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01.
arXiv (CS.CV) 2026-06-12

Modality-Aware Feature Matching in Visual and Vision-Language Applications: A Comprehensive Survey

Feature matching is a cornerstone task in computer vision, essential for applications such as image retrieval, stereo matching, 3D reconstruction, and SLAM. This survey comprehensively reviews modality-based feature matching, exploring traditional handcrafted methods and emphasizing contemporary deep learning approaches across various modalities, including RGB images, depth images, 3D point clouds, LiDAR scans, medical images, and vision-language interactions. Traditional methods, leveraging detectors like Harris corners and descriptors such as SIFT and ORB, demonstrate robustness under moderate intra-modality variations but struggle with significant modality gaps. Contemporary deep learning-based methods, exemplified by detector-free strategies like CNN-based SuperPoint and transformer-based LoFTR, substantially improve robustness and adaptability across modalities. We highlight modality-aware advancements, such as geometric and depth-specific descriptors for depth images, sparse and dense learning methods for 3D point clouds, attention-enhanced neural networks for LiDAR scans, and specialized solutions like the MIND descriptor for complex medical image matching. Cross-modal applications, particularly in medical image registration and vision-language tasks, underscore the evolution of feature matching to handle increasingly diverse data interactions.

02.
arXiv (CS.CV) 2026-06-16

Sex-based Network-Specific Differences in Connectomes: A Krakencoder-Based Analysis

This study examines how deficiencies in one brain connectome modality propagate to the other, using the Krakencoder as a simulation framework. Structural and functional connectomes from 702 healthy participants in the Human Connectome Project were analyzed, with the impact of each of the Yeo-7 functional networks assessed separately. Seven scenarios were considered, each involving the removal of a single network while the remaining networks were preserved. The resulting perturbations in cross-modal predictions were quantified using three complementary metrics: KL divergence on eigenvalue spectra, Frobenius norm, and Wasserstein distance. In addition, the persistence of sex-specific information within the predicted connectomes was evaluated. Across all metrics and both prediction directions, the Default Mode Network produced the largest perturbations, whereas the Somatomotor network yielded the smallest. Sex differences in network-level perturbation signatures were subtle, with the best result being an accuracy of 66.09% from connectomes predicted under network-removal conditions. In contrast, connectomes predicted from intact inputs achieved substantially higher sex classification accuracy, reaching up to 84.76%. These findings confirm that full predicted connectomes retain considerably more sex-discriminative information than perturbation-derived signatures alone.

03.
Nature Biotechnology 2026-06-11

Large-scale, spatially resolved panoramic CRISPR screening in native tissue environments using Perturb-DBiT

作者:

Spatially resolved CRISPR screening in vivo has been limited to small perturbation panels and subsets of protein-coding RNAs. We present Perturb-DBiT, a method for co-sequencing of spatial total RNA whole transcriptomes and single guide RNAs (sgRNAs) on the same tissue section in situ. In a human cancer metastatic colonization model, we applied large (80,000+) sgRNA panels across tumor colonies in multiple consecutive tissue sections alongside their corresponding total RNA transcriptomes. We linked perturbations affecting long noncoding RNA covariation, microRNA–mRNA interactions and distinct amino acid-specific tRNA alterations to tumor migration and growth. By integrating transcriptional pseudotime trajectories, we further observed the impact of perturbations on clonal dynamics and cooperation. In an immune-competent syngeneic mouse model, investigation of the tumor immune microenvironment indicated distinct, synergistic effects on immune infiltration and suppression. Perturb-DBiT provides a spatially resolved comprehensive view of perturbation responses in complex tissues, including small and large RNA regulation, tumor proliferation, migration, metastasis and immune interactions. In vivo CRISPR genetic perturbations are spatially mapped at scale.

04.
arXiv (CS.CL) 2026-06-11

Improving Cross-Format Robustness in Language Models with Multi-Format Training

Large language models often remain sensitive to answer format: a question solved correctly in one form may fail in another semantically equivalent form. To study this gap, we define cross-format robustness as the extent to which a model answers the same underlying question consistently across formats. We then compare full-format training with FormatMix, which expands only a subset of training items into multiple equivalent formats using either random or targeted selection. Across GLM4 and Llama-3.1, multi-format supervision consistently improves both task performance and cross-format robustness, whereas Multiple-choice question (MCQ)-only supervision alone brings little benefit and can even reduce robustness. We further find that expanding only about 30% of the training set into multiple formats often recovers most of the gain from full-format training, and this effect appears across the model families and sizes we study. These results suggest that format diversity, rather than additional supervision alone, is the key driver of robustness. That lightweight multi-format augmentation is a practical way to make LLMs less sensitive to answer format without changing the base model.

05.
medRxiv (Medicine) 2026-06-15

A More-Than-Human Approach to Designing for Mental Health: Remixing Prototypes for the Contexts of Complex Healthcare Infrastructures

Digital mental health tools (DMHTs) often fail to be successfully implemented in clinical settings. While user- and human-centred design frameworks are frequently proposed for developing effective tools, they are insufficient to address the sociotechnical complexity of healthcare environments. This paper addresses this limitation by detailing the application of a more-than-human design framework to incorporate wider contextual factors into design decisions. To demonstrate the application of this more-than-human design framework, we present a case study showcasing the design of one specific feature within a DMHT intended to support Health Improvement Practitioners (HIPs) in New Zealand's Integrated Primary Mental Health and Addictions (IPMHA) service. Our process blends usage-context storyboards with interface prototypes, using think-aloud interviews to test the contextual fit of our prototypes. The initial design concept failed due to contextual factors such as inconsistent wait times and the administrative burden on clients and clinic staff. This led to a pivot to a more context-appropriate, practitioner-focused, in-session concept for digital psychometric administration and automated scoring. This case study demonstrates that for DMHTs to be viable within complex healthcare environments, design must focus on more than the needs of a single user, incorporating multiple stakeholders and contextual variables across the wider service-delivery context.

06.
arXiv (quant-ph) 2026-06-19

General circuit mapping algorithm for neutral atom quantum computers

arXiv:2606.20503v1 Announce Type: new Abstract: Neutral atom quantum computers (NAQC) are emerging as a promising, scalable quantum computing platform because of their long qubit coherence, flexible qubit arrangement, and multiqubit gate capabilities. However, circuit execution often requires physically moving qubits, making compilation a critical optimization challenge. We propose a circuit independent mathematical framework built on graph-theoretic combinatorial optimization that determines the minimal number of required qubit transfers. This model captures spatial constraints specific to NAQC platforms with zone-limited gate operations and multi-qubit gates. From this framework, we encode the qubit mapping problem as a nonlinear integer program and solve it using a genetic algorithm, enabling trade-offs between minimizing the total traveled distance and the number of parallel transfer operations. Compared to the state-of-the-art scalable compiler for zoned architectures, our approach consistently finds fewer transfers. Depending on the optimization focus, our method produces shorter traveled distances or fewer parallel transfer operations. This work provides both theoretical guaranties and a practical tool for efficient, architecture-aware quantum circuit compilation. As a result, practitioners can generate hardware-aware mappings that reduce movement-induced errors and better exploit atom transfer parallelism, directly improving execution efficiency on NAQC devices.

07.
arXiv (CS.LG) 2026-06-11

A prior-free blind detection of information leakage from model predictions

arXiv:2606.11267v1 Announce Type: new Abstract: Data leakage – contamination of a model with information unavailable at baseline – is the dominant reproducibility failure in machine-learning-based science, yet detection tools require training code, external data, or domain expertise. None operates on the artifact an auditor most often holds: the model's output. We ask what can be decided about leakage from predictions and outcomes alone. We give a decision-theoretic framework in which leakage diagnostics are functionals of the predicted-risk/outcome law, parameterized by a threshold-weighting linked to proper scoring rules and decision-curve analysis. We prove a sharp impossibility: a recalibrated leak matching an honest model's calibration and discrimination is indistinguishable from honest performance by any function of the predictions, so the broad class is detectable only against an externally supplied ceiling on achievable discrimination. We then prove what leakage cannot hide: a near-deterministic subgroup – the signature of a near-label leak – produces a sustained unit-purity head that no legitimate predictor of a non-deterministic outcome can manufacture, yielding a prior-free test. These results organize leakage into a trichotomy – miscalibrated, broad-calibrated, and deterministic – each with a matched detector and failure mode. We validate on UK Biobank using time-windowed comorbidity leakage with known, graded severity, measuring a detection floor of $\Delta\cstar \approx 0.007$ on this endpoint, below which residual leakage is undetectable from output and too small to alter conclusions. The numerical floor is cohort- and endpoint-specific; the structural lesson is general: output-only detection fails where residual leakage is indistinguishable from an honestly stronger predictor. The test returns a verdict on a prediction vector in under a second on commodity hardware.

08.
arXiv (CS.AI) 2026-06-12

(Human) Attention Is (Still) All You Need: Human oversight makes AI-assisted social science reliable

arXiv:2606.12848v1 Announce Type: new Abstract: Large language models (LLMs) are increasingly used for tasks once reserved for trained researchers, including hypothesis generation, specification choice, and drafting conclusions. We argue that the reliability of AI-assisted research depends not only on model capability, but also on how cognitive labour is structured between humans and machines. We study this problem through Human-in-the-Loop Economic Research (HLER), a decision architecture based on pre-commitment, decision sequencing, accountability, and attention allocation. In a pre-specified 2*4 factorial experiment with 280 complete research runs across four datasets, an unconstrained multi-agent baseline produced critical failures in 72% of runs. Using the same underlying model, the same agent decomposition, and identical prompts for the shared reasoning agents, HLER reduced the failure rate to 16% by imposing three architectural commitments: LLMs reason but do not execute data work, data and estimation are handled deterministically, and three human decision gates bind the workflow. Fisher's exact test rejects equality of failure rates at p

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

The Theory of Mind Utility: Formal Specification of a Mentalizing Mechanism

arXiv:2606.12721v1 Announce Type: new Abstract: Inferring others' beliefs requires more than reading surface signals; it requires tracking who told them what, in what order, and how credibly. The Theory of Mind Utility (ToM-U) formalizes this epistemic state inference problem at the computational level of analysis, specifying what mentalizing computes and why without commitment to algorithmic or neural implementation. ToM-U achieves this by constructing Local Epistemic World Models (LEWMs) – directed typed graphs that represent agents, state nodes, and the epistemic relationships among them – and evaluating discrete candidate LEWMs against observed behavior until one achieves sufficient confidence. Five formal definitions specify the LEWM structure, agent node properties including ordered information access history, a bounded proliferation mechanism for recursive mentalizing, three inference procedures, and a residue function that captures the structured trace left by failed mentalizing attempts. ToM-U differs from Bayesian Theory of Mind and adjacent formal accounts, which presuppose rather than derive belief states, and from simulation theory and theory-theory, which lack a formal apparatus for epistemic state inference. The architecture generates directional, falsifiable predictions about mentalizing failure that follow from structural properties of the model rather than auxiliary assumptions, and positions ToM-U as a domain-agnostic mechanism upstream of goal inference and other downstream social cognitive processes.

10.
arXiv (quant-ph) 2026-06-19

Exploiting More Than Symmetry in Variational Quantum Machine Learning

arXiv:2606.20316v1 Announce Type: new Abstract: The success of variational quantum learning models crucially depends on choosing parametrizations that reflect the structure of the problem at hand. Symmetries provide one of the clearest such structures: whenever transformations of the input leave the desired outcome unchanged, this invariance should be built into the model rather than discovered during training. However, imposing a symmetry does not by itself determine a useful ansatz. Even within the symmetry-preserving space, one must decide where the trainable degrees of freedom should be placed. In this work, we study this remaining design freedom in equivariant variational quantum circuits. Building on symmetry-based parameter sharing, we disentangle two architectural choices: how much symmetry should be enforced, and which symmetry-respecting interactions should be trainable. Using Tic-Tac-Toe as a fully enumerable and structurally transparent test case, we find that suitable subgroups preserve most of the generalization benefit. By contrast, the dominant gains arise from gates acting directly on decisive task motifs. Thus, symmetry defines the admissible design space, while effective ansatze require an additional task-informed choice of trainable interactions.

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

HawkesNest: A Multi-Axis Synthetic Benchmark for Spatiotemporal Pattern Complexity

arXiv:2606.16863v1 Announce Type: new Abstract: Evaluation of spatiotemporal point process (STPP) models relies heavily on opaque real-world datasets, where latent generative structure is unknown and model failures are difficult to attribute. We introduce HawkesNest, a generator-aligned benchmark for controlled spatiotemporal pattern complexity built on a multivariate Hawkes backbone. HawkesNest defines four complexity axes: space–time entanglement, background heterogeneity, cross-type interaction, and domain topology. Each axis is associated with a deterministic index computed from the latent data-generating mechanism. By varying these axes while holding global rate, stability, and simulation budget fixed, HawkesNest enables diagnostic stress tests of STPP models under known structural difficulty. We verify that the indices are monotone and nearly orthogonal under controlled sweeps. We illustrate its use by showing that Hawkes-family baselines degrade under joint heterogeneity–entanglement complexity, even though they are structurally aligned with the Hawkes data-generating backbone. We further show that HawkesNest exposes neural-model sensitivity: AutoSTPP remains vulnerable under isolated increases in space–time entanglement. Code. Available at https://github.com/YahyaAalaila/HawkesNest

12.
arXiv (math.PR) 2026-06-15

Laws of Large Numbers for Non-Independent Random Variables on Hyperspaces with respect to the Hausdorff Metric

arXiv:2011.07199v5 Announce Type: replace Abstract: This paper investigates the limit behavior of the Minkowski sums for sequences of set-valued random variables. When the underlying space is finite dimensional, by using the support function, we establish the weak and strong laws of large numbers for non-independent random variables in the hyperspace with respect to the Hausdorff metric $d_H$.

13.
Nature (Science) 2026-06-17

<i>CHPO</i> coordinates chilling recovery and nitrogen use in rice

作者:

Global rice production faces mounting challenges from abnormal temperature fluctuations and nitrogen-fertilizer-driven environmental pollution1–7. Developing varieties that balance chilling resilience and nitrogen-use efficiency (NUE) offers a promising solution, but the molecular networks coordinating these traits remain poorly understood. Here we identify CHILLING PHOENIX (CHPO), a major gene underlying the quantitative trait locus shared by both chilling tolerance and resilience. It encodes a MYB transcription factor that acts as a key regulator coordinating post-chilling recovery with nitrogen use in rice. Natural variation in a GCG-repeat-encoded polyalanine tract alters CHPO DNA-binding preference and redirects regulatory outputs between the japonica-type (CHPOjap) and indica-type (CHPOind), causing opposing effects on chilling tolerance and resilience. This allelic variation is shaped by domestication selection, with the CHPOjap allele probably derived from Chinese wild rice. CHPOjap directly targets OsTCP19 and OsNRT2.4 to fine-tune NUE, thereby enhancing chilling tolerance and resilience. These findings provide a mechanistic framework for a chilling-induced high-nitrogen-utilization module that alleviates the damage caused by chilling stress, and a potential molecular design&nbsp;strategy for breeding rice varieties with both chilling resilience and high NUE at the&nbsp;recovery stage. A rice gene, CHPO, links chilling resilience with nitrogen-use efficiency, revealing a domestication-shaped regulatory mechanism that could guide breeding of climate-resilient, sustainable rice varieties.

14.
arXiv (CS.LG) 2026-06-15

Temporally Consistent Graph Q-Networks for Intelligent Network Control

arXiv:2606.13848v1 Announce Type: cross Abstract: Mobile networks continue to grow in complexity and next generation networks are expected to support both increasing traffic loads and more diverse services. As network complexity rises, optimizing antenna parameters under dynamic or changing objectives becomes increasingly challenging. We propose a novel multi-agent reinforcement learning (MARL) algorithm for high-level control and orchestration of mobile networks. The Temporally Consistent Graph Q-Network (TC-GQN) algorithm learns a self-predicting representation of the whole network that is task-independent and aggregates information from all base-stations. A graph neural network is trained using a global reward function to assign coordinated local actions based on the learned encoding of the global network state. We evaluate the algorithm in a simulated environment to orchestrate an energy-saving feature across multiple sectors and multiple carriers under different quality of service (QoS) constraints. The proposed algorithm outperforms state-of-the-art graph-based baselines and a competitive rule-based controller by improving hardware sleep time while maintaining QoS. Moreover, the learned representation enables rapid adaptation to changing intents.

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

EquiDexFlow: Contact-Grounded SE(3)-Equivariant Dexterous Grasp Generative Flows

Most learned dexterous grasp generators relegate contact forces to a downstream verification step, so a kinematically-plausible pose can still violate the conditions for a stable physical grasp. We address this with EquiDexFlow, an SE(3)-equivariant flow-matching model that jointly predicts wrist pose, joint angles, fingertip contacts, surface normals, and contact forces from an object point cloud. Our architecture projects contacts onto the object surface and forces into the Coulomb friction cone by construction, so placement and friction compliance hold without loss penalties. We prove end-to-end SE(3) equivariance and verify it empirically over 200 rotations, with wrist residuals below $0.04^\circ$ and exactly zero joint deviation. Trained on 8,100 force-closure grasps across 81 objects for the 16-DoF Allegro Hand, our model achieves zero friction violations, the best composite score, and the lowest wrench residual among all ablation variants. We retarget decoded fingertip contacts to a 16-DoF LEAP Hand via per-finger inverse kinematics, and our hardware-feasible refinement places every joint at least 5% inside its actuator envelope while preserving wrench balance. On the physical robot, retargeted EquiDexFlow-decoded grasps complete open-loop pick-and-hold trials on all six test objects, with every asymmetric object succeeding at both the canonical pose and a $120^\circ$ co-rotation. Videos, code, and checkpoints are available at https://equidexflow.github.io.

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

Critically Engaged Pragmatism: Scientific Norm and Social, Pragmatist Epistemology for AI Science Evaluation Tools

arXiv:2601.09753v2 Announce Type: replace-cross Abstract: AI science evaluation tools aim to assess research credibility. As with traditional metrics such as impact factors, their edicts can be decontextualised and repurposed in problematic ways. To address this, I propose Critically-Engaged Pragmatism as a scientific norm enjoining scientific communities to scrutinise the purposes and purpose-specific reliability of AI science evaluation tools. To foster Critically Engaged Pragmatism, creators of AI science evaluation tools should transparently and fully report design, training, and benchmarking details to facilitate assessments of purpose-specific reliability, liability to different types of error, and bias. What count as best practices for the transparent reporting of AI science evaluation tools should be updated as new forms of error, bias, and gamesmanship are discovered. Under this framework, AI science evaluation tools are not objective arbiters of scientific credibility. Rather, they are the object of critical discursive practices that ultimately ground the credibility of scientific communities.

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

Algorithmic Prompt Generation for Diverse Human-like Teaming and Communication with Large Language Models

Understanding how humans collaborate and communicate in teams is essential for improving human-agent teaming and AI-assisted decision-making. However, relying solely on data from large-scale user studies is impractical due to logistical, ethical, and practical constraints, necessitating synthetic models of multiple diverse human behaviors. Recently, agents powered by Large Language Models (LLMs) have been shown to emulate human-like behavior in social settings. But, obtaining a large set of diverse behaviors requires manual effort in the form of designing prompts. On the other hand, Quality Diversity (QD) optimization has been shown to be capable of generating diverse Reinforcement Learning (RL) agent behavior. In this work, we combine QD optimization with LLM-powered agents to iteratively search for prompts that generate diverse team behavior in a long-horizon, multi-step collaborative environment. We first show, through a human-subjects experiment, that humans exhibit diverse coordination and communication behavior in this domain. We then present a series of experiments showing that our approach captures behaviors that are difficult to observe without large-scale data collection, and a follow-up user study to show that these generated behaviors are human-like. Our findings highlight the combination of QD and LLM-powered agents as an effective tool for studying teaming and communication strategies in multi-agent collaboration.

18.
arXiv (CS.LG) 2026-06-19

Comparative Study of Neural Surrogate Architectures for Autoregressive Prediction of Internal Battery States

arXiv:2606.20053v1 Announce Type: new Abstract: The Doyle-Fuller-Newman (DFN) model resolves internal electrochemical states in lithium-ion batteries with high fidelity. However, the numerical solution of its governing equations is computationally prohibitive for real-time deployment, limiting scalability from individual cells to pack and fleet-scale applications. While machine learning surrogates can substantially reduce inference latency through GPU acceleration, most existing approaches learn solution approximations tied to specific operating conditions rather than learning generalizable state-evolution dynamics. This work presents a systematic comparison of four neural network architectures (MLP, ResNet, U-Net, FNO) formulated as autoregressive state-transition operators that predict full DFN internal states across a wide range of operating conditions. To ensure a controlled architectural comparison, all models are trained under a unified framework using multi-step unrolling and current-conditioning, isolating the impact of spatial inductive bias. Results demonstrate that the U-Net's multi-scale feature hierarchy achieves a mean final-step nRMSE of 3% averaged across all internal state variables after 300-step autoregressive rollouts, while providing a 5.38x speed-up over the numerical solver. These findings highlight spatial inductive bias as a critical determinant of surrogate performance, advancing the development of surrogates for internal state observability for next-generation battery management systems and digital twins.

20.
arXiv (CS.LG) 2026-06-11

Self-Supervised Multisensory Pretraining for Contact-Rich Robot Reinforcement Learning

arXiv:2511.14427v4 Announce Type: replace-cross Abstract: Effective contact-rich manipulation requires robots to synergistically leverage vision, force, and proprioception. However, Reinforcement Learning agents struggle to learn in such multisensory settings, especially amidst sensory noise and dynamic changes. We propose MultiSensory Dynamic Pretraining (MSDP), a novel framework for learning expressive multisensory representations tailored for task-oriented policy learning. MSDP is based on masked autoencoding and trains a transformer-based encoder by reconstructing multisensory observations from only a subset of sensor embeddings, leading to cross-modal prediction and sensor fusion. For downstream policy learning, we introduce a novel asymmetric architecture, where a cross-attention mechanism allows the critic to extract dynamic, task-specific features from the frozen embeddings, while the actor receives a stable pooled representation to guide its actions. Our method demonstrates accelerated learning and robust performance under diverse perturbations, including sensor noise, and changes in object dynamics. Evaluations in multiple challenging, contact-rich robot manipulation tasks in simulation and the real world showcase the effectiveness of MSDP. Our approach exhibits strong robustness to perturbations and achieves high success rates on the real robot with as few as 6,000 online interactions, offering a simple yet powerful solution for complex multisensory robotic control. Website: https://msdp-pearl.github.io/

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

DisjunctiveNet: Neural Symbolic Learning via Differentiable Convexified Optimization Layers

arXiv:2605.30456v2 Announce Type: replace Abstract: Many learning tasks in science and engineering are characterized by sparse datasets, which limits the effectiveness of purely data-driven approaches. At the same time, these problems are often accompanied by rich domain knowledge derived from physical laws, operational requirements, and expert heuristics. Such knowledge is frequently expressed as rules involving logical propositions and linear inequalities. Existing neuro-symbolic methods typically enforce these rules approximately through soft penalties, assume input-independent rules when designing specialized architectures, or rely on non-differentiable post-processing at inference time to achieve hard constraint satisfaction. While recent advances in differentiable optimization layers enable end-to-end feasibility enforcement within neural networks, extending these approaches to logical or mixed-integer rules remains challenging due to inherent nonconvexity. In this work, we propose a unified end-to-end framework for enforcing hard, input-dependent mixed integer linear constraints within neural networks. Our approach represents rules as disjunctive constraints and applies hierarchical convex relaxations to obtain convex hull formulations. These relaxations yield tractable linear constraints that can be embedded as differentiable optimization layers while enabling exact rule satisfaction. We demonstrate the effectiveness of the proposed framework on real-world datasets, achieving perfect rule satisfaction and strong predictive performance.

22.
bioRxiv (Bioinfo) 2026-06-11

DModE: An end-to-end framework for Differential Modification and Expression Analysis of Nanopore direct RNA sequencing data

Summary: Nanopore direct RNA sequencing (DRS) enables simultaneous quantification of transcript abundance and RNA modifications from native RNA molecules, providing a unique opportunity to study transcriptional and epitranscriptomic regulation within a single experiment. However, comprehensive analysis of DRS data remains challenging, as existing workflows typically focus on individual processing steps and often require manual integration of multiple software packages for expression analysis, modification detection, statistical testing, and visualization. Furthermore, integrated differential expression and differential RNA modification analysis at both gene and isoform resolution remains poorly supported by current workflows. Here, we present DModE (Differential Modification and Expression Analysis), an end-to-end framework for integrated analysis of Nanopore DRS data. DModE combines an Epi2ME-compatible Nextflow preprocessing workflow with a dedicated Python package for downstream statistical analysis, visualization, and reporting. The framework supports differential gene and isoform expression analysis, differential RNA modification analysis at genome and transcript level, metagene profiling, exploratory epitranscriptomic analyses, and integrated assessment of relationships between expression and modification dynamics. Results are automatically summarized in interactive HTML reports, facilitating reproducible and accessible data interpretation. By integrating transcriptomic and epitranscriptomic analyses within a single framework, DModE substantially simplifies comprehensive DRS data analysis and lowers the barrier for studying RNA modification biology using Nanopore sequencing.

23.
arXiv (CS.AI) 2026-06-12

CausalMoE: A Billion-Scale Multimodal Foundation Model for Granger Causal Discovery with Pattern-Routed Heterogeneous Experts

arXiv:2606.13024v1 Announce Type: cross Abstract: Granger Causal Discovery (GCD) is fundamental for analyzing temporal dependencies in complex systems. However, existing neural GCD methods predominantly rely on a "one-size-fits-all" paradigm, struggling to capture distribution shifts and dynamic regime changes inherent in real-world time series. This often leads to entangled representations and spurious causal graphs. In this paper, we propose CausalMoE, a billion-scale multimodal Granger causal foundation model that explicitly models patch-level heterogeneity. CausalMoE introduces a Pattern-Routed Mixture of Heterogeneous Experts, which dynamically identifies latent temporal patterns and routes patches to specialized domain experts, effectively decoupling regime-specific mechanisms from shared dynamics. To ensure interpretable graph recovery, we design a Causality-Aware Self-Attention mechanism operating across variables, yielding sparse Granger causal graphs via proximal optimization. Furthermore, CausalMoE is the first to integrate LLMs and VLMs to align numerical signals with textual and visual priors, regularizing causal estimation in complex scenarios. Extensive experiments demonstrate that CausalMoE establishes a new state-of-the-art on fully supervised benchmarks, while effectively generalizing to few-shot settings where traditional methods fail.

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

HypOProto: Hyperbolic Ordinal Prototypes for Left Ventricular Filling Pressure Classification

Echocardiography (echo) is a widely used imaging modality for assessing cardiac function, with Left Ventricular Filling Pressure (LVFP) serving as a critical physiological marker for conditions such as heart failure. Standard LVFP classification into normal vs elevated categories relies on the Doppler-derived $E/e'$ ratio, which is operator-dependent and often unavailable in resource-limited settings, motivating methods that infer LVFP directly from B-mode echo. Existing deep learning approaches achieve high performance but remain largely black-box, limiting clinical interpretability. We propose HypOProto, a hyperbolic, ordinal prototype-based framework for interpretable LVFP classification using a frozen, explainable foundation model backbone. HypOProto arranges prototypes along the physiological $E/e'$ scale, placing borderline cases near the hyperboloid root where small angular differences separate similar cases, while normal and elevated cases occupy outward positions reflecting increasing diagnostic certainty. This hyperbolic geometry encodes clinically meaningful ordinal relationships and improves interpretability. We also introduce a novel Hyperbolic Prototype Angular Separation (HyperPAS) loss, enforcing inter-class prototype separation in hyperbolic space. HypOProto achieves SOTA performance while maintaining transparency, and highlights clinically relevant regions in visualizations. This work represents the first prototype-based framework for LVFP classification in echo. Our code can be found at https://github.com/DeepRCL/HypOProto.

25.
medRxiv (Medicine) 2026-06-17

Womens intentions and motivations towards health behaviour change before pregnancy: a cross-sectional survey of pregnant women in Australia

Introduction: The preconception period (i.e. the weeks and months before pregnancy) is a critical window during which parental health behaviours can influence pregnancy outcomes and the childs long-term health. Modifiable factors such as nutrition, physical activity, substance use, and environmental exposures play a key role, yet womens ability to adopt and sustain healthy behaviours is shaped by complex psychological, social and environmental influences. This study applies the Theory of Planned Behaviour to identify the beliefs underpinning womens preconception behaviours, with the aim of informing support for effective and sustained health behaviour change. Methods: An Australian national retrospective cross-sectional survey of pregnant women (18-49 years), recruited through social media platforms. The 92-item survey captured respondent socio-demographics, pregnancy status and health conditions, health behaviours, and beliefs regarding preconception health behaviours. Respondents level of pregnancy planning was categorised using the London Measure of Unplanned Pregnancy (LMUP). Items regarding preconception beliefs were structured in accordance with the Theory of Planned Behaviour, with a focus on regular exercise, healthy diet, and alcohol avoidance. These beliefs variables were analysed using structured equation modelling to identify paths between latent variables and the items used to estimate each concept. Results: The study was completed by 430 pregnant women of whom 72.7% had a planned pregnancy. Most had a partner, were university educated and in good health. Structural equation modelling showed intention strongly predicted exercise ({beta}=0.65), healthy diet ({beta}=0.54) and alcohol avoidance ({beta}=0.64). Perceived control and partner norms influenced intentions, whereas health professional norms had limited effect. Positive beliefs were associated with folate supplement use and smoking cessation. Conclusion: These findings highlight intention as a key driver of preconception health behaviours, with perceived control and partner influences playing a more significant role than individual beliefs or health professional input. Effective interventions should therefore address structural barriers and actively involve partners, while respecting womens autonomy. Overall, couples-focused, multi-level strategies are likely essential to support meaningful and sustained preconception health behaviour change.