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

PMOF: A Dataset and Benchmark for Passenger Monitoring Using Overhead Fisheye Cameras

Autonomous staff-free public transport requires reliable in-vehicle passenger monitoring. However, perception inside moving vehicles is challenged by confined spaces, variable illumination, motion-induced background variation, occlusion, and limited viewpoints. To mitigate these spatial constraints, ceiling-mounted fisheye cameras provide full-scene coverage from a single viewpoint. Yet existing public overhead fisheye datasets are recorded in static environments and do not capture the domain shift introduced by vehicle motion. To fill this gap, we introduce PMOF, Passenger Monitoring using Overhead Fisheye cameras, the first public dataset of top-view fisheye imagery captured inside a moving vehicle, comprising over 19k manually annotated frames. PMOF provides rotated bounding boxes, tracking identifiers, and action labels, supporting object detection, tracking, and action recognition. We benchmark PMOF using YOLO26m-obb models fine-tuned under multiple dataset configurations that combine PMOF with existing overhead fisheye datasets. Cross-domain fine-tuning with custom rotation-aware augmentation achieves 94.8% AP50 on PMOF and 96.5% AP50 on an unseen overhead fisheye dataset from a different domain. Our results highlight the domain gap between static and moving environments and show that incorporating PMOF improves detection performance and advances generalization beyond passenger monitoring to broader fisheye-based person detection tasks. The dataset and code are available at https://swermuth.github.io/pmof/.

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

Track2View: 4D-Consistent Camera-Controlled Video Generation via Paired 3D Point Tracks

Re-rendering an existing video from a novel camera viewpoint requires the output to follow the prescribed camera trajectory while preserving the appearance and dynamics of the original scene across every frame. Existing methods rely on per-frame pose embeddings, noisy point-cloud renderings, or implicit learned correspondences, none of which provides an explicit, temporally continuous link between source and target pixels. We propose Track2View, which conditions a video diffusion transformer on paired 3D point tracks: sparse trajectories of scene points projected into both the source and target camera views. These tracks provide explicit spatiotemporal correspondences that are temporally continuous by construction, encoding what content should appear where and when. At the core of Track2View is a dual-view track conditioner that transfers visual context from source to target view through parameter-free geometric operations and learned temporal aggregation, ensuring generalization to arbitrary camera trajectories without memorizing specific motions. We further introduce a data curation pipeline that extracts one-to-one track correspondences by running a 3D point tracker on temporally concatenated multi-camera view pairs. On a 400-video benchmark spanning static and dynamic scenes, Track2View achieves state-of-the-art results across visual quality, view synchronization, and camera accuracy, reducing rotation error by 30-65% and translation error by 61-72% relative to leading baselines. Project page is available at this https URL: https://qjizhi.github.io/track2view

03.
arXiv (quant-ph) 2026-06-12

Trading symmetry for Hilbert-space dimension in Bell-inequality violation

arXiv:2601.02893v3 Announce Type: replace Abstract: In quantum information, asymmetry, i.e., the lack of symmetry, is a resource allowing one to accomplish certain tasks that are otherwise impossible. Similarly, in a Bell test using any given Bell inequality, the maximum violation achievable using quantum strategies respecting or disregarding a certain symmetry can be different. In this work, we focus on the symmetry involved in the exchange of parties and explore when we have to trade this symmetry for a lower-dimensional quantum strategy in achieving the maximal violation of given Bell inequalities. For the family of symmetric Collins-Gisin-Linden-Massar-Popescu inequalities, we provide evidence showing that there is no such trade-off. However, for several other Bell inequalities with a small number of dichotomic measurement settings, we show that symmetric quantum strategies in the minimal Hilbert space dimension can only lead to a suboptimal Bell violation. In other words, there exist symmetric Bell inequalities that can only be maximally violated by asymmetric quantum strategies of minimal dimension. In contrast, one can also find examples of asymmetric Bell inequalities that are maximally violated by symmetric correlations. The implications of these findings on the geometry of the set of quantum correlations and the possibility of performing self-testing therefrom are briefly discussed.

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

ForceForget: Reinforcement Concept Removal for Enhancing Safety in Text-to-Image Models

With the advance of generative AI, the text-to-image (T2I) model has the ability to generate various contents. However, T2I models still can generate unsafe contents. To alleviate this issue, various concept erasing methods are proposed. However, existing methods tend to excessively erase unsafe concepts and suppress benign concepts contained in harmful prompts, which can negatively affect model utility. In this paper, we focus on eliminating unsafe content while maintaining model capability in safe semantic meaning interpretation by optimizing the concept erasing reward (CER) with reinforcement learning. To avoid overly content erasure, we introduce the Safe Adapter to project partial text embedding for efficient concept regulation in cross-attention layers. Extensive experiments conducted on different datasets demonstrate the effectiveness of the proposed method in alleviating unsafe content generation while preserving the high fidelity of benign images compared with existing state-of-the-art (SOTA) concept erasing methods. In terms of robustness, our method outperforms counterparts against red-teaming tools. Moreover, we showcase the proposed approach is more effective in emerging image-to-image (I2I) scenarios compared with others. Lastly, we extend our method to erase general concepts, such as artistic styles and objects. Disclaimer: This paper includes discussions of sexually explicit content that may be offensive to certain readers. All images used in this work are synthesized or from public datasets.

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

Evidence of an Emergent "Self" in Continual Robot Learning

arXiv:2603.24350v3 Announce Type: replace-cross Abstract: A key challenge to understanding self-awareness has been a principled way of quantifying whether an intelligent system has a concept of a "self", and if so how to differentiate the "self" from other cognitive structures. We propose that the "self" can be isolated by seeking the invariant portion of cognitive process that changes relatively little compared to more rapidly acquired cognitive skills - because our self is the most persistent aspect of our experiences. We used this principle to analyze the cognitive structure of robots under two conditions: One robot learns a constant task, while a second undergoes continual learning under variable tasks. We find that robots subjected to continual learning develop an invariant subnetwork that is significantly more stable (p < 0.001) compared to the control, and that this subnetwork is also functionally important: preserving it aids adaptation while damaging it impairs performance. We validate this pattern across three different robots spanning locomotion and manipulation.

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

Side-Channel Attacks Bypass Protection in 3D Printers

arXiv:2606.13952v1 Announce Type: cross Abstract: Active Motor Noise Cancellation (AMNC) ships in commercial fused deposition modeling (FDM) 3D printers as a hardware countermeasure against acoustic side-channel attacks that target intellectual property (IP). We present the first empirical evaluation of a deployed AMNC countermeasure, using a public dataset of synchronized acoustic and vibration recordings from two AMNC-equipped Bambu Lab printers across 12 object classes. AMNC fully neutralizes the acoustic channel: classification accuracy is indistinguishable from the 8.33% random baseline. The vibration channel, which AMNC does not target, still leaks. With summary statistics the leak is coarse and amplitude-driven (vibration accuracy approximately 31% pooled, 36-47% within-printer), while the waveform shape carries essentially nothing (frequency-only features at chance). A full-sequence temporal model that ingests the ordered evolution of the print raises accuracy to approximately 61%, and an order-shuffling control (approximately 33%) shows that a substantial component is genuinely sequential and tied to print progression. The leak is device-specific: a classifier trained on one printer transfers near chance to the other. We conclude that AMNC is an acoustic-only defense: vibration remains a partial, geometry-correlated side channel it does not address, but one that does not, on this dataset, support full geometric reconstruction; reconstruction-grade attacks would require the magnetic or power channels AMNC also leaves untouched. We release all code.

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

Recurrent Reasoning on Symbolic Puzzles with Sequence Models

arXiv:2606.15686v1 Announce Type: new Abstract: Large language models often appear strong on symbolic and algorithmic tasks, yet this apparent strength can hide brittle behaviour when problems become longer, harder, or slightly out of distribution. A major limitation of current reasoning benchmarks is that many primarily test whether a model can produce a valid answer, while paying less attention to whether the solution is minimal, robust, and stable under controlled difficulty scaling. We introduce RecurrReason, a difficulty-controlled benchmark of four recurrent logic puzzles (Tower of Hanoi, River Crossing, Block World, and Checkers Jumping) with BFS-optimal trajectories and a single interpretable difficulty parameter $N \in \{1,\dots,10\}$, totalling 10{,}817 unique puzzles and 285{,}933 moves. We benchmark two Transformer families, an encoder-decoder model (T5-style) and a decoder-only model (GPT-2-style), under consistent data splits and evaluation criteria, training on $N{=}1$ to $7$ and evaluating on both held-out in-distribution instances and harder out-of-distribution instances at $N{=}8$ to $10$. Fine-tuned pre-trained T5 achieves 97.27\% validation and 81.00\% OOD accuracy on Block World; all models score 0.00\% on River Crossing under all conditions. Failure mode analysis reveals that architecture is a stronger determinant of success than scale. Pre-training transfers only to puzzles with locally structured transition functions. Our code and dataset will be open-sourced upon acceptance.

08.
arXiv (CS.LG) 2026-06-17

SpatioTemporal Causal Network Diagnostics for Geographic Tipping Point Early Warning

arXiv:2606.17553v1 Announce Type: new Abstract: Geographic tipping points in ecosystems, climate subsystems, or ice sheets pose severe challenges for localized early warning. Classical spatial indicators such as Moran's I summarize global spatial structure, but they struggle with three issues: spatial dilution, Euclidean assumptions, and correlated noise. This paper introduces SpatioTemporal Causal Network Diagnostics (ST-CND), a framework that addresses these three issues by representing the geographic field as a time-evolving directed causal network. The core workflow is as follows: (1) infer which spatial nodes help predict other nodes via transfer entropy, replacing fixed Euclidean neighborhoods with data-driven information-flow topology; (2) estimate local recovery rates within each candidate subnetwork via dynamic mode decomposition; and (3) identify the most vulnerable subnetwork by combining three signals, namely high internal fluctuation, high internal synchronization, and low external coupling, thereby suppressing false alarms from spatially correlated noise. Validated on synthetic bifurcations and two observational sea-surface temperature benchmarks, namely Indo-Pacific SST and North Atlantic AMOC, ST-CND delivers localized and interpretable warnings. On the AMOC task, it achieves an AUROC of 0.783 and a critical-subnetwork IoU of 0.378, outperforming recurrence-network and lambda-AR1 baselines. The framework provides an interpretable and scalable pipeline for spatial early warning in Earth system science.

09.
arXiv (CS.AI) 2026-06-15

Optimizing Agentic Reasoning with Retrieval via Synthetic Semantic Information Gain Reward

arXiv:2602.00845v3 Announce Type: replace Abstract: Agentic reasoning enables large reasoning models (LRMs) to dynamically acquire external knowledge, but yet optimizing the retrieval process remains challenging due to the lack of dense, principled reward signals. In this paper, we introduce InfoReasoner, a unified framework that incentivizes effective information seeking via a synthetic semantic information gain reward. Theoretically, we redefine information gain as uncertainty reduction over the model's belief states, establishing guarantees, including non-negativity, telescoping additivity, and channel monotonicity. Practically, to enable scalable optimization without manual retrieval annotations, we propose an output-aware intrinsic estimator that computes information gain directly from the model's output distributions using semantic clustering via bidirectional textual entailment. This intrinsic reward guides the policy to maximize epistemic progress, enabling efficient training via Group Relative Policy Optimization (GRPO). Experiments across seven question-answering benchmarks demonstrate that InfoReasoner consistently outperforms strong retrieval-augmented baselines, achieving up to 5.4% average accuracy improvement. Our work provides a theoretically grounded and scalable path toward agentic reasoning with retrieval. The code is available at https://github.com/dl-m9/InfoReasoner

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

An Improved Generative Adversarial Network for Micro-Resistivity Imaging Logging Restoration

An improved GAN-based imaging logging image restoration method is presented in this paper for solving the problem of partially missing micro-resistivity imaging logging images. The method uses FCN as the generative network infrastructure and adds a depth-separable convolutional residual block to learn and retain more effective pixel and semantic information; an Inception module is added to increase the multi-scale perceptual field of the network and reduce the number of parameters in the network; and a multi-scale feature extraction module and a spatial attention residual block are added to combine the channel attention. The multi-scale module adds a multi-scale feature extraction module and a spatial attention residual block, which combine the channel attention mechanism and the residual block to achieve multi-scale feature extraction. The global discriminative network and the local discriminative network are designed to gradually improve the content and semantic structure coherence between the restored parts and the whole image by playing off each other and the generative network. According to the experimental results, the average structural similarity measure of the five sets of imaged logging images with different sizes of missing regions in the test set is 0.903, which is an improvement of about 0.3 compared with other similar methods. It is shown that the method in this study can be used for the restoration of micro-resistivity imaging log images with good improvement in semantic structural coherence and texture details, thus providing a new deep learning method to ensure the smooth advancement of the subsequent interpretation of micro-resistivity imaging log images.

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

Recover Semantics First, Generate Better: Improved Latent Modeling for 3D MRI Reconstruction and Cross-Contrast Synthesis

Multi-contrast magnetic resonance imaging (MRI) provides complementary information for clinical diagnosis. However, acquiring all MRI sequences is often time-consuming and costly. Recent generative models perform cross-contrast synthesis to address this issue by inferring absent contrasts from the available ones. Nevertheless, synthesizing 3D MRI presents significant challenges. Due to the massive volume sizes, operating directly in the pixel space is computationally prohibitive; therefore, a common approach is to first compress the 3D volumes into a latent space and subsequently train generative models in that space. We observe that existing compression architectures face several critical issues: they under-preserve long-range anatomical coherence, discard clinically meaningful semantics, and rely on optimization objectives that lead to over-smoothed reconstructions. Ultimately, these shortcomings compromise the performance of subsequent generative models. In this work, we propose a semantics-first latent modeling framework for 3D MRI reconstruction and cross-contrast synthesis. Specifically, we introduce a Latent Harmonization Encoder (LHE) to capture global anatomical dependencies, ensuring coherent volumetric representations. To mitigate semantic degradation during latent compression, we further design a Semantic Recovery Block (SRB) that injects high-level priors from a self-supervised semantic teacher, enhancing contrast-aware separability in the latent space. Additionally, we propose an Anatomy-aware Frequency Loss (AFL) to adaptively preserve diagnostically relevant high-frequency structures. Extensive experiments on two public multi-contrast MRI datasets demonstrate consistent improvements in reconstruction fidelity and cross-contrast synthesis quality. Our code is available at https://github.com/script-Yang/RSF.

12.
arXiv (CS.LG) 2026-06-19

Flow Matching for Efficient and Scalable Data Assimilation

arXiv:2508.13313v4 Announce Type: replace-cross Abstract: Data assimilation (DA) estimates a dynamical system's state from noisy observations. Recent generative models like the ensemble score filter (EnSF) improve DA in high-dimensional nonlinear settings but are computationally expensive. We introduce the ensemble flow filter (EnFF), a training-free, flow matching (FM)-based framework that accelerates sampling and offers flexibility in flow design. EnFF uses Monte Carlo estimators for the marginal flow field, localized guidance for observation assimilation, and utilizes a novel flow path that exploits the Bayesian DA formulation. It generalizes classical filters such as the bootstrap particle filter and ensemble Kalman filter. Experiments on high-dimensional benchmarks demonstrate EnFF's improved cost-accuracy tradeoffs and scalability, highlighting FM's potential for efficient, scalable DA. Code is available at https://github.com/Utah-Math-Data-Science/Data-Assimilation-Flow-Matching.

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

Testing For Distribution Shifts with Conditional Conformal Test Martingales

arXiv:2602.13848v2 Announce Type: replace Abstract: We propose a sequential test for detecting arbitrary distribution shifts that allows conformal test martingales (CTMs) to work under a fixed, reference-conditional setting. Existing CTM detectors construct test martingales by continually growing a reference set with each incoming sample, using it to assess how atypical the new sample is relative to past observations. While this design yields anytime-valid type-I error control, it suffers from test-time contamination: after a change, post-shift observations enter the reference set and dilute the evidence for distribution shift, increasing detection delay and reducing power. In contrast, our method avoids contamination by design by comparing each new sample to a fixed null reference dataset. Our main technical contribution is a robust martingale construction that remains valid conditional on the null reference data, achieved by explicitly accounting for the estimation error in the reference distribution induced by the finite reference set. This yields anytime-valid type-I error control together with guarantees of asymptotic power one and bounded expected detection delay. Empirically, our method detects shifts faster than standard CTMs, providing a powerful and reliable distribution-shift detector.

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

Gaze Heads: How VLMs Look at What They Describe

How a vision-language model internally solves the task of describing an image is far from obvious. We find that the model develops a specific mechanism for this: a small set of attention heads in its language-model backbone, which we call gaze heads, whose attention tracks the image region the model is currently describing. We find them with a simple correlation score from a few forward passes, using comic strips as a controlled testbed where narrative order is laid out spatially. These gaze heads do not just track the image tokens being described: redirecting their attention to a chosen region forces the VLM to describe that region instead. A single attention-mask intervention on the top-100 gaze heads, fewer than 9% of all heads, steers the model's answer to any chosen comic panel at 83.1% accuracy, while the same intervention on random heads fails to redirect the answer, and intervening on all heads destroys generation. The same lever also extends to continuous control: switching the gaze target mid-generation makes the model wrap up its current panel description and move to the new one within a few tokens. Beyond comics, the same intervention redirects answers to chosen regions in natural COCO images. The mechanism further recurs across model sizes from 2B to 32B parameters and across other VLM architectures, although some frozen-encoder families show no comparable head set. More broadly, this shows that targeted edits identified through mechanistic analysis can serve as practical inference-time levers for steering multimodal model behavior, without any retraining. Our code, interactive demo, and datasets are available at https://gaze.baulab.info/

15.
arXiv (CS.CV) 2026-06-11

FitVTON: Fit-aware Virtual Try-On via Body-Garment Size Control

While diffusion-based virtual try-on has achieved impressive visual realism, most methods treat the task as 2D inpainting, prioritizing texture preservation over physical plausibility. Consequently, they often produce plausible-looking images that fail to reflect authentic garment fit across diverse body shapes. We present FitVTON, a Fit-aware virtual try-on model on different bodies in the wild. FitVTON encodes garment-body size through structured text prompts, and learn from simulated try-on triplets from parameterized garment model. To improve the fitting effects over garment silhouettes, we introduce two auxiliary head to predict the masks for both the garment and the exposed body. We further introduce a texture rectification stage to improve realistic appearance from simulated data. To evaluate the fitting fidelity, we curate a real-world dataset, FittingEffect3K, combining VLM-based scoring protocol. Both subjective and quantitive experiments show that FitVTON demonstrate authentic fitting fidelity, with significant sizing accuracy and shape preservation over state-of-the-art methods while maintaining competitive image quality. Project Page: https://zenoning.github.io/FitVTON/.

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

The Critical Role of Model Selection in Causal Inference: A Comparative Analysis of Classification Models within the InferBERT Framework for Pharmacovigilance

Distinguishing causal adverse drug events (ADEs) from spurious correlations remains a central challenge in pharmacovigilance. The InferBERT framework integrates transformer models with Do-calculus, but its success hinges on the underlying classification model. This study evaluates the impact of model choice in InferBERT, assessing whether simpler models suffice, if domain-specific pre-training helps, whether scaling to LLMs improves causal detection, and the effect of post-hoc calibration. We performed a comparative study on two benchmarks: Analgesics-induced Acute Liver Failure (AILF) and Tramadol-related Mortalities (TRAM). Four models were evaluated-XGBoost (baseline), ALBERT (original InferBERT), BioBERT (biomedical transformer), and Med-LLaMA (medical LLM)-using 5-fold cross-validation repeated over 20 runs. We measured accuracy, Expected Calibration Error (ECE) pre- and post-isotonic regression, and Jaccard concordance of causal terms with PRR, ROR, and EBGM; significance was tested with paired t-tests. BioBERT achieved the highest accuracy on both datasets, while Med-LLaMA underperformed despite its size and parameter-efficient fine-tuning. Domain-specific pre-training was decisive. Calibration improved ECE but had mixed effects on accuracy and causal discovery. BioBERT's superiority also yielded the strongest concordance with traditional pharmacovigilance signals. These results show that domain-specific pre-training provides a clear advantage over simpler baselines and larger LLMs. Investing in manageable, domain-aware models is more effective for computational pharmacovigilance than simply scaling model size.

18.
arXiv (CS.CV) 2026-06-11

Semantically-Aware Diver Activity Recognition Framework for Effective Underwater Multi-Human-Robot Collaboration

Effective multi-human-robot collaboration is essential for expanding human-led operations in the challenging and high-risk underwater environment. For autonomous underwater vehicles (AUVs) to become true teammates, they must be able to comprehend their surroundings and recognize a diver's activities to offer assistance and ensure safety. Towards this goal, we introduce DAR-Net, a novel transformer-based framework that analyzes complex underwater scenes to classify diver activities. Our contribution lies in a semantically guided learning formulation that couples transformer-based temporal reasoning with pixel-level scene supervision. This multi-loss training strategy explicitly aligns global activity recognition with local human-robot interaction semantics, which is particularly critical in low-visibility underwater conditions. To address the significant challenge of data scarcity in this domain, we present the first-ever Underwater Diver Activity (UDA) dataset, a foundational resource containing over 2,600 annotated images with pixel-level masks. Through rigorous experimental evaluations in a controlled environment, we demonstrate that DAR-Net achieves promising accuracy in recognizing six distinct diver activities, outperforming state-of-the-art models. While this dataset provides a crucial baseline, our work serves as a pioneering step, laying the groundwork for future research and facilitating the development of more intelligent, collaborative underwater robotic systems.

19.
arXiv (CS.AI) 2026-06-16

STRIDE: Strategic Trajectory Reasoning via Discriminative Estimation for Verifiable Reinforcement Learning

arXiv:2606.15866v1 Announce Type: new Abstract: Reinforcement Learning with Verifiable Rewards (RLVR) has become an effective post-training paradigm for improving the reasoning abilities of large language models. However, existing RLVR methods typically rely on final-answer correctness to assign trajectory-level rewards, providing sparse supervision and treating all tokens uniformly regardless of their actual contribution to reasoning. Although recent studies introduce intermediate signals such as process rewards, high-entropy tokens, and semantic uncertainty, these signals are often not inherently verifiable and may fail to distinguish beneficial strategic patterns from harmful ones. To address this limitation, we propose STRIDE (Strategic Trajectory Reasoning with Discriminative Estimation), a fine-grained RLVR framework that derives strategic reasoning supervision from verifiable outcomes. STRIDE contrasts successful and failed trajectories within each response group to estimate the outcome-discriminative preference of each $n$-gram strategic pattern, and further combines this signal with reasoning saliency entropy to identify decision-relevant strategic patterns. These patterns are assigned differentiated advantage values during RL optimization, enabling more precise credit assignment while preserving the verifiability of RLVR. Extensive experiments demonstrate that STRIDE consistently improves reasoning performance across diverse models, tasks, and extended settings, including VLMs and agent-based systems.

20.
bioRxiv (Bioinfo) 2026-06-17

MetaHarmonizer: robust biomedical metadata harmonization and a contamination control for inflated LLM performance on public benchmarks

Public biomedical repositories hold substantial reuse potential, but inconsistent metadata routinely blocks integration across studies. Recent LLM-based harmonization approaches address scale but suffer from non-determinism, hallucinated ontology terms, and, in their highest-accuracy configurations, dependence on proprietary APIs or labeled fine-tuning data. A more fundamental concern is that LLM accuracies on widely-used public benchmarks may substantially inflate transferable capability: under a contamination-controlled evaluation protocol we developed, the apparent LLM-only advantage on the GDC schema-mapping benchmark is inverted, and three out of five LLMs recover 80 -100% of GDC identifiers from zero-schema context, suggesting direct memorization. Building on this insight, we present MetaHarmonizer, an automated metadata harmonization system designed to be robust by construction: SchemaMapper aligns attribute names across schemas, and OntologyMapper standardizes values to controlled vocabularies. Both modules implement a multi-stage cascade that escalates to more resource-intensive methods only when earlier stages fall short, with all candidates grounded in pre-defined controlled vocabularies to preclude hallucinated outputs and LLMs used only as bounded preprocessing components rather than inference-time dependencies. On the GDC schema-matching benchmark, SchemaMapper with the deployment-optimized LLM-generated alias dictionary achieved 71.6% Top-1 accuracy and the higher Recall@GT than Magneto bipartite variants, recovering significantly more ground-truth mappings; with the best performing alias dictionary, it reached the highest Top-1/Top-5/Recall@GT, and also matched the best Magneto reranker (fine-tuned LLM-reranker) on MRR; and it also outperforms LLM-only performance under contamination-controlled conditions. On four EFO benchmarks, OntologyMapper achieved 77.9 - 95.5% Top-1 accuracy, outperforming text2term by up to 16.4 pp and direct LLM inference (against the smaller corpus) by 19.2 pp because memorization is not a viable shortcut for this task. Across both modules, calibrated confidence scores separate correct from incorrect predictions (AUC 0.73 - 0.94), enabling principled human-in-the-loop triage. Inference is fully local, deterministic, and computationally efficient - seconds on schema mapping and under a minute for ontology mapping of up to ~7,000 terms against the pre-indexed 33,230-term corpus. Released as a Python package with a domain-agnostic architecture, MetaHarmonizer provides a scalable foundation for improving the FAIRness of biomedical data and enabling cross-study integration, alongside an evaluation methodology applicable to any LLM-augmented bioinformatics benchmark built on public benchmarks.

21.
medRxiv (Medicine) 2026-06-15

Non-Parametric Ancestry Adjustment for Polygenic Scores

Modern polygenic risk scores (PRS) exhibit shifts correlated with ancestry, leading to erroneous predictions for non-European individuals when models are trained on predominantly European cohorts. Such shifts arise from, among other factors, (1) algorithmic limitations in the ability of PRS model training to detect causal variants, rather than nearby variants with ancestry-dependent correlations to the causal one, (2) under-representation of alleles with higher prevalence in non-European populations in the association study training, and (3) gene-by-environment interactions where the environment is correlated with genetic ancestry. Current ancestry-adjustment methodologies often discretize individuals into population categories and apply a simple affine mapping to reduce these genetic ancestry biases. However, such approaches provide suboptimal adjustments, particularly for admixed individuals. In this work, we introduce a detailed theoretical characterization of ancestry-dependent biases and propose novel methods based on non-parametric neighborhood techniques that provide more accurate empirical results and admit statistical consistency guarantees. Extensive experiments using the UK Biobank demonstrate the effectiveness of the proposed methods.

22.
arXiv (math.PR) 2026-06-12

Branching-selection particle systems and inverse first passage problems

Authors:

arXiv:2606.13487v1 Announce Type: new Abstract: A generalised inverse first passage problem asks whether, given a probability measure $p$ on $[0,\infty]$, one can find a boundary $b:[0,\infty]\to \mathbb{R}$ such that the stopping time:\[\tau:=\inf\left\{t:\Lambda\int_0^t \omega(W_s-b(s))ds \geq U\right\}\] has distribution $p$, where $U\sim Exp(1)$, $\Lambda\in(0,\infty)$ and $\omega$ is a monotonic decreasing function. We construct a branching-selection particle system whose hydrodynamic limit is governed by a free boundary problem and connect this to the generalised inverse first passage problem. In the $N$-particle system, particles move as independent Brownian motions, branch at a prescribed rate, and are removed at a rate proportional to their location relative to a position $b^N(t)$ which is a function of the empirical distribution. We identify the limit of $b^N$ as the solution of the inverse first passage problem.

23.
medRxiv (Medicine) 2026-06-11

Corticospinal tract risk modifies motor recovery after minimally invasive surgery for intracerebral hemorrhage: a secondary analysis of MISTIE-III

Objective: Outcome after surgical hematoma evacuation for intracerebral hemorrhage (ICH) depends on hematoma location. As corticospinal tract (CST) integrity affects motor recovery after stroke, we hypothesized that CST integrity drives heterogeneity in surgical outcomes and investigated this in a secondary analysis of MISTIE-III participants. Methods: Risk of CST injury was categorized into four levels, based on the interaction between the CST, the hematoma, and perihematomal edema (PHE) on automatically segmented stability CT: no risk, PHE infiltration, hematoma infiltration, and complete interruption of the CST. Associations with outcome were tested using multivariable linear regression for motor National Institutes of Health Stroke Scale (NIHSS) at day 180 and ordinal regression for modified Rankin Scale (mRS) at day 365, introducing an interaction term between CST risk and treatment group. Results: Day 180 motor NIHSS was significantly lower for 'no risk' ({beta}:-3.77, [95% confidence interval [CI]: -5.8 to -1.70], p=0.0003) and 'PHE infiltration' ({beta}:-2.3, [95%CI: -3.5 to -1.1]; p=0.0002) vs. 'complete interruption'. Surgery was associated with lower Day 180 motor NIHSS in participants with hematoma infiltration ({beta}:-2.07, [95%CI: -3.8 to -0.4], p=0.016). Compared to complete interruption, 'no risk' (adjusted odds ratio [aOR]:0.27, [95%CI: 0.10 to 0.74], p=0.01) and 'PHE infiltration' (aOR:0.41, [95%CI: 0.23 to 0.74]; p=0.003) were associated with lower odds of unfavorable day 365 mRS. Surgery was associated with lower mRS in participants with no risk (aOR:0.23, [95%CI: 0.05 to 0.97, p=0.045). Interpretation: Increasing CST risk is associated with worse motor recovery (day 180) and disability (day 365). CST risk modifies the effect of the MISTIE-III procedure on motor recovery and disability.

24.
PLOS Medicine 2026-06-23

Parental body mass index and offspring childhood body size and eating behaviour: A structural equation modelling analysis in the Norwegian Mother, Father and Child Cohort Study

Authors:

by Tom A. Bond, Tom A. McAdams, Nicole M. Warrington, Laurie J. Hannigan, Espen Moen Eilertsen, Ziada Ayorech, Fartein A. Torvik, George Davey Smith, Deborah A. Lawlor, Eivind Ystrom, Alexandra Havdahl, David M. Evans Background The intergenerational transmission of obesity-related traits could propagate an accelerating cycle of obesity, if parental adiposity causally influences offspring adiposity. The extent to which intergenerational obesity associations are due to such causal effects, as opposed to genetic confounding (inheritance), is unclear. We aimed to establish whether associations between parental peri-pregnancy body mass index (BMI) and offspring birth weight (BW), BMI until 8 years of age, and 8-year-old eating behaviour are due to genetic confounding. Methods and findings Data were from the Norwegian Mother, Father and Child Cohort Study, a prospective population-based birth cohort born between 1999 and 2009 at 50 out of 52 hospital maternity units in Norway. We compared the strength of the associations of maternal pre-pregnancy BMI versus paternal BMI during pregnancy, with offspring outcomes including birth weight and BMI assessed between age 6 months and 8 years of age, and appetite-related eating behaviour traits assessed at age 8 years via the Child Eating Behaviour Questionnaire (CEBQ), adjusting for potential confounders including parity, parental/grandparental language group and parental age, smoking, education and income). We then used an extended children of twins structural equation model (SEM) to quantify the extent to which associations were due to genetic confounding. Up to 85,866 children (51.3% male) were included in linear regression models, whereas SEM models included up to 50,999 children. Maternal BMI was more strongly associated than paternal BMI with offspring BW, but the maternal-paternal difference decreased for offspring BMI after birth. Greater parental BMI was associated with obesity-related offspring eating behaviours. SEM results indicated that genetic confounding did not explain the association between parental BMI and offspring BW, but explained the majority of the association with offspring BMI from 6 months onwards. For 8-year BMI, genetic confounding explained 79% (95% CI [62, 95]; p = 1.9 × 10−12) of the covariance with maternal BMI and 94% (95% CI [72, 113]; p = 2.7 × 10−14) of the covariance with paternal BMI. Limitations of this study include selective recruitment and attrition, potential bias due to parental assortative mating, and that findings may not generalise beyond high-income country settings with high obesity prevalence. Conclusions We found strong evidence that parent–child BMI associations may primarily be due to genetic confounding. When considered alongside prior evidence, this finding may argue against a strong causal effect of maternal or paternal adiposity on childhood adiposity via intrauterine or periconceptional mechanisms.

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arXiv (CS.CV) 2026-06-16

NEXUS: Neural Energy Fields for Physically Consistent Contact-Rich 3D Object Dynamics

Physics-grounded video generation requires controllable 3D object dynamics that remain physically consistent under contact, deformation, and external forcing. Existing trajectory-based methods often model isolated physical effects, making it difficult to compose conservative and non-conservative dynamics in contact-rich 3D scenes. We present NEXUS, a neural energy-field framework for contact-rich 3D object dynamics. NEXUS represents each object as a structural graph and constructs dynamic object-object and object-environment contact graphs. Inspired by Hamiltonian Neural Networks, NEXUS formulates motion through scalar energy and dissipation terms rather than directly predicting states or accelerations. Conservative effects, including gravity and elastic deformation, are composed as additive energy terms, while non-conservative effects such as damping and impact-induced energy loss are modeled with learned Rayleigh-style dissipation. Forces are derived by differentiating the energy and dissipation functions and rolled out with a multi-substep semi-implicit integrator. Across controlled trajectory benchmarks, NEXUS improves long-horizon accuracy over representative learned and physics-structured dynamics baselines under varying mechanical properties and physical-effect compositions. We further show that NEXUS trajectories provide effective guidance for contact-rich video generation, improving physical plausibility while maintaining competitive visual quality.