbed for developing and evaluating related work generation systems that are better aligned with scholarly writing practices.

07.
PLOS Computational Biology 2026-06-01

BeetleAtlas 2: An enhanced <i>Tribolium castaneum</i> web resource for tissue and developmental transcriptomics allowing refinement of gene predictions

by David P. Leader, Muhammad T. Naseem, Janina L. Rinke, Kenneth Veland Halberg BeetleAtlas is an online resource for tissue- and stage-specific transcriptomics in the red flour beetle, Tribolium castaneum. On updating from the original Tcas5.2 genome assembly to the more recent improved icTriCast1.1 genome assembly it became evident that there were major discrepancies between the gene models of the two genome annotations in use: the OGS3 and the NCBI gene sets. As neither was clearly superior we implemented a new design in BeetleAtlas 2 (beetleatlas.org) comprising two parallel ‘modes’ — one incorporating results using the NCBI gene models and a second incorporating those using the OGS3 gene models. This allows direct comparison where equivalent gene models exist: 50–57% of cases. To aid resolution of discrepancies between the two gene model sets and verification of results, gene models are linked to a custom visualization of RNA-seq read coverage of the genome in the UCSC Genome Browser. This displays reads from 22 tissues and life stages superimposed on the icTriCast1.1 genome assembly. Reference tracks show the NCBI gene models, the OGS3 gene models after translation of their coordinates from the Tcas5.2 assembly, and 1050 discontinued NCBI gene models from the previous assembly after a similar transfer of coordinates. We document various situations in which distinct patterns of expression of the tissues can be used to confirm and extend correlations between the two gene sets, resolve discrepancies between them, make corrections and identify putative genes or exons absent from the current gene sets. BeetleAtlas 2 allows those involved in Tribolium research to avoid the pitfalls inherent in incorrect gene models when planning experiments on specific genes and interpreting the results. It also demonstrates how BeetleAtlas 2 might play an important role in establishing a revised gene set for Tribolium castaneum in the future.

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

Automating SKILL.md Generation for Computer-Using Agents via Interaction Trajectory Mining

arXiv:2606.20363v1 Announce Type: new Abstract: Explicit skill libraries make computer-using agents easier to inspect, but it remains unclear whether such libraries can be mined from interaction data in a way that improves downstream policies. We study this question through a three-stage pipeline that segments GUI trajectories, clusters segments into candidate skills, and trains a skill-aware policy from the resulting annotations. The mined clusters are readable on the source benchmark: five of eight clusters have at least 0.95 purity against InteraSkill Workflows labels. However, readability does not imply transfer. GRPO improves IW skill-step accuracy only from 18.5\% to 20.5\%, leaves BrowseComp+ essentially unchanged, and underperforms trivial frequency priors on key source-domain metrics. We therefore present the method as a diagnostic study: trajectory mining can expose inspectable skill structure, but the current boundary detector, orderless segment representation, and offline reward model are insufficient for reliable cross-domain policy improvement.

09.
arXiv (CS.AI) 2026-06-25

Agentic System as Compressor: Quantifying System Intelligence in Bits

arXiv:2606.25960v1 Announce Type: new Abstract: Large language models are turning from isolated predictors into agentic systems: they call tools, retrieve evidence, obey environment constraints, use verifiers, and complete tasks through search and multi-turn interaction. We adopts an analytical viewpoint based on "compression is intelligence": under a fixed task distribution, interface, and compute budget, a stronger agentic system lets a target object be reconstructed with fewer bits. We operationalize the measure with arithmetic coding, seed coding, and a fallback, and evaluate it in five settings: reversed text, chess moves, protein sequences, retrieval-augmented question answering, and semantic story compression; in all of them agentic components reduce codelength. These small, controlled experiments cover component types typical of real agentic systems, show that codelength can analyze how components, observers, and budgets change residual uncertainty, and offer guidance for evaluating real agent systems.

10.
arXiv (quant-ph) 2026-06-15

Quantum Simulation of Spin-Dependent Electron Transfer in a Synthetic Chiral Lattice with a Trapped Ion

arXiv:2606.13930v1 Announce Type: new Abstract: Electron transfer through chiral structures can exhibit spin asymmetry, known as the chiral-induced spin selectivity effect, whose microscopic origin remains an open question. While path-interference within the chiral moiety has been proposed as a key mechanism, its experimental validation requires precise and versatile tunability of system parameters. Here we implement a programmable quantum simulation of spin-dependent electron transfer in a donor–chiral-bridge–acceptor model using a trapped ion. The bridge is encoded in internal states of the ion with tunable nearest- and next-nearest-neighbor couplings, while donor and acceptor states are coupled via a spectator bosonic motional mode. We observe spin-dependent interference within the bridge, and further reveal spin-dependence in donor-to-acceptor transfer dynamics, controlled by amplitude and phase of the coupling parameter. Our results identify interference among spin-dependent pathways as a microscopic origin of spin-dependent transfer, and open a route toward quantum simulations of complex chiral lattices with multi-level and bosonic degrees of freedom.

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

MVTrack4Gen: Multi-View Point Tracking as Geometric Supervision for 4D Video Generation

Synthesizing a novel-view video from a monocular reference video along a target camera trajectory requires both geometric consistency and motion fidelity with respect to the reference video. Existing methods based on explicit 3D representations are limited by the accuracy of off-the-shelf reconstruction modules, which often produce inaccurate geometry for dynamic objects in monocular videos. In contrast, camera-conditioning-only methods can achieve high visual quality but often struggle to preserve geometric and motion consistency. In this work, we introduce MVTrack4Gen (Multi-View point Tracking for Novel-View Generation), a motion-aware training framework that leverages multi-view point tracking as an additional geometric and motion supervision signal for camera-conditioning-only novel-view video diffusion models. Our key finding is that specific attention layers encode strong correspondence cues, where query features attend to key features at geometrically corresponding locations across views and over time, and the misalignment of these correspondences causes motion inconsistency. Based on this observation, we route these features into an auxiliary multi-view tracking head and jointly train the diffusion model with a point-tracking objective. By explicitly strengthening these motion-aware correspondences, MVTrack4Gen improves existing models to better follow the motion in the reference view and maintain cross-view geometric consistency. Across diverse benchmarks, our method achieves state-of-the-art geometric consistency and competitive camera accuracy.

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

Physics-Driven Zero-Shot MRI Reconstruction with Non-local Image Priors

Zero-Shot Self-Supervised Learning (ZS-SSL) has emerged as a promising paradigm for accelerated Magnetic Resonance Imaging (MRI) reconstruction, eliminating the reliance on fully-sampled external datasets. However, learning solely from a single under-sampled scan suffers from supervision scarcity and optimization instability, often leading to overfitting or artifacts. To address these challenges, we propose a robust physics-driven ZS-SSL framework that synergizes physical consistency with image-domain non-local priors. Our method introduces three core innovations: (1) a Coil Sensitivity Map (CSM)-Guided Dynamic Repository, which stabilizes the training trajectory by filtering physically inconsistent artifacts based on coil sensitivity constraints; (2) a SPIRiT-based regularization, which enforces k-space self-consistency via a learned correlation kernel and stochastic masking; (3) a Non-Local Self-Similarity (NSS) Pixel Bank, which leverages the high-fidelity reference established by the former modules to explicitly mine non-local anatomical similarities, thereby augmenting supervision in the image domain. Extensive experiments on the FastMRI dataset demonstrate that our approach achieves state-of-the-art performance, particularly under high acceleration factors, effectively bridging the gap between zero-shot learning and supervised methods. The code is available at https://github.com/Zolento/NS-SSL.

13.
arXiv (CS.AI) 2026-06-16

Agent Economics: An Entropy-Controlled Pluralistic Alignment Framework for Preventing Artificial Hivemind in Autonomous Agents

Authors:

arXiv:2606.09039v2 Announce Type: replace Abstract: This study proposes the Behavioral Protocol Framework (BPF), an entropy-controlled pluralistic alignment framework designed to address two critical challenges in autonomous agent economies: the hivemind effect arising from excessive strategic convergence among agents and the lack of transparency in autonomous decision-making processes. The proposed BPF consists of three core modules: Mentalizing-based Social Intelligence (MbSI) grounded in Theory of Mind (ToM), Pluralistic Alignment (PA), and a Verifiable Execution Kernel (VEK). These modules are organically integrated within a closed-loop architecture that governs the entire lifecycle of agent behavior, from decision-making and execution to verification and feedback. To evaluate the proposed framework, a simulation environment implemented in Python and a Streamlit-based user interface will be developed. Through empirical experimentation, the study aims to examine whether the entropy-control mechanism of the PA module can effectively preserve strategic diversity among agents and mitigate collective convergence, while the VEK module provides a comprehensive and transparent audit trail of the decision-making process. The anticipated results are expected to demonstrate that the proposed framework can simultaneously enhance the stability, efficiency, and trustworthiness of autonomous agent economies. Consequently, this research offers a practical approach for developing robust, transparent, and accountable agent-native economic systems.

14.
arXiv (math.PR) 2026-06-25

Exponential Rank Bounds for Random Matrices

arXiv:2606.25204v1 Announce Type: new Abstract: Fix $b\in(0,1)$, let $1\leq k\leq n$, and let $A=(A_{ij})$ be an $n\times n$ random matrix with independent real entries satisfying $$ \sup_{x\in\mathbb{R}}\mathbb{P}\{A_{ij}=x\}\leq b0$ such that $$ \mathbb{P}\{\operatorname{rank} A\leq n-k\}\leq \exp(-cnk), \qquad 1\leq k\leq n. $$

15.
Science (Express) 2026-06-18

Indium-free perovskite/silicon tandem solar cells with tin oxide recombination layer and electrodes | Science

Authors: Unknown Author

Indium-based transparent conductive oxides are widely used as electrodes and recombination layers in perovskite/silicon tandem solar cells, yet their scalability is constrained by indium scarcity and sputtering-induced damage. Here we report high efficiency and stable indium-free perovskite/silicon tandem solar cells enabled by reactive plasma deposited tin oxide (RPD-SnO x ). For RPD-SnO x as the recombination layer, a certified efficiency of 33.6% is achieved. Fully indium-free tandems that used RPD-SnO x as both recombination layer and electrodes delivering a champion PCE of 33.2% (1 cm 2 ) and a mini-module with a certified efficiency of 31.0% (207.9 cm 2 ). Dense and uniform self-assembled monolayer anchoring enabled by RPD-SnO x suppressed non-radiative recombination and reduced halide migration. Indium-free mini-modules exhibited high thermal, damp-heat, and outdoor operational stability and retained 65% of their maximum initial efficiency after 105 days of outdoor operation.

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

Simulation-Based Multi-Fillet Evaluation of Woody Breast Poultry Fillets

Woody breast (WB) is a myopathy in modern broiler chickens that causes the breast muscle to become unusually stiff and fibrous, leading to decreased meat quality and significant economic losses. State-of-the-art automated WB detection relies on a side-view imaging system to analyze the bending behavior of a single fillet as it falls off a conveyor belt. While highly accurate, this approach is constrained by its single-fillet field of view, creating throughput bottlenecks on commercial processing lines. In this paper, we address this limitation via a novel multi-fillet detection architecture utilizing a top-down camera configuration. To validate our approach, we first develop a high-fidelity digital twin of an industrial conveyor system. Next, we synthesize a diverse dataset of 3D fillet meshes and model their viscoelastic bending dynamics using a physics-based simulation engine. Lastly, a continuous 2D shape deformation score is extracted from the top-down perspective as the simulated fillets traverse the roller precipice. Experimental results demonstrate that the top-down shape score effectively captures the contour changes of the fillets as it bends, providing a robust and scalable alternative to a side-view imaging system for simultaneous multi-fillet WB evaluation.

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

Reinforcement Learning for Neural Model Editing

Authors:

Editing pretrained neural networks requires specialized algorithms tailored to specific objectives. Designing such algorithms is often time-consuming and demands significant effort. We present an exploratory framework that formulates neural model editing as a reinforcement learning problem, where agents modify models using reward feedback. We introduce two environments: MaskWorld, where agents scale weights multiplicatively, and ShiftWorld, where agents apply additive weight updates. The reward function combines a utility-preservation objective with a task-specific editing objective, enabling agents to learn targeted modifications while maintaining overall model performance. We evaluate the framework on bias mitigation in text classification and machine unlearning in image classification, both of which traditionally rely on specialized algorithms. Our results show that the learned policies reduce forget set accuracy to nearly 0% while preserving over 90% retain set accuracy on the unlearning task. In the bias mitigation setting, the learned policies improve bias-related performance by more than 5% while maintaining general classification utility. Our findings show that neural model editing can be cast as a reinforcement learning problem, allowing editing policies to be learned from reward feedback rather than manually engineered for each task.

18.
arXiv (CS.CV) 2026-06-16

iTRIALSPACE: Programmable Virtual Lesion Trials for Controlled Evaluation of Lung CT Models

We introduce iTRIALSPACE, a programmable evaluation framework for controlled assessment of lung CT models. Standard benchmarks are static retrospective collections that entangle lesion size, lobe prevalence, anatomy, and acquisition context, making it difficult to determine what structurally drives model accuracy. iTRIALSPACE addresses this limitation by composing real clinical CTs and lesion profiles into controlled virtual lesion trials through a four-stage pipeline: multidataset nodule profiling, explicit trial specification, anatomy-aware mask insertion, and ControlNet-conditioned CT synthesis. The framework is built on a unified 54-attribute nodule-profile dataset spanning 13,140 annotated nodules from seven public CT sources and instantiated as 13 trial modes. We evaluate iTRIALSPACE in a 55,469-sample Virtual Lesion Study spanning three medical VLMs, four spatialguidance conditions, and three clinical tasks. Across all 13 modes, the synthetic substrate remains within the real-to-real FID baseline, and synthetic performance rankings transfer strongly to real clinical data ($\rho$ = 0.93, p < 10$^{-15}$). Controlled trial modes expose findings unavailable to fixed-distribution benchmarks, including shortcut-driven size prediction collapse under lobe-equalized sampling and hostto-donor variance ratios of 8.9x and 3.3x in twin-cross analysis. These results position iTRIALSPACE as an auditable evaluation infrastructure for controlled, falsifiable testing beyond static retrospective benchmarks.

19.
arXiv (math.PR) 2026-06-25

Haagerup property and group-invariant percolation

arXiv:2303.17429v3 Announce Type: replace-cross Abstract: Let $\mathcal G$ be the Cayley graph of a finitely generated, infinite group $\Gamma$. We show that $\Gamma$ has the Haagerup property if and only if for every $\alpha\alpha\mathrm{deg}_{\mathcal G}(g)$ for every vertex $g$ and with the two-point function $\tau(g,h)=\mathbb P\big[g\leftrightarrow h\big]$ vanishing as $d(g,h)\to\infty$. On the other hand, we show that $\Gamma$ has Kazhdan's property (T) if and only if there exists a threshold $\alpha^*\alpha^*\mathrm{deg}(o)$ implies that the two-point function is uniformly bounded away from zero. These results in particular answer questions raised by Lyons (J. Math. Phys. 41. 1099-1126 (2000)) about characterizations of properties of groups beyond amenability through group-invariant percolations. The method of proof is new and is based on a construction of percolations with suitable dependence structures built from invariant point processes on spaces with measured walls. This construction furthermore leads to quantitative bounds on the two-point functions, exhibiting in particular exponential decay of the two-point function in several prominent examples of Haagerup groups, including co-compact Fuchsian groups, co-compact discrete subgroups of $\mathrm{Isom}(\mathbb H^n)$ and lamplighters over free groups. This method also allows us to extend the aforementioned characterization of property (T) to the setting of relative property (T) and provide an application to Bernoulli percolation at the uniqueness threshold.

20.
PLOS Computational Biology 2026-05-29

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

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

21.
arXiv (CS.LG) 2026-06-17

Sign-Rank, Index, and List Replicability: Connections and Separations

arXiv:2606.18236v1 Announce Type: new Abstract: In learning theory, the sign rank of a binary concept class captures the smallest dimension in which it can be represented by points and halfspaces. Despite tremendous interest, lower bounds on sign rank are notoriously difficult to come by. Two recent approaches to the problem establish lower bounds on sign rank by measures that are easier to analyze: the $\mathbb{Z}_2$-index and the list replicability number. We order these measures, showing that the $\mathbb{Z}_2$-index is upper-bounded by a linear function of the list replicability number. As a main consequence, we obtain a strong separation between sign rank and $\mathbb{Z}_2$-index, thereby resolving a question of Frick, Hosseini, and Vasileuski. This motivates a thorough study of list replicability, the stronger of the two lower-bounding measures. We establish upper bounds on the list replicability number by two combinatorial measures: height and minimum star number. We also prove a fundamental composition result, showing that the product of two concept classes has list replicability number bounded by the sum of the list replicability numbers of the two classes.

22.
arXiv (CS.AI) 2026-06-15

Universal Manipulation Exoskeleton: Learning Compliant Whole-body Policies with Real-time Torque Feedback

arXiv:2606.14218v1 Announce Type: cross Abstract: For robots to work safely in household environments, they need to be compliant and react to torque and force feedback during contact. However, the majority of existing data collection pipelines still lack the ability to capture force and torque data for learning active compliant policies. In this paper, we present Universal Manipulation Exoskeleton (UME), an upper-limb exoskeleton that provides real-time haptic torque feedback while recording whole-arm configurations and joint torque signals for teleoperation. With transparent torque feedback, human operators can even unsheathe kinematically constrained objects while blindfolded. UME is low-cost, lightweight, and portable. Equipped with an embedded IMU, it enables teleoperation for mobile manipulation. With our proposed universal retargeting algorithm, UME can teleoperate a range of robots, including the 7DoF OpenArm, 7DoF Franka, and 6DoF X-ARM. We demonstrate that this combination of capabilities enables learning bimanual, whole-body, and active compliant policies that operate effectively in highly constrained spaces. The learned robust autonomous policies achieve high success rates across a variety of tasks, including long-horizon mobile manipulation, force-mediated box flipping, visually occluded box pushing, and space-constrained tabletop manipulation. Videos, code, and additional information can be found at https://ume-exo.github.io.

23.
medRxiv (Medicine) 2026-06-11

Conversational Speech for Respiratory Triage in Primary Care: A Pilot Study

Authors:

Background. Respiratory complaints account for a substantial share of adult ambulatory care visits, and triaging them accurately has direct consequences for antibiotic stewardship and pathogen-specific therapy. Prior work has investigated voice as a triage signal, but that literature is dominated by single-condition detection from scripted speech in crowdsourced or controlled clinical settings and has not been evaluated at primary care scale on conversational ambient audio. Methods. A dataset of 514,377 ambient-recorded primary care visits from 379,225 adult patients at a US clinic network was used, with per-visit clinically assigned ICD-10 diagnosis codes and de-identified demographic and geographic metadata. Patient audio was extracted from each doctor-patient conversation, and spectral, voice quality, and prosodic features were computed. Eleven binary classification tasks were defined, aligned with a respiratory triage cascade (e.g., acute respiratory versus acute non-respiratory illness, and lower versus upper respiratory tract infection). An acoustic model (feed-forward network) was trained independently for each task using patient-stratified five-fold cross-validation and evaluated on a held-out test set. Each task's model was also compared against six non-acoustic baselines using a single demographic, geographic, or temporal variable. The 11 trained classifiers were composed into a hierarchical cascade and illustrated as case studies on selected patients. Results. Test-set AUC across the 11 tasks ranged from 0.602 (95% CI: 0.588-0.614) to 0.745 (95% CI: 0.742-0.748), with a mean expected calibration error of 0.018. Six of eleven binaries outperformed all confounder baselines. Four binaries showed median within-stratum AUC of 0.62-0.70 when the confounder was held fixed, indicating acoustic discrimination beyond what the confounder alone explains. The exception was the pneumonia versus non-pneumonia lower respiratory tract infection binary, which failed against the patient-city confounder baseline, plausibly reflecting a clinic-level difference in ICD-10 coding. Conclusion. Conversational primary care audio carries acoustic signal that discriminates clinically meaningful respiratory contrasts. Absolute performance is moderate, but the conditions are stricter than prior work: conversational speech and differential-diagnosis contrasts among sick patients. This pilot study is a baseline for voice-based clinical AI moving beyond sick-versus-healthy detection toward differential-diagnosis panels and a proof-of-concept for hierarchical reasoning.

24.
arXiv (CS.CL) 2026-06-17

Do Large Language Models Always Tell The Same Stories?

Recent advances in large language models (LLMs) have enabled the generation of high-quality prose, yet the question of whether these models are capable of generating diverse outputs remains contested. In this work, we investigate the diversity of LLM-generated stories through the framework of narrative similarity. Using a contrastive framework and a dataset of human-written stories and prompts from r/WritingPrompts, we collect narrative similarity judgments across 10 representative LLMs, utilizing both human evaluations and three different automatic annotation methods. Our findings reveal a consistent trend: LLM-generated narratives are consistently more similar to each other than human-written stories are. We demonstrate that frontier models in particular converge on a ``mean'' generic narrative that approximates individual human stories but lacks the collective diversity of human authors. Finally, we show that common mitigation strategies, including negative prompting and temperature scaling, fail to meaningfully address this homogeneity.

25.
bioRxiv (Bioinfo) 2026-06-22

Multivariate Random Forests for Cross-Modal Multi-Omics Integration

Multi-omics studies are widely used across many areas of biomedical research. In many diseases, some signals are shared across data types, while others are strongest in a single omics layer. Current multi-omics clustering methods often either merge all data types into a single representation, which can blur biology that is strong in one layer, or rely on linear structure that may miss more complex relationships across data types. We introduce multiRF, a random-forest-based method that handles complex data types and separates shared and modality-specific structure for multi-omics data. multiRF learns sample similarities across omics layers from multivariate random forests, combines them across data types, and uses the resulting weights to estimate the part of each omics layer that is predictable from the others. The remaining residual is treated as modality-specific signal, allowing shared and modality-specific similarities to be clustered separately. In simulations, multiRF recovered shared clusters as well as or better than established integrative methods while more reliably separating modality-specific signal under nonlinear data structures. In TCGA head and neck squamous cell carcinoma, the shared component aligned with the main subtype structure across established reference classifications, while gene- and miRNA-specific components revealed additional immune and developmental biology. In the ADNI cohort with matched blood DNA methylation and structural MRI, the shared cross-modal aging signal was associated with future conversion to mild cognitive impairment or Alzheimer's disease, and a DNAm-specific residual signal showed exploratory additional information. These results show that multiRF can recover a common disease axis while retaining biologically meaningful signals specific to one data type. multiRF is available as an open-source R package at https://github.com/novawz/multiRF.