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01.
medRxiv (Medicine) 2026-06-15

Instrumental Activities of Daily Living in Older Adults with Epilepsy: A Cross-Sectional and Longitudinal Multicenter Study

Objective: Instrumental activities of daily living (IADLs) represent a critical but understudied measure of day-to-day function in persons with epilepsy(PWE). In the multicenter Brain Aging and Cognition in Epilepsy (BrACE) study of PWE aged greater than or equal to 55 years, we examined the proportion, clinical correlates, epilepsy-related predictors, and longitudinal trajectory of IADL impairment. Methods: IADLs were assessed using the Functional Activities Questionnaire (FAQ; range=0 to 30; higher=more impaired); a FAQ greater than or equal to 2 defines MCI-level impairment, and a FAQ greater than or equal to 5 defines dementia-level functional impairment. Multivariable logistic regression identified predictors of baseline function. Global cognition (Montreal Cognitive Assessment [MoCA]), individual cognitive measures, and quality of life (QOL) were compared between the impaired and unimpaired groups. Linear regression evaluated predictors of longitudinal functional decline. Results: Of 57 participants (mean age=66.6 years; female=52.6%), 38.6% (n=22) had MCI-level functional impairment and 17.5% (n=10) had dementia-level functional impairment. In univariate analyses, worse FAQ scores were associated with lower education, higher area deprivation index, early-onset epilepsy (EOE less than 60 years), antiseizure medication polytherapy, and epilepsy localization. In multivariable analysis, temporal lobe epilepsy (OR=4.46, 95% CI=1.09, 21.83,p=0.047), EOE(OR=7.14, 95% CI=1.16, 59.97, p=0.046), and lower education(OR=0.70,95% CI=0.49, 0.93, p=0.025) remained independently associated with baseline MCI-level functional-impairment. Lower education (OR=0.55,95% CI=0.29, 0.84, p=0.021) was the only factor associated with dementia-level IADL-impairment. IADL-impaired participants demonstrated lower verbal memory scores (adjusted p=0.041) and MoCA scores (adjusted p

02.
arXiv (CS.AI) 2026-06-19

Mitigating Simplicity Bias in OOD Detection through Object Co-occurrence Analysis

arXiv:2605.07821v2 Announce Type: replace-cross Abstract: Out-of-distribution (OOD) detection is crucial for ensuring the reliability of deep learning models. Existing methods mostly focus on regular entangled representations to discriminate in-distribution (ID) and OOD data, neglecting the rich contextual information within images. This issue is particularly challenging for detecting near-OOD, as models with simplicity bias struggle to learn discriminative features in disentangled representations. The human visual system can use the co-occurrence of objects in the natural environment to facilitate scene understanding. Inspired by this, we propose an Object-Centric OOD detection framework that learns to capture Object CO-occurrence (OCO) patterns within images. The proposed method introduces a new OOD detection paradigm that understands object co-occurrence within an image by predicting disentangled representations for the test sample, then adaptively divides patterns into three scenarios based on object co-occurrence patterns observed in ID training data, and finally performs OOD detection in a divide-and-conquer manner. By doing so, OCO can distinguish near-OOD by considering the semantic contextual relationships present in their images, avoiding the tendency to focus solely on simple, easily learnable regions. We evaluate OCO through experiments across challenging and full-spectrum OOD settings, demonstrating competitive results and confirming its ability to address both semantic and covariate shifts. Code is released at https://github.com/Michael-McQueen/OCO.

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

Real-rootedness of the Poincaré polynomials of $\overline{\mathcal M}_{0,n}$: an AI-assisted proof

arXiv:2605.29151v2 Announce Type: replace-cross Abstract: We prove real-rootedness for the Poincaré polynomial \[ P_n(t)=\sum_{i=0}^{n-3} \dim H^{2i}(\overline{\mathcal M}_{0,n};\mathbb{Q})t^i \] of the Deligne–Mumford moduli space $\overline{\mathcal M}_{0,n}$ of stable $n$-pointed rational curves, proving a conjecture of Aluffi–Chen–Marcolli. The proof starts from the Keel–Manin–Getzler recurrence, but its main new idea is a bivariate deformation $F_m(y,t)$ of the Poincaré polynomial. This deformation reveals a hidden interlacing structure not visible in the one-variable recurrence. For fixed $t

04.
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).

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

Variational Network with Wavelet-based UNET in Accelerated MRI Reconstruction from Under Sampled K-space Data

Fully sampled MRI requires dense k-space acquisition, leading to long scan times, reduced clinical throughput, and increased sensitivity to patient motion. Accelerated MRI addresses this by acquiring undersampled k-space data and reconstructing the missing information computationally. However, reconstruction from undersampled measurements is highly ill-posed and can introduce aliasing artifacts, noise amplification, and loss of anatomical detail. Although conventional parallel imaging and compressed sensing methods mitigate these issues, and deep learning methods have further improved reconstruction quality, preserving high-frequency structures under aggressive undersampling remains challenging. In this work, we propose a Variational Network with a Wavelet-based U-Net (W-UNet) for accelerated MRI reconstruction. The framework combines physics-guided iterative reconstruction with learnable multi-scale frequency representations. Standard pooling operations are replaced with Discrete Wavelet Transform and Inverse Wavelet Transform modules, enabling lossless downsampling while preserving low-frequency structure and high-frequency edge details. Integrated into the refinement and sensitivity map estimation stages, the proposed design improves artifact suppression, feature preservation, and reconstruction fidelity in both single-coil and multi-coil settings. Experiments on fastMRI knee and M4Raw brain datasets show state-of-the-art performance. Ablation studies further confirm the effectiveness of wavelet-based feature decomposition for accelerated MRI reconstruction.

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

Anti-causal domain generalization: Leveraging unlabeled data

arXiv:2602.17187v2 Announce Type: replace-cross Abstract: The problem of domain generalization concerns learning predictive models that are robust to distribution shifts when deployed in new, previously unseen environments. Existing methods typically require labeled data from multiple training environments, limiting their applicability when labeled data are scarce. In this work, we study domain generalization in an anti-causal setting, where the outcome causes the observed covariates. Under this structure, environment perturbations that affect the covariates do not propagate to the outcome, which motivates regularizing the model's sensitivity to these perturbations. Crucially, estimating these perturbation directions does not require labels, enabling us to leverage unlabeled data from multiple environments. We propose two methods that penalize the model's sensitivity to variations in the mean and covariance of the covariates across environments, respectively, and prove that these methods have worst-case optimality guarantees under certain classes of environments. Finally, we demonstrate the empirical performance of our approach on a controlled physical system and a physiological signal dataset.

07.
arXiv (CS.LG) 2026-06-16

A Multimodal Approach to Alzheimer's Diagnosis: Geometric Insights from Cube Copying and Cognitive Assessments

arXiv:2512.16184v2 Announce Type: replace Abstract: Early and accessible detection of Alzheimer's disease (AD) remains a critical clinical challenge, and cube-copying tasks offer a simple yet informative assessment of visuospatial function. This work proposes a multimodal framework that converts hand-drawn cube sketches into graph-structured representations capturing geometric and topological properties, and integrates these features with demographic information and neuropsychological test (NPT) scores for AD classification. Cube drawings are modeled as graphs with node features encoding spatial coordinates, local graphlet-based topology, and angular geometry, which are processed using graph neural networks and fused with age, education, and NPT features in a late-fusion model. Experimental results show that graph-based representations provide a strong unimodal baseline and substantially outperform pixel-based convolutional models, while multimodal integration further improves balanced classification performance and discriminative ability. SHAP-based interpretability analysis identifies specific graphlet motifs associated with corner integrity and edge continuity as key predictors, closely aligning with clinical observations of distorted cube drawings in AD. Together, these findings establish graph-based analysis of cube-copying behavior as an interpretable, non-invasive, and scalable framework for Alzheimer's disease screening.

08.
arXiv (CS.CL) 2026-06-16

AthDGC: An Open Diachronic Greek Treebank with Indo-European Parallels

AthDGC ("Athens-PROIEL") is an open, end-to-end workflow and dataset. It is, to the best of our knowledge, the first openly licensed dependency-parsed treebank of Greek that spans eight diachronic periods, namely Archaic, Classical, Koine, Late Antique, Byzantine, Late Byzantine, Early Modern, and Modern Greek, under a single PROIEL XML 2.0 schema, with verse-level cross-alignment of the New Testament to Latin (Vulgate), Gothic (Wulfila), Old Church Slavonic (Marianus), and Classical Armenian. AthDGC builds on the PROIEL Treebank Family (Haug and Johndal 2008; Eckhoff et al. 2018), which established the schema and the Koine-Greek reference set for the project. Annotation uses the Stanford Stanza PROIEL-trained workflow; sentence-level alignment uses LaBSE, a multilingual sentence-embedding model; word-level alignment uses multilingual-BERT attention through the AwesomeAlign procedure. The v0.4 release provides curated samples and the open-source toolkit; the full annotated corpus partitions remain under v0.5 audit on the Greek national HPC. Quantitative scale, per-witness verse counts, and per-period annotated-row counts are reported in the v0.5 release notes, after the audit pass completes. Concept DOI: 10.5281/zenodo.20439182.

09.
arXiv (CS.LG) 2026-06-12

The Urysohn Machine: A Metric-Topological Model of Computation

作者:

arXiv:2508.14143v2 Announce Type: replace Abstract: We introduce the Urysohn Machine, an effective model of classification-oriented computation in which metric separation, frontier structure, and contraction are explicit parts of the computational state. Its basic object is a Urysohn Triple: a support region, a target partition, and a separating classifier stored in a reusable Metric Library. The topological foundation is a constructive Urysohn Realization theorem for finite simplicial settings. It builds separators from dyadic ladders of nested polyhedral regions and equips their frontiers with a chain-level calculus: frontiers are cycles, and shells between levels have boundaries given by differences of frontiers. This construction yields two related complexity measures: decision-boundary width, the geometric measure of a single classifier's boundary, and Urysohn width, the total frontier mass represented by a library or realization. We prove an Amortized Separation Theorem showing that approximating a boundary of width to accuracy requires a number of simple basis triples proportional to boundary width and inversely proportional to resolution, under explicit boundary-footprint assumptions. We also introduce a contrastive separation operator whose graph-cut functional consistently estimates decision-boundary width from sampled metric data, while its Laplacian spectrum certifies class-component structure and conductance. Finally, we analyze the dynamic Urysohn ladder and prove four guarantees: separability under quotient collapse, stability of committed frontiers, bounded capacity under contraction, and scalability with quotient distance. Together, these results give a metric-topological account of classification complexity, amortized inference, and compositional reuse that preserves classical computability while exposing geometric structure hidden by purely symbolic descriptions.

10.
arXiv (math.PR) 2026-06-16

Exponential Convengence of DLRA for SDEs

arXiv:2606.15843v1 Announce Type: new Abstract: We study dynamical orthogonal (DO) approximations of stochastic differential equations and investigate their long-time behaviour. The DO formulation represents the solution by a low-rank decomposition and leads to a coupled system consisting of an evolution equation on the Stiefel manifold and a reduced stochastic process. We establish the well-posedness of the strong DO system and derive quantitative error estimates between the original stochastic differential equation and its low-rank approximation in the Wasserstein distance. Our main contribution is the analysis of invariant probability measures for the DO dynamics. Under suitable dissipativity, Lipschitz continuity, and non-degeneracy assumptions on the coefficients, we prove the existence of an invariant probability measure for the strong DO system. The proof combines uniform moment estimates, a Krylov–Bogoliubov argument for an associated frozen system, and a Kakutani-Fan-Glicksberg fixed-point theorem to recover the self-consistent dynamics. We further show that the induced low-rank process admits an invariant probability measure and discuss the structure of invariant measures through several illustrative examples. These results provide a rigorous foundation for the use of dynamical low-rank approximations in the approximation of long-time statistical properties of stochastic dynamical systems.

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

No One-Size-Fits-All Neurons: Task-based Neurons for Artificial Neural Networks

arXiv:2405.02369v2 Announce Type: replace-cross Abstract: In the past decade, many successful networks are on novel architectures, which almost exclusively use the same type of neurons. Recently, more and more deep learning studies have been inspired by the idea of NeuroAI and the neuronal diversity observed in human brains, leading to the proposal of novel artificial neuron designs. Designing well-performing neurons represents a new dimension relative to designing well-performing neural architectures. Biologically, the brain does not rely on a single type of neuron that universally functions in all aspects. Instead, in our brain, neurons are often task-based. In this study, we address the following question: since the human brain is a task-based neuron user, can the artificial network design go from the task-based architecture design to the task-based neuron design? Since methodologically there are no one-size-fits-all neurons, given the same structure, task-based neurons can enhance the feature representation ability relative to the existing universal neurons due to the intrinsic inductive bias for the task. Specifically, we propose a two-step framework for prototyping task-based neurons. As the initial step, we evaluate the proposed framework using polynomials as base functions. Empirically, systematic experimental results on synthetic data, classic benchmarks, and real-world applications show that the proposed task-based neuron design is not only feasible but also delivers competitive performance over other state-of-the-art models.

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

Advances in 4D Representation: Geometry, Motion, and Interaction

We present a survey on 4D generation and reconstruction, a fast-evolving subfield of computer graphics whose developments have been propelled by recent advances in neural fields, geometric and motion deep learning, as well as 3D generative artificial intelligence (GenAI). While our survey is not the first of its kind, we build our coverage of the domain from a unique and distinctive perspective of 4D representations, to model 3D geometry evolving over time while exhibiting motion and interaction. Specifically, instead of offering an exhaustive enumeration of many works, we take a more selective approach by focusing on representative works to highlight both the desirable properties and ensuing challenges of each representation under different computation, application, and data scenarios. The main take-away message we aim to convey to the readers is on how to select and then customize the appropriate 4D representations for their tasks. Organizationally, we separate the 4D representations based on three key pillars: geometry, motion, and interaction. Our discourse will not only encompass the most popular representations of today, such as neural radiance fields (NeRFs) and 3D Gaussian Splatting (3DGS), but also bring attention to relatively under-explored representations in the 4D context, such as structured models and long-range motions. Throughout our survey, we will reprise the role of large language models (LLMs) and video foundational models (VFMs) in a variety of 4D applications, while steering our discussion towards their current limitations and how they can be addressed. We also provide a dedicated coverage on what 4D datasets are currently available, as well as what is lacking, in driving the subfield forward. Project page:https://mingrui-zhao.github.io/4DRep-GMI/

13.
arXiv (CS.LG) 2026-06-15

Decompose Sparsely Where You Should, Absorb Densely Where You Should No

arXiv:2606.14040v1 Announce Type: new Abstract: Sparse autoencoders (SAEs) are typically trained to reconstruct the entire residual stream through a sparse dictionary, implicitly assuming that all activation content is amenable to sparse, monosemantic decomposition. We question this assumption and hypothesize that activations contain a low-rank, dense component that is computationally important to the model yet inherently unsuitable for sparse representation, which serves as a major source of the persistent dense latents widely observed in trained SAEs. To test this, we add a small rank-$r$ linear bottleneck in parallel with standard SAEs (BatchTopK and Matryoshka), allowing dense structure to be absorbed before sparse reconstruction. On Gemma-2-2B layer 12, a rank-24 bottleneck reduces dense latent count by up to 84\% while improving sparse probing and targeted probe perturbation on both architectures at matched sparsity. The absorbed component is (i) structurally identifiable as the top principal components and outlier dimensions; (ii) causally necessary, with removing it raising next-token cross-entropy by 7.5$\times$, far exceeding the 2.8$\times$ from removing the geometrically near-identical top-24 PCA directions; and (iii) redundantly encoded by sparse dictionaries, with ablating 787 maximally aligned sparse features raising cross-entropy by only 2.9$\times$ and ablating 2,048 topic-aligned features leaving MMLU topic classification virtually unchanged, whereas removing the scaffold drops it from 98.7\% to chance. Together, our findings identify a compact, semantically informative and causally important component of residual stream activations (which we term a computational scaffold) that standard sparse dictionaries represent inefficiently, suggesting that the scope of sparsity-based interpretability methods warrants careful re-examination.

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

From Noise to Order: Learning to Rank via Denoising Diffusion

arXiv:2602.11453v3 Announce Type: replace-cross Abstract: Learning-to-rank (LTR) methods have traditionally been limited to discriminative machine learning approaches that model the probability of the document being relevant to the query given some feature representation of the query-document pair. We propose an alternative denoising diffusion-based generative approach to LTR that instead models the full joint distribution over features and relevance labels. While in discriminative LTR, an over-parameterized ranking model may find different ways to fit the training data, we posit that candidate solutions that can explain the full data distribution under the generative setting maybe better at estimating relevance. Thus, we propose DiffusionRank that extends TabDiff, an existing diffusion model for tabular datasets, to create generative alternatives to classical discriminative pointwise and pairwise LTR objectives. Our work demonstrates improvements from DiffusionRank over discriminative counterparts on four standard LTR datasets and points to a rich space for future exploration to leverage ongoing advancements in deep generative models for LTR. Our code is publicly available at https://github.com/sadjadeb/DiffusionRank.

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

Recovering Stranded Discrimination in Knowledge Tracing: Per-Item Bias Correction via Empirical-Bayes Shrinkage

arXiv:2606.14123v1 Announce Type: cross Abstract: Deployed knowledge-tracing models are typically frozen after training, yet systematic per-item logit bias arises, from limited per-item expressivity in backbone architectures and from post-deployment shifts in item properties, degrading prediction quality. Global post-hoc calibrators such as Platt scaling, temperature scaling, and isotonic regression improve probability estimates but leave discriminative ability, as measured by AUC, unchanged. This AUC invariance is a structural consequence of monotone score-only transforms; recovering the stranded discrimination requires conditioning on item identity. We propose SLC (State-space Logit Correction), which converts binary observations to Gaussian pseudo-observations via Laplace/IRLS, applies empirical-Bayes shrinkage through a Kalman smoother, and fits an offset-Platt link. The state-space formulation also yields a detectability bound that characterizes the Bernoulli information floor, explaining why temporal tracking provides no benefit at current data densities. Across four datasets, five backbones, and three seeds, SLC improves AUC on all four datasets and NLL on three, with the advantage concentrating on sparse items. Cross-domain controls suggest that the same phenomenon can arise beyond education when the deployed backbone leaves entity-level bias.

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

Optimizing Lithium Production Decisions under Geological, Demand, and Pricing Uncertainties: A POMDP Framework for Multi-Objective Decision Making

arXiv:2606.18598v1 Announce Type: new Abstract: Decision making in lithium production is challenging, whether from an investor's perspective or a strategic production standpoint. Determining which mines to open and when to open them involves not only geological and price uncertainties, but also complexities around the choice of extraction method, from direct lithium extraction to hard rock mining. Prior work explored models of this problem and different methods to optimize mining decisions; these models did not account for uncertainty in pricing, uncertainty in demand, or different mining technologies to extract lithium. Incorporating different pricing models and extraction technology into these models enables more robust strategies for determining not only when and where to open a mine, but also which method of production to pursue. We frame the problem as a partially observable Markov decision process (POMDP) and solve using belief state planning methods to get optimal decision making. In our study, we show that POMDP solvers outperform human inspired heuristics by dynamically adapting to shifting lithium price regimes (static, linear, exponential, and stochastic) through belief state planning and explicit uncertainty management. By optimally sequencing exploration, production, and technology choice, the framework achieves higher demand fulfillment and more balanced economic environmental outcomes over the projects lifetime in all different pricing and deposit scenarios.

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

Remember, Don't Re-read: Stateful ReAct Agents for Token-Efficient Autonomous Experimentation

arXiv:2606.14945v1 Announce Type: new Abstract: The autoresearch pattern enables autonomous experimentation by having a large language model (LLM) iteratively modify code to optimize a target metric. Its stateless design, however, reconstructs experimental context from scratch at every iteration, incurring $O(n)$ token cost per iteration and $O(n^{2})$ total. This work reformulates the pattern as a stateful ReAct agent using LangGraph, where typed persistent state carries experimental history across iterations via a tool-calling interface. Two benchmarks are evaluated: hyperparameter tuning (15 iterations, small per-iteration observations) and code performance optimization (40 iterations, large per-iteration observations containing full source code and benchmark results). On hyperparameter tuning, the stateful agent consumes 90\% fewer tokens (2{,}492 vs.\ 24{,}465). On code optimization, the stateful agent consumes 52\% fewer tokens (627K vs.\ 1{,}275K) while achieving comparable optimization quality on both tasks. The token reduction is structural: the stateless agent re-reads the full history at $O(n)$ cost per iteration, while the stateful agent operates within a fixed-size conversation window at $O(1)$ cost. This paper describes the architecture in sufficient detail for practitioners to implement a stateful autoresearch agent for their own workflows.

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

OneFocus: Enabling Real-World X-ray Security Screening with a Unified Vision-Language Model

X-ray contraband detection is critical for security in large-scale logistics and transportation, yet conventional detectors struggle to adapt to emerging contraband types and lack fundamental visual understanding. Vision-language models (VLMs) offer strong generalization but are hindered by the scarcity of high-quality X-ray image-caption data. To bridge this critical gap, we present MMXray, a meticulously curated benchmark of 52,124 image-caption pairs spanning 28 fine-grained classes of X-ray contraband. To enrich MMXray with realistic occlusion patterns, we further introduce CleanDET, a dedicated synthesis dataset containing clean foreground contraband images from 28 categories and background images with diverse density levels, together with AnyContraSyn, a controllable synthesis method designed to operate on CleanDET. We also develop OnePipe, an extensible pipeline for systematic data curation. Built on MMXray, we propose OneFocus, a unified VLM that supports four core tasks: visual question answering, contraband localization, classification, and image understanding. OneFocus achieves state-of-the-art performance in X-ray contraband understanding and demonstrates robust cross-domain generalization, establishing a strong vision-language baseline for security screening.

19.
bioRxiv (Bioinfo) 2026-06-20

Ribosomes are covered by a coat of flexible protein fragments

Ribosomal proteins contain flexible terminal regions that are averaged out during electron density reconstructions, rendering them absent from experimental models derived by X-ray crystallography or cryogenic electron microscopy. These flexible protein fragments (FPFs) collectively form an invisible coat on the ribosome surface whose presence has been systematically overlooked. Here we analysed FPFs from 36 ribosomes spanning bacteria, eukaryotes, and mitochondria. We found that mitoribosomes harbour the most numerous and longest FPFs. Structural predictions confirmed that FPFs are predominantly disordered across all ribosome classes. Comparison of FPF amino acid composition against proteome-wide background frequencies revealed strong and domain-specific compositional biases. The balance between arginine and lysine content tracks the cardiolipin content of the membrane each ribosome class contacts. The arginine enrichment in mitoribosomal FPFs may additionally reflect selection arising from the RNA-rich environment of mitochondrial RNA granules, membraneless condensates where mitoribosomes are assembled. FPFs are uniformly depleted in aromatic residues, arguing against protein-driven liquid–liquid phase separation propensity. Our findings suggest that the flexibly tethered coat is a highly functional intrinsic part of all ribosomes.

20.
medRxiv (Medicine) 2026-06-18

Device assessed 24-hour movement behaviour and cardiovascular disease mortality amongst cancer survivors.

Background: Cancer survivors face elevated risks of mortality from cardiovascular disease (CVD). The potential importance of physical activity (PA) and other behaviours across the 24-hour day (e.g. sedentary behaviour (SB) and sleep) for CVD-mortality risk is not well understood in this at-risk population. Objectives: To assess the importance of 24-hour movement behaviour, using a compositional approach, for mitigating CVD-mortality amongst cancer survivors. Methods: Participants with a prior cancer diagnosis were drawn from the UK Biobank accelerometry sub-study (n=6,158). Accelerometer-derived movement (moderate-to-vigorous PA (MVPA), vigorous PA (VPA), moderate PA (MPA), light PA (LPA), SB, sleep) was examined in relation to CVD-mortality, identified from health record linkage data (using Fine-Gray Cox proportional-hazards models adjusted for demographic, health, lifestyle covariates). Results: Median follow-up was 8.0 years (Q1-Q3: 7.4-8.5), with n=500 (8.2%) deaths (CVD-deaths: n=118). Greater MVPA, in place of any other behaviour, was inversely associated with CVD-mortality with e.g. 10% lower hazard if MVPA theoretically replaced 7 minutes (mins)/day SB (Hazard ratio (HR): 0.91, (95% Confidence Interval: 0.86-0.95)), 9 mins/day LPA (HR: 0.90, 0.83-0.97), or 11 mins/day sleep (HR: 0.90, 0.83-0.97). The VPA component of MVPA proved critical, requiring only ~1-2 additional mins/day for equivalent hazard reduction. Sleep duration, was also inversely associated with CVD-mortality. A 10% lower hazard required replacing 29 mins/day of SB with sleep (HR: 0.90, 0.84-0.96); no other behavioural replacement amongst SB, sleep or LPA could provide an equivalent risk reduction. Conclusions: Among cancer survivors, the most potent reduction in CVD-mortality followed theoretically reallocating time to higher intensity movement.

21.
PLOS Computational Biology 2026-06-15

Fung-AI: An AI/ML-driven pipeline for antifungal peptide discovery

by Daniel S. Berman, Libby M. Lewis, Tom D. Curtis, Olivia N. Tiburzi, Daniel F. Q. Smith, Arturo Casadevall, Laura J. Dunphy Emerging fungal pathogens represent a concerning threat to both global health and food security. In this study, we aimed to address our rising vulnerability to fungal pathogens through the development of the Fung-AI pipeline: an AI/ML-driven approach for antifungal discovery. A generative adversarial network (GAN) was trained to generate novel candidate antifungal peptide sequences. Next, in silico antifungal and hemolytic classifiers were built to further prioritize AI-generated peptides for experimental validation. From a pool of ~10,000 candidates, thirteen peptides were selected for testing over two-stages of experimentation. Five peptides were found to display mild antifungal activity against the wheat pathogen, Fusarium graminearum, with minimal inhibitory concentrations (MICs) ranging from 250 µg/mL to 500 µg/mL. Four of the five peptides also showed activity against the human pathogen, Candida albicans (MIC: 500 µg/mL). Two of our AI-generated antifungal peptides additionally demonstrated low cytotoxicity in HepG2 human liver carcinoma cells (LC50 > 704.2 µg/mL) indicating that they may be useful as scaffolds for future optimization for therapeutic applications. None of our peptides were found to considerably inhibit the emerging pathogen C. auris, suggesting the need for pathogen-specific down-selection of candidate peptides. Overall, we present a proof-of-principle, generative-AI-based approach for the rapid design of de novo antifungal peptides.

22.
arXiv (quant-ph) 2026-06-11

A Cryogenic Uniaxial Strain Cell for Quantum Devices

arXiv:2606.11485v1 Announce Type: new Abstract: Mechanical strain is a powerful resource for tuning quantum systems, but existing piezoelectric strain cells are generally optimized for fragile, high-aspect-ratio single crystals rather than the thick, square-profile chips typical of semiconductor quantum devices. Furthermore, adapting these cells for qubits requires accommodating dense RF and DC wiring while maintaining strict electrical isolation from high-voltage piezo actuators. Here, we present a piezoelectric uniaxial strain cell designed to homogeneously strain thick, square-profile substrates. We introduce a highly symmetric dual-chip loading configuration that effectively suppresses flexural deformation and shear stress. The cell integrates a high-density RF/DC interposer to support standard wire bonding and encloses the actuators in a grounded Faraday cage to prevent unwanted Stark shifts in the device layer. Finite element simulations confirm that combining stiff actuators with this symmetric mounting drastically improves strain homogeneity. Finally, we validate the apparatus experimentally by applying uniaxial strain to a 200 $\mu$m thick silicon die. Surface strain measurements demonstrate an applied strain of 215 $\mu\epsilon$ for 200 V applied piezo bias.

23.
PLOS Medicine 2026-06-01

The NIH 2025 Public Access Policy: Immediate access, unequal costs

by Caitlin R. Ryus, Caroline Raymond King, Edward R. Melnick The NIH 2025 Public Access Policy eliminates embargo periods for federally funded research, expanding who can read science. Yet without addressing article processing charges and market concentration, the policy risks creating new barriers to who can afford to perform and publish their science. In this Perspective, Caitlin Ryus and colleagues discuss the NIH 2025 Public Access Policy, highlighting that while expanding who can read science, the policy risks creating new barriers to who can afford to perform and publish their science.

24.
arXiv (CS.CV) 2026-06-18

Pyramid Self-Contrastive Learning for Single-shot Test-time Ultrasound Image Denoising

The inherent electronic and speckle noise complicates clinical interpretation of ultrasound images. Conventional denoising methods rely on explicit noise assumptions whose validity diminishes under composite noise conditions. Learning-based methods are usually pretrained in a limited image domain using a labeled dataset, which implies inevitable domain shift in complex in vivo environments. This study proposes a Pyramid Self-Contrastive Learning (PSCL) framework for test-time ultrasound image denoising without pretraining. Given multiple noisy samples from only one-shot imaging, PSCL disentangles anatomical similarity and noise randomness into separate pyramid latent spaces. The clean image is then decoded from the anatomy space while discarding the noise space. We first apply PSCL to synthetic aperture ultrasound (SAU), where an Aperture-to-Aperture loop serves as a self-supervised proxy task to ensure denoising fidelity. Simulation experiments, including noise levels from 0 to 30 dB and inclusion geometries from simple to complex, demonstrated improvements of 69.3% in SNR and 34.4% in CNR. The in vivo results showed 84.8% SNR and 25.7% CNR gains using only two aperture data of the heart in six echocardiographic views, liver, and kidney. PSCL delivers clear images across diverse imaging targets and configurations, paving the way for more reliable anatomical visualization without domain shift and pretraining costs.

25.
bioRxiv (Bioinfo) 2026-06-18

Bayesian modeling of longitudinal metatranscriptomes of broiler meat spoilage microbiomes shows shared predictive signature associated with spoilage at refrigerated temperatures

Microbial spoilage of packaged meat is driven by complex microbial succession and related metabolic activity, yet conventional shelf-life assessment is mainly based on shelf-life studies relying on culturing and sensory analysis. In routine quality assurance, results are obtained retrospectively, and they are only indirectly linked to the metabolic activity related to sensory deterioration. Functional, time informative approaches that capture the active metabolic state of the spoilage microbiome and predict the rate of spoilage are lacking. We developed a censoring-aware Gaussian process (CAGP) framework to model longitudinal pathway expression profiles from broiler meat metatranscriptomes collected over consecutive storage days at 4 or 6{degrees}C. Samples were annotated using odor-based sensory scores defining fresh, early-spoilage, and late-spoilage phases. Because observed zeros in pathway-level data may reflect non-detection rather than true absence, the model treats low values as left-censored observations below a detection threshold while estimating smooth temporal trajectories with uncertainty. In leave-one-out prediction within the 4{degrees}C time series, predicted sampling days differed from the true days by an average of 0.43 days, and predicted spoilage phases agreed with the sensory classification. Trajectories learned at 4{degrees}C also transferred to an independent 6{degrees}C time series at the spoilage-phase level, suggesting that shared functional spoilage programs are preserved despite temperature-dependent changes in spoilage rate. Cross-entropy ranking further identified pathway modules carrying time- and phase-informative signals across temperatures. Overall, this framework provides a probabilistic approach for linking metatranscriptomic functional dynamics to sensory spoilage progression, supporting shelf-life assessment beyond retrospective microbial enumeration.