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01.
PLOS Computational Biology 2026-06-24

Variable selection-combined causal mediation analysis for continuous treatments with application to large-dimensional biomedical data

Authors:
Yajing Zhou↗

by Yajing Zhou, Kecheng Wei, Yahang Liu, Zhaoyang Li, Chen Huang, Guoyou Qin, Yongfu Yu Substantial progress has been made in the area of causal inference utilizing large-scale data, among which the estimation of causal mediation effects has attracted a lot of attention. However, existing large-dimensional causal inference primarily focuses on total effects or typical causal mediation effects under binary variable settings, placing less emphasis on large-scale covariate selection with continuous treatment and mediator. To address this, we propose a weighted semiparametric estimation framework that integrates the generalized outcome-adaptive LASSO method into generalized propensity score modeling to achieve estimation of causal mediation effects under continuous variable settings. Simulation results show that our proposed method outperforms other regularization-based methods in selection accuracy and estimation efficiency, which is achieved by incorporating outcome-related key variables and excluding noise covariates. From the perspective of achieving a stable balance between efficiency and bias, as well as high-dimensional information filtering, our method may serve as a compelling alternative that balances estimation efficiency with model interpretability and inferential robustness. We further conduct a real-world application based on the UK Biobank database, quantifying the causal mediation effects of apolipoprotein B levels within the association between potential diabetes risk and cancer incidence using large-scale healthcare and medical data.

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02.
medRxiv (Medicine) 2026-06-22

Clinical-grade Cuffless Blood Pressure Monitoring via Deep-tissue Diffuse Speckle Pulsatile Flowmetry

Authors:
Choo↗T. W. J↗Yap↗A. A. M↗Kawaja↗Chao↗V. T. T↗Ng↗C. J↗Olivo↗Bi↗

Blood pressure (BP) is a vital sign which is measured to diagnose and manage hypertension. However, current methods to measure BP use inflatable cuffs which cause discomfort and limit the frequency at which measurements can be made, or intra-arterial catheters which are invasive and pose infection risks. Here, we propose and evaluate the use of Diffuse Speckle Pulsatile Flowmetry (DSPF) as a cuffless BP measurement method to address these limitations. DSPF is a laser speckle-based technique which simultaneously records blood flow rate and blood volume (i.e. photoplethysmography or PPG) signals from relatively deep vascular tissue. Using information from these signals, we studied DSPFs effectiveness in measuring systolic BP (SBP) and diastolic BP (DBP) through an outpatient study in which 133 patients were recruited, and in measuring beat-to-beat BP waveforms through an inpatient study in which two patients were recruited. In the outpatient study, the DSPF method was able to achieve mean absolute errors (MAEs) of 4.17 mmHg and 2.42 mmHg for SBP and DBP respectively compared to conventional cuff-based methods. It was also able to fulfil the requirements of the AAMI/ESH/ISO 81060-2:2018 standard for BP measurement devices and attain an "A" grade according to the British Hypertension Society grading scheme. For the inpatient study, it produced BP waveforms which had MAEs of 2.35 mmHg and 3.06 mmHg compared to arterial-line measurements for the two patients, respectively. Compared to PPG which has been studied more extensively as a cuffless BP measurement method, we found through ablation studies that DSPF was able to reach significantly lower MAEs and hence better accuracies. DSPF augments the performance of PPG-only methods by leveraging additional information from the blood flow rate signal, and we therefore find it to be a superior cuffless BP measurement method which can potentially be used in outpatient, inpatient, and remote settings.

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03.
arXiv (CS.AI) 2026-06-25

Fuzzy Quantification over OWL Ontologies and Knowledge Graphs

Authors:
Enrique Palac\'in↗Fernando Bobillo↗Ignacio Huitzil↗Francesca A. Lisi↗Umberto Straccia↗

arXiv:2606.25778v1 Announce Type: new Abstract: This paper presents a versatile framework for evaluating fuzzy quantification queries over both standard and fuzzy ontologies as well as knowledge graphs. The primary objective is the retrieval of individuals that satisfy queries articulated via Type I or Type II fuzzy quantified expressions. A key advantage of the proposed approach is its inherent adaptability: it remains entirely agnostic to the quantifier type, the underlying evaluation method, and the specific data source of the ontology (i.e., OWL ontologies or RDFS knowledge graphs). Furthermore, we present Q2S2, a publicly accessible implementation of this system developed to support future research.

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04.
arXiv (quant-ph) 2026-06-16

Decoherence-free algebras in quantum dynamics

Authors:
Daniele Amato↗Paolo Facchi↗Arturo Konderak↗

arXiv:2403.12926v2 Announce Type: replace Abstract: In this Article we analyze the algebraic properties of the asymptotic dynamics of finite-dimensional open quantum systems in the Heisenberg picture. In particular, a natural product (Choi-Effros product) can be defined in the asymptotic regime. Motivated by this structure, we introduce a new space called the Choi-Effros decoherence-free algebra. Interestingly, this space is both a C*-algebra with respect to the composition product, and a B*-algebra with respect to the Choi-Effros product. Moreover, such space admits a direct-sum decomposition revealing a clear relationship with the attractor subspace of the dynamics. In particular, the equality between the attractor subspace and the Choi-Effros decoherence-free algebra is a necessary and sufficient condition for a faithful dynamics. Finally, we show how all the findings do not rely on complete positivity but on the much weaker Schwarz property.

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05.
arXiv (quant-ph) 2026-06-24

Unitary Designs from Doped Matchgate Circuits

Authors:
Fabian Ballar Trigueros↗Zheng-Hang Sun↗Xhek Turkeshi↗Piotr Sierant↗Poetri Sonya Tarabunga↗

arXiv:2606.23800v1 Announce Type: new Abstract: Matchgate circuits realize free-fermion dynamics: they are efficiently classically simulable, yet cannot on their own generate the generic randomness required for universal computation or unitary design formation. We study a controlled route beyond this integrable limit by doping matchgate circuits with non-Gaussian gates-physically, the injection of fermionic interactions into an otherwise free system. Using the matchgate commutant framework, we obtain analytic control over unitary $2$-design formation. For globally scrambled dynamics, the design problem maps exactly onto a classical birth-death Markov chain with an Ornstein-Uhlenbeck continuum limit, recasting the emergence of quantum randomness in terms of spectral gaps and mixing times and yielding rigorous bounds on the number of non-Gaussian gates needed for approximate $2$-designs. These bounds hold for a broad class of parity-preserving non-Gaussian gates, independently of microscopic details, with numerics indicating that the same mechanism governs higher-order designs. Used as local building blocks in a glued-circuit architecture, they yield approximate parity-preserving $2$-designs in polylogarithmic depth with a sparse non-Gaussian gate count, with implications for Page-like entanglement growth and fermionic classical-shadow protocols. Finally, locality reshapes this picture: in local brickwork dynamics, design formation is diffusion-limited and far slower. Our results establish doped matchgate circuits as a controlled, analytically tractable route from free fermions to interaction-generated quantum designs.

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

Complete Relational Description of Spin in a Quantum Background

Authors:
Hannah Troger↗Ofek Bengyat↗Thomas D. Galley↗Marios Christodoulou↗

arXiv:2606.15873v1 Announce Type: new Abstract: The standard description of the state of a spin in quantum mechanics presupposes externally fixed directions – a classical background. Can a spin be fully described instead in relation to other quantum mechanical systems? Poulin suggested twenty years ago group averaging over rotations the joint state of a fundamental spin and a reference spin with large angular momentum which, however, yields a classical bit in a probabilistic mixture. We revisit this idea and show that when the quantum reference system is augmented to two large spins, the standard quantum mechanical description of a spin is recovered in the limit of large quantum numbers for the reference system.

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07.
arXiv (CS.CL) 2026-06-19

DeFrame: Debiasing Large Language Models Against Framing Effects

Authors:
Kahee Lim↗Soyeon Kim↗Steven Euijong Whang↗

As large language models (LLMs) are increasingly deployed in real-world applications, ensuring their fair responses across demographics has become crucial. Despite many efforts, an ongoing challenge is hidden bias: LLMs appear fair under standard evaluations, but can produce biased responses outside those evaluation settings. In this paper, we identify framing – differences in how semantically equivalent prompts are expressed (e.g., "A is better than B" vs. "B is worse than A") – as an underexplored contributor to this gap. We first introduce the concept of "framing disparity" to quantify the impact of framing on fairness evaluation. By augmenting fairness evaluation benchmarks with alternative framings, we find that (1) fairness scores vary significantly with framing and (2) existing debiasing methods improve overall (i.e., frame-averaged) fairness, but often fail to reduce framing-induced disparities. To address this, we propose a framing-aware debiasing method that encourages LLMs to be more consistent across framings. Experiments demonstrate that our approach reduces overall bias and improves robustness against framing disparities, enabling LLMs to produce fairer and more consistent responses.

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08.
PLOS Medicine 2026-05-13

Contribution of nosocomial transmission to <i>Klebsiella pneumoniae</i> neonatal sepsis in Africa and South Asia: An observational study of infection clusters inferred from pathogen genomics and temporal data

Authors:
Erkison Ewomazino Odih↗

by Erkison Ewomazino Odih, Jabir A. Abdulahi, Anne V. Amulele, Matthew Bates, Eva Heinz, Weiming Hu, Kajal Jain, Rindidzani Magobo, Courtney P. Olwagen, John M. Tembo, Tolbert Sonda, Jonathan Strysko, Caroline C. Tigoi, Kyle Bittinger, Jennifer Cornick, Ebenezer Foster-Nyarko, Wilson Gumbi, Steven M. Jones, Chileshe L. Musyani, Carolyn M. McGann, Ahmed M. Moustafa, Patrick Musicha, James C. L. Mwansa, Moreka L. Ndumba, Thomas D. Stanton, Donwilliams O. Omuoyo, Oliver Pearse, Laura T. Phillips, Paul J. Planet, Charlene M. C. Rodrigues, Fatou Secka, Kirsty Sands, Erin Theiller, Allan M. Zuza, Sulagna Basu, Grace J. Chan, Kenneth C. Iregbu, Jean-Baptiste Mazarati, Semaria Solomon Alemayehu, Timothy R. Walsh, Rabaab Zahra, Angela Dramowski, Sombo Fwoloshi, Appiah-Korang Labi, Lola Madrid, Noah Obeng-Nkrumah, David Ojok, Boaz D. Wadugu, Andrew C. Whitelaw, Anudita Bhargava, Atul Jindal, Ramesh K. Agarwal, Alexander M. Aiken, James A. Berkley, Susan E. Coffin, Nicholas A. Feasey, Nelesh P. Govender, Davidson H. Hamer, Shabir A. Madhi, Mari Jeeva Sankar, Kelly L. Wyres, Kathryn E. Holt Background Klebsiella pneumoniae is the leading cause of sepsis among neonates in low- and middle-income countries (LMICs) in Africa and Asia, contributing substantially to the overall burden of antimicrobial-resistant infections and mortality among neonates globally. Pathogen sequencing has been used to investigate case clusters and confirm nosocomial transmission in a small number of neonatal units. Here we utilise pathogen sequence data to estimate the fraction of K. pneumoniae neonatal sepsis attributable to nosocomial transmission in African and South Asian countries. Methods and findings We estimated the proportion of invasive K. pneumoniae disease involved in nosocomial transmission clusters in a given neonatal unit, using single-linkage clustering based on pairwise temporal and genetic distances estimated from bacterial whole-genome sequences aggregated from 10 contributing studies. Analysing 1,523 K. pneumoniae isolates from 27 units in 13 countries in Africa and South Asia between 2013 and 2023, we inferred 156 nosocomial transmission clusters, ranging from 2 to 188 neonates each (83 of the clusters comprised ≥3 cases). Overall, we estimated that 1,035 neonatal infections (68.0%) were part of nosocomial transmission clusters. Excluding the first infection in each cluster as a potential index case, we estimate at least 879 (57.7%) infections were acquired via nosocomial transmission. Sensitivity analyses showed that results were robust to the choice of genetic distance estimation methods and thresholds used to define clusters, and cluster estimates were stable over temporal distance thresholds ranging from 2 to 8 weeks. Isolates were mostly extended-spectrum beta-lactamase (ESBL) producers (90.9%) and included 172 multi-locus sequence types (STs). Fourteen STs, including several globally recognised multidrug-resistant lineages, were associated with transmission clusters at multiple units, and these were collectively responsible for two-thirds of all infections. Carriage of carbapenemase genes (adjusted odds ratio, aOR = 2.08 [95% confidence interval, CI: 1.04, 4.14]; p = 0.04) and ESBL genes (aOR = 2.48 [95% CI: 1.26, 4.90]; p = 0.006) were significantly positively associated with transmission in a logistic regression model with site as a covariate. Limitations of this study include the lack of sufficient clinical data to allow high-resolution investigation of transmission dynamics and lack of facility-level data to investigate contributors to the observed differences in transmission burden across sites. Conclusions Nosocomial transmission contributes to a substantial proportion of K. pneumoniae sepsis in neonatal care units in Africa and South Asia. Reducing transmission within these settings through improved infection prevention and control and other measures could substantially reduce the neonatal sepsis burden. A high burden of transmission clusters is associated with the same drug-resistant lineages that are recognised as high-risk clones associated with hospital outbreaks in high-income countries, indicating global connectivity of the antimicrobial-resistant pathogen population.

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09.
arXiv (quant-ph) 2026-06-24

Multipartite synchronization residuals in driven-dissipative spin networks

Authors:
Jatin Ghildiyal↗Shubhrangshu Dasgupta↗Asoka Biswas↗

arXiv:2606.24360v1 Announce Type: new Abstract: We introduce a phase-space measure of quantum synchronization that quantifies relative phase localization for two-qubit and three-qubit systems. This measure is built from the first angular moments of phase distributions obtained from Husimi-Q quasiprobability functions. Using this framework, we formulate a new class of synchronization residuals, motivated by subadditivity-type hierarchies of information-theoretic measures. We investigate these residuals in a driven-dissipative quantum Rabi network in the dispersive adiabatic regime. We show that, for two qubits, collective synchronization remains bounded by single-qubit contributions yielding a non-negative bipartite residual. The three-qubit nonequilibrium steady state exhibits a negative tripartite residual, which indicates collective phase synchronization, which cannot be described by pairwise decomposition. The corresponding entropy-based residuals, however, remain non-negative in both cases. Our results therefore, underscore that phase-sensitive synchronization measures and entropic correlation measures probe distinct aspects of open-system dynamics.

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

Not All Retrievals are Useful: Cross-Attention for Input-Aware RAG in Time Series Forecasting

Authors:
Seunghan Lee↗Jaehoon Lee↗Jun Seo↗Sungdong Yoo↗Minjae Kim↗Tae Yoon Lim↗Dongwan Kang↗Hwanil Choi↗SoonYoung Lee↗Wonbin Ahn↗

arXiv:2603.14709v2 Announce Type: replace Abstract: Retrieval-augmented generation (RAG) enhances zero-shot time series (TS) forecasting by leveraging external knowledge bases, yet existing approaches overlook input-level relevance when fusing retrieved samples with the query. We argue that not all retrievals are equally useful, and irrelevant ones can degrade performance. To this end, we propose Cross-RAG, a zero-shot RAG-based forecasting framework that selectively attends to query-relevant retrieved samples via query–retrieval cross-attention. By modeling input-level relevance between the query and retrieved samples, Cross-RAG jointly incorporates three sources of information: 1) the query itself, 2) the retrieved samples, and 3) their relational interactions. In particular, this input-aware design enables Cross-RAG to remain stable as the number of retrieved samples $k$ grows, whereas prior methods without cross-attention require careful $k$ tuning to avoid degradation from irrelevant retrievals. Extensive experiments demonstrate that Cross-RAG consistently improves zero-shot forecasting performance across multiple TSFM backbones and various RAG methods, with additional analyses confirming its effectiveness across various retrieval scenarios. Code is available at https://github.com/seunghan96/cross-rag/.

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11.
bioRxiv (Bioinfo) 2026-06-10

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

Authors:
Petrov↗P. B↗Oshinjo↗Roning↗Izzi↗

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/).

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12.
medRxiv (Medicine) 2026-06-22

Hyperlipidemia Pharmacotherapy in Skilled Nursing Facilities: A Real-World Evidence Study

Authors:
Ashraf↗Mathers↗K. E↗Wagner↗Saumur↗

Objectives: To estimate hyperlipidemia medication order prevalence and associated variables in U.S. skilled nursing facility (SNF) residents. Design: Retrospective, observational study. Setting and Participants: Electronic Health Record data from 447,080 SNF residents with a hyperlipidemia diagnosis identified in PointClickCare's Life Sciences clinical database (January-April 2025) were reviewed. Methods: The presence and absence of medication orders for hyperlipidemia treatments recommended by the American Heart Association were assessed. Descriptive analyses summarized demographic and clinical characteristics, and a modified Poisson regression model was used to estimate risk ratios for having a medication order, adjusting for demographic, clinical, and facility characteristics. Results: Overall, 83.3% of residents diagnosed with hyperlipidemia had at least one hyperlipidemia medication order. Statins were ordered by 96.2% of active order residents, while other medication classes i.e., omega-3 fatty acids, cholesterol absorption inhibitors, fibrates were less common (

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13.
arXiv (quant-ph) 2026-06-15

Who can compete with quantum computers? Lecture notes on quantum inspired tensor networks computational techniques

Authors:
Xavier Waintal↗Chen-How Huang↗Christoph W. Groth↗

arXiv:2601.03035v2 Announce Type: replace Abstract: This is a set of lectures on tensor networks with a strong emphasis on the core algorithms involving Matrix Product States (MPS) and Matrix Product Operators (MPO). Compared to other presentations, particular care has been given to disentangle aspects of tensor networks from the quantum many-body problem: MPO/MPS algorithms are presented as a way to deal with linear algebra on extremely (exponentially) large matrices and vectors, regardless of any particular application. The lectures include well-known algorithms to find eigenvectors of MPOs (the celebrated DMRG), solve linear problems, and recent learning algorithms that allow one to map a known function into an MPS (the Tensor Cross Interpolation, or TCI, algorithm). The lectures end with a discussion of how to represent functions and perform calculus with tensor networks using the "quantics" representation. They include the detailed analytical construction of important MPOs such as those for differentiation, indefinite integration, convolution, and the quantum Fourier transform. Three concrete applications are discussed in detail: the simulation of a quantum computer (either exactly or with compression), the simulation of a quantum annealer, and techniques to solve partial differential equations (e.g. Poisson, diffusion, or Gross-Pitaevskii) within the "quantics" representation. The lectures have been designed to be accessible to a first-year PhD student and include detailed proofs of all statements.

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14.
arXiv (CS.AI) 2026-06-17

FinAcumen: Financial Multimodal Reasoning via Self-Evolving Experience Memory Harness

Authors:
Pianran Guo↗Pengcheng Zhou↗Yucheng Jian↗Shuhua Chen↗

arXiv:2606.17642v1 Announce Type: new Abstract: Financial multimodal reasoning requires agents to coordinate numerical computation, retrieval, visual interpretation, and temporal grounding across heterogeneous evidence sources. Existing tool-augmented agents improve execution fidelity, yet remain largely stateless across episodes, repeatedly rediscovering reasoning strategies and failure patterns. In high-stakes financial settings, this leads to unreliable tool routing, noisy retrieval, and hallucination-prone reasoning. We present FinAcumen, a financial reasoning agent framework centered on selective experience memory for tool-augmented multimodal reasoning. FinAcumen accumulates financially grounded reasoning experience from prior trajectories, distilling successful strategies and failure-derived cautionary rules into a persistent memory bank. During inference, retrieved experiences condition reasoning only when semantic relevance exceeds a calibrated threshold, while irrelevant memory is explicitly suppressed through a fallback mechanism. A deterministic financial tool environment further grounds numerical computation, retrieval, visual decoding, and answer verification.Across four financial multimodal reasoning benchmarks, FinAcumen consistently improves a frozen 8B vision-language model over finance-specialized models and approaches leading proprietary general-purpose models. Further analysis shows that selective experience activation improves reasoning reliability under retrieval uncertainty. Our code is anonymously available at https://anonymous.4open.science/r/FinAcumen

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

Beyond Trajectory Imitation: Strategy-Guided Policy Optimization for LLM Reasoning

Authors:
Tianyuan Shi↗Canbin Huang↗Bei Li↗Xin Chen↗Xiaojun Quan↗Jingang Wang↗Qifan Wang↗

arXiv:2606.24064v1 Announce Type: new Abstract: Distilling reasoning capabilities from strong to weak language models typically involves imitating specific solution trajectories, effectively transferring what to answer rather than how to reason. This trajectory-level imitation encourages memorization of instance-specific steps rather than acquisition of transferable problem-solving skills, limiting generalization to novel problems. We propose Strategy-Guided Policy Optimization (SGPO), which replaces instance-level trajectory imitation with reusable strategy distillation. SGPO extracts structured strategy descriptions from strong-model responses and, for each problem, constructs both autonomous and strategy-guided trajectories to enable direct comparison of the model's behavior with and without strategic guidance. The framework then addresses two key questions. For how to distill, a token-level forward-KL objective selectively transfers the distributional shift induced by strategy conditioning into the unguided policy, with proximal constraints ensuring stability. For when to distill, adaptive instance-level weighting strengthens guidance when autonomous exploration falls short and reduces it as the model's own competence grows. Experiments on four mathematical benchmarks across two model families show that SGPO consistently outperforms SFT, on-policy RL, and hybrid-policy baselines, improving the average score by 2.2 points over the strongest baseline on Qwen2.5-7B-Instruct. Analysis reveals that the forward-KL objective provides an inherently selective distillation signal that outperforms direct trajectory imitation, and that strategy distillation exhibits complementary scaling with base model capability.

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

Data-driven Lake Water Quality Forecasting for Time Series with Missing Data using Machine Learning

Authors:
Rishit Chatterjee↗Tahiya Chowdhury↗

arXiv:2601.15503v2 Announce Type: replace Abstract: Volunteer-led lake monitoring yields irregular, seasonal time series with many gaps arising from ice cover, weather-related access constraints, and occasional human errors, complicating forecasting and early warning of harmful algal blooms. We study Secchi Disk Depth (SDD) forecasting on a 30-lake, data-rich subset drawn from three decades of in-situ records collected across Maine lakes. Missingness is handled via Multiple Imputation by Chained Equations (MICE), and we evaluate performance with a normalized Mean Absolute Error (nMAE) metric for cross-lake comparability. Among six candidates, ridge regression provides the best mean test performance. Using ridge regression, we then quantify the minimal sample size, showing that under a backward, recent-history protocol, the model reaches within 5% of full-history accuracy with approximately 176 training samples per lake on average. We also identify a minimal feature set, where a compact four-feature subset matches the thirteen-feature baseline within the same 5% tolerance. Bringing these results together, we introduce a joint feasibility function that identifies the minimal training history and fewest predictors sufficient to achieve the target of staying within 5% of the complete-history, full-feature baseline. In our study, meeting the 5% accuracy target required about 64 recent samples and just one predictor per lake, highlighting the practicality of targeted monitoring. Hence, our joint feasibility strategy unifies recent-history length and feature choice under a fixed accuracy target, yielding a simple, efficient rule for setting sampling effort and measurement priorities for lake researchers.

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

EventRadar: Long-Range Visual UAV Discovery through Spatiotemporal Event Sensing

Authors:
Zhiting Zhou↗Xingchen Liu↗Xinglin Yu↗Jiashen Chen↗Haoyang Wang↗Jingao Xu↗Yunhao Liu↗Xinlei Chen↗

Unauthorized unmanned aerial vehicle (UAV) activity around airports, public venues, and other sensitive sites has made protected-airspace monitoring increasingly important. A practical sensing system must search a wide angular region, find small long-range targets, and return both bearing support and UAV-specific evidence before a restricted perimeter is breached. Existing UAV detection paths often rely on spatially organized evidence, such as body extent, silhouette, or track continuity. At long range, however, these cues become difficult to preserve and verify as the target footprint weakens and its image-plane support shrinks. EventRadar follows a complementary cue: propeller-induced temporal periodicity, which recent event-camera sensing studies have shown can reveal UAV-specific motion after appearance becomes weak. We extend this cue to kilometer-scale active sensing with an event-camera prototype. Scene-Anchored Geometry Evidence (SAGE) fuses scanning events with IMU pose to maintain a bearing-indexed scene memory, separating transient candidate support from persistent background clutter. Comb-guided Harmonic-Group Learned Iterative Shrinkage and Thresholding Algorithm (CHG) then treats each candidate as a weak high-rate timing signal and recovers phase-insensitive harmonic evidence with fixed compute. Compared with related event-camera baselines on 700-1500 m UAV event recordings, EventRadar achieves 0.990 mAP$_{.3}$ and 0.949 F1$_{.3}$, reduces FN$_{.3}$ to 0.009, and shows real-time feasibility in prototype profiling.

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18.
bioRxiv (Bioinfo) 2026-06-17

AMaNITA: an end-to-end workflow for native tRNA nanopore sequencing data analysis

Authors:
Katopodi↗X.-L↗Pryszcz↗L. P↗Llovera↗Ollivier↗Cozzuto↗Ponomarenko↗Novoa↗E. M↗

Transfer RNA (tRNA) molecules serve as essential adapters during protein translation. While direct RNA sequencing (DRS) via Oxford Nanopore Technologies has emerged as a powerful platform for systematic tRNAome profiling, we currently lack a simple and robust statistical framework for nanopore tRNA data analyses. Here, we address this gap by developing AMaNITA (Abundance, Modifications, and Nanopore Intensity Toolbox Application), an end-to-end bioinformatic workflow that enables simplified, robust, and scalable analyses of nanopore native tRNA sequencing datasets. AMaNITA streamlines the entire analytical trajectory: from upstream processing (basecalling, mapping, filtering, batch effect correction) to downstream assessment of differential tRNA abundance and modification stoichiometry. The workflow generates an interactive HTML report for data exploration and analysis, allowing the user to download the source data files and resulting plots. AMaNITA can be executed using Singularity from the command line, without requiring installation of dependencies.

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19.
medRxiv (Medicine) 2026-06-24

Structural variant discovery and diagnostic impact in rare diseases from short-read and long-read sequencing

Authors:
Sanchis-Juan↗Mostovoy↗Stenton↗S. L↗Ganesh↗V. S↗Weisburd↗Yenkin↗Kurtas↗N. E↗Zhao↗Shin↗…

Rare diseases collectively affect 1 in 10 individuals, yet current genetic testing fails to identify a causal variant for most cases. At present, cytogenetic methods and/or sequencing approaches such as exome (ES) or short-read genome sequencing (srGS) represent the state-of-the-art for comprehensive clinical discovery of sequence and structural variants (SVs), including copy number variants, balanced SVs, complex SVs, and tandem repeats (TRs). Recently, long-read genome sequencing (lrGS), coupled with multiomics data, has presented great promise to resolve variation in genomic regions recalcitrant to characterization by srGS such as highly repetitive simple repeat sequences and segmental duplications. However, there are few guidelines to enable clinical interpretation of genetic variation in these highly repetitive genomic regions, and the enthusiasm of the field in adopting lrGS has made it difficult to assess the true added diagnostic yield of this technology due to widely variable and inconsistently applied analytic pipelines and variable degrees of pre-screening by ES or srGS. Here, we investigated the contribution of SVs to rare diseases using srGS as a front-line strategy when paired with highly sensitive SV discovery and evaluate the added diagnostic yield of incorporating lrGS for a subset of cases. Our srGS analysis encompassed 1,462 families (3,450 individuals) recruited through the Broad Institute Center for Mendelian Genetics and the Genomics Research to Elucidate the Genetics of Rare Diseases (GREGoR) programs. Diagnostic SVs were identified in 5.4% of cases (79/1,462), of which 80% were uniquely detectable by srGS compared to standard cytogenetic techniques. For 96 families (including 10 families with a heterozygous variant observed in a known recessive gene of clinical relevance), we performed lrGS with methylation profiling, as well as long-read transcriptomic analyses in a subset of 20 trios. Analyses with lrGS yielded over 25,000 SVs per genome, 63% of which were not captured by srGS, along with an additional ~200 rare SNV/indels per genome not previously captured and 12 differentially methylated regions per genome. Among these, we identified only one diagnostic variant not interpreted by srGS, an apparently mosaic de novo SNV in CASK that was absent in the srGS callset due to allelic imbalance. No new diagnoses were supported by long-read transcriptomics or episignatures. In this well characterized rare disease cohort, the added diagnostic yield was thus 1.04% (1/96 families). Following a systematic literature review of prior lrGS studies, we find that most reported diagnoses were detectable by srGS and that our added diagnostic yield is consistent with those prior studies. These studies emphasize the significant impact of comprehensive SV discovery in rare disease cases and further demonstrate the power for increased discovery of novel genomic variation and episignatures from lrGS. Nonetheless, they also serve to temper expectations of dramatic diagnostic advances in rare disease patients until there is more extensive annotation of the functional and clinical impact of all coding and noncoding variation uniquely accessible to lrGS with extensive reference databases spanning highly repetitive genomic sequencing that could be enabled by this transformative technology.

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20.
arXiv (CS.CL) 2026-06-19

Sign-Language Datasets at Scale: A Comprehensive Survey on Resources, Benchmarks, and Annotation Standards

Authors:
Yiming Ni↗Zhi-Qi Cheng↗Jiayu Li↗Wei Cheng↗

Sign languages are expressive visual languages used by Deaf and Hard-of-Hearing (DHH) communities. Despite substantial progress in sign-language recognition, translation, and production, advances remain constrained by fragmented datasets, inconsistent annotations, and limited linguistic coverage. Existing benchmarks often fail to reflect real-world communication needs, and systematic analyses of these limitations remain limited. In this survey, we present a comprehensive index of sign-language datasets, covering 120 resources across 35 sign languages. We analyze key challenges such as modality imbalance, annotation granularity, and signer bias, and outline considerations for future dataset design. We also introduce a 24-field Sign-Language Datasheet and release a public GitHub repository (https://github.com/Ginqwerty/Open-Sign-Language) to support standardized documentation and reproducible evaluation. Overall, our work provides a unified and practical foundation for developing inclusive, robust, and scalable sign-language technologies in real-world applications.

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21.
arXiv (CS.AI) 2026-06-12

From Digital to Physical: Digital Agents as Autonomous Coaches for Physical Intelligence

Authors:
Zixing Lei↗Genjia Liu↗Yuanshuo Zhang↗Qipeng Liu↗Yuzhu Cai↗Sixiang Chen↗Jixian Wu↗Yunhong Wang↗Weixin Li↗Chuan Wen↗Bo Zhao↗Shanghang Zhang↗…

arXiv:2601.21570v2 Announce Type: replace Abstract: The field of Embodied AI is witnessing a rapid evolution toward general-purpose robotic systems, fueled by high-fidelity simulation and large-scale data collection. However, this scaling capability remains severely bottlenecked by a reliance on labor-intensive manual oversight from intricate reward shaping to hyperparameter tuning across heterogeneous backends. Inspired by LLMs' success in software automation and science discovery, we introduce \textsc{EmboCoach-Bench}, a benchmark evaluating the capacity of LLM agents to autonomously engineer embodied policies. Spanning 32 expert-curated RL and IL tasks, our framework posits executable code as the universal interface. We move beyond static generation to assess a dynamic closed-loop workflow, where agents leverage environment feedback to iteratively draft, debug, and optimize solutions, spanning improvements from physics-informed reward design to policy architectures such as diffusion policies. Extensive evaluations yield three critical insights: (1) autonomous agents can qualitatively surpass human-engineered baselines by 26.5\% in average success rate; (2) agentic workflow with environment feedback effectively strengthens policy development and substantially narrows the performance gap between open-source and proprietary models; and (3) agents exhibit self-correction capabilities for pathological engineering cases, successfully resurrecting task performance from near-total failures through iterative simulation-in-the-loop debugging. Ultimately, this work establishes a foundation for self-evolving embodied intelligence, accelerating the paradigm shift from labor-intensive manual tuning to scalable, autonomous engineering in embodied AI field.

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22.
arXiv (CS.CL) 2026-06-16

PathRouter: Aligning Rewards with Retrieval Quality in Agentic Graph Retrieval-Augmented Generation

Authors:
Bo Wang↗Heyan Huang↗Yaolin Li↗Wei Tang↗Yuan Zhang↗Wenbo Li↗Mingze Gao↗Ge Shi↗Chong Feng↗

Agentic GraphRAG trains language-model agents to iteratively retrieve and reason over graph-structured evidence, enabling more accurate and context-aware decision-making by efficiently navigating complex information networks. However, outcome-only reinforcement learning suffers from answer-path reward aliasing, where correct answers may come from shortcuts rather than useful evidence paths. It also exhibits search-update ambiguity, as scalar trajectory-level feedback does not indicate which retrieval actions to adjust. To mitigate these shortcomings, we present PathRouter, a path-aware training framework for agentic GraphRAG. PathRouter jointly evaluates each trajectory along answer correctness and evidence-path overlap, yielding four trajectory categories with differentiated GRPO advantage scaling that suppresses shortcut reinforcement while preserving evidence-seeking behavior. For evidence-poor trajectories, a frozen gold-evidence teacher provides token-level KL guidance on reasoning and search-query tokens, excluding answer tokens to avoid direct response imitation. Experiments on six QA benchmarks across three model sizes show that PathRouter consistently improves answer F1 and evidence-path overlap, achieving average F1 gains of 3.1 on 3B and 4.9 on 7B models compared to a strong baseline.

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23.
bioRxiv (Bioinfo) 2026-06-22

PhaseWY: A pipeline for haplotype phasing, sex chromosome identification and extraction of sex-limited sequences

Authors:
Ellerstrand↗S. J↗Churcher↗A. M. J↗Kutschera↗V. E↗Hansson↗

Sex chromosomes are central to many ecological and evolutionary processes. Evidence has accumulated that sex chromosome systems vary extensively in age, turnover and transitions, motivating renewed efforts to study the diversity of sex chromosome systems across the tree of life. However, successful genomic detection of sex chromosomes depends on several factors, including the size and divergence time, background genetic diversity, and the number of sequenced females and males. In addition, technical challenges associated with sequencing and analysing the sex-limited Y/W chromosome remain. Here, we present PhaseWY, an automated Snakemake pipeline that uses whole-genome sequencing data from multiple female and male individuals to identify sex-chromosomal regions and extract the corresponding Y/W sequences. PhaseWY (i) detects sex differences in alignment depth, (ii) applies read-based and statistical haplotype phasing, (iii) identifies sex-linked regions using haplotype clustering, and (iv) subsets autosomal, X/Z- and Y/W-linked variants for downstream analyses. We applied PhaseWY to simulated data to benchmark factors influencing sex-linkage detection and successful extraction of Y/W-linked variants. To demonstrate its practical utility, we further applied PhaseWY to the neo-sex chromosome system in Alauda larks (Alaudidae) and performed a range of downstream analyses demonstrating the scope of applications of the PhaseWY output. We conclude that PhaseWY provides an easy-to-use and reproducible tool for population-genomic analyses in non-model organisms, with particular importance for advancing our understanding of sex-chromosome evolution.

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

Mordal: Automated Pretrained Model Selection for Vision Language Models

Authors:
Shiqi He↗Insu Jang↗Mosharaf Chowdhury↗

Incorporating multiple modalities into large language models (LLMs) is a powerful way to enhance their understanding of non-textual data, enabling them to perform multimodal tasks. Vision language models (VLMs) form the fastest growing category of multimodal models because of their many practical use cases, including in healthcare, robotics, and accessibility. Unfortunately, even though different VLMs in the literature demonstrate impressive visual capabilities in different benchmarks, they are handcrafted by human experts; there is no automated framework to create task-specific multimodal models. We introduce Mordal, an automated multimodal model search framework that efficiently finds the best VLM for a user-defined task without manual intervention. Mordal achieves this both by reducing the number of candidates to consider during the search process and by minimizing the time required to evaluate each remaining candidate. Our evaluation shows that Mordal can find the best VLM for a given problem using $8.9\times$–$11.6\times$ lower GPU hours than grid search. We have also discovered that Mordal achieves about 69\% higher weighted Kendall's $\tau$ on average than the state-of-the-art model selection method across diverse tasks.

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25.
arXiv (CS.AI) 2026-06-16

An Empirical Investigation of Pre-Trained Deep Learning Model Reuse in the Scientific Process

Authors:
Nicholas M. Synovic↗Karolina Ryzka↗Alessandra V. Vellucci Solari↗Kenny Lyons↗James C. Davis↗George K. Thiruvathukal↗

arXiv:2603.13584v2 Announce Type: replace-cross Abstract: Deep learning has achieved recognition for its impact within natural sciences, yet the prohibitive financial and technical cost of training models from scratch inhibit adoption. Following software engineering community guidance, natural scientists are reusing pre-trained deep learning models (PTMs) to amortize these costs. While prior works recommend PTM reuse patterns, we present the first empirical study of PTM reuse patterns in the natural sciences, quantifying the utilization and impact of PTM reuse within the scientific process across 17,718 peer reviewed, open access papers. Our results show that "Biochemistry, Genetics and Molecular Biology" has outpaced other natural scientific fields in PTM reuse, "adaptation" reuse is the most prevalent PTM reuse pattern identified across all natural science fields, and the "testing" stage of the scientific process has been most impacted by PTM integration.

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