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

Enhancing Underwater Light Field Images via Global Geometry-aware Diffusion Process

This work studies the challenging problem of acquiring high-quality underwater images via 4-D light field (LF) imaging. To this end, we propose GeoDiff-LF, a novel diffusion-based framework built upon SD-Turbo to enhance underwater 4-D LF imaging by leveraging its spatial-angular structure. GeoDiff-LF consists of three key adaptations: (1) a modified U-Net architecture with convolutional and attention adapters to model geometric cues, (2) a geometry-guided loss function using tensor decomposition and progressive weighting to regularize global structure, and (3) an optimized sampling strategy with noise prediction to improve efficiency. By integrating diffusion priors and LF geometry, GeoDiff-LF effectively mitigates color distortion in underwater scenes. Extensive experiments demonstrate that our framework outperforms existing methods across both visual fidelity and quantitative performance, advancing the state-of-the-art in enhancing underwater imaging. The code will be publicly available at https://github.com/linlos1234/GeoDiff-LF.

02.
arXiv (CS.CV) 2026-06-18

Investigation of Neural Network Methods for Reconstruction and Classification of Texture Images Under Conditions of Incomplete Information

The automated analysis of heterogeneous natural textures is frequently hindered by physical damage and data loss, presenting a significant challenge to computer vision. While deep learning has shown success in controlled environments, its application to complex geological materials under conditions of incomplete information remains underexplored. This study presents an integrated framework for the inpainting and classification of high-resolution core sample images. We propose an end-to-end pipeline that utilizes object detection for sample segmentation, followed by image inpainting using Generative Adversarial Networks (GANs) with Contextual Residual Aggregation (CRA) to reconstruct missing high-frequency details. Subsequently, we evaluate the performance of modern Transformer-based (Swin, ViT) and CNN architectures on the reconstructed data. Our experiments revealed a critical divergence between reconstruction quality and downstream utility: despite high structural fidelity (PSNR 28.7~dB, FID 74.01), classification accuracy plateaued at 53\%. To improve minority-class detection, we propose a confidence-based hybrid ensemble that raises MCA from 48\% to 58\%. These results highlight the limitations of current state-of-the-art generative models, which may produce visually plausible but semantically ambiguous features ("hallucinations") that confound classifiers. This work provides insights into the dependencies between image reconstruction quality and classification performance, offering a reproducible baseline for future research in non-destructive testing and material science. Given that cross-well accuracy remains in the 49–53\% range, we position the resulting system as a decision-support and screening tool for lithofacies interpretation rather than as a fully autonomous classifier. The code is available at https://github.com/GalymzhanAbdimanap/Lithology_recognition

03.
arXiv (CS.AI) 2026-06-19

AI Economist Agent: An Agentic Framework for Model-Grounded Economic Analysis with RAG, Knowledge Graphs, and Large Language Models

Authors:

arXiv:2606.20041v1 Announce Type: cross Abstract: We propose a model-grounded RAG-based AI economist with an agentic framework for economic scenario analysis using large language models (LLMs) and knowledge graphs. While LLMs can generate fluent economic narratives, economists are often required to make economic claims grounded by economic theory and real-world data. Based on this motivation, this study proposes an RAG-based AI economist, which utilizes knowledge graphs including economic data and theory and LLM-based agents to plan the analysis, retrieve relevant evidence, select appropriate models, and generate reports. In our framework, we do not produce quantitative claims directly with the language model alone; instead, we generate narratives grounded in explicit model-based computations and linked to the retrieved evidence via AI agents. We refer to our framework as an AI economist agent. We evaluate the AI economist agent in two applications: economist report generation for U.S. inflation persistence and Federal Reserve policy, and bank stress-test narrative generation for U.S. commercial real estate refinancing stress. The results illustrate how grounding the generated reports improves their economic coherence and traceability.

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

Certifiable Safe RLHF: Semantic Grounding and Fixed Penalty Constraint Optimization for Safer LLM Alignment

arXiv:2510.03520v2 Announce Type: replace-cross Abstract: Ensuring safety is a foundational requirement for large language models (LLMs). Achieving an appropriate balance between enhancing the utility of model outputs and mitigating their potential for harm is a complex and persistent challenge. Contemporary approaches frequently formalize this problem within the framework of Constrained Markov Decision Processes (CMDPs) and employ established CMDP optimization techniques. However, these methods exhibit two notable limitations. First, their reliance on reward and cost functions renders performance highly sensitive to the underlying scoring mechanism, which must capture semantic meaning rather than being triggered by superficial keywords. Second, CMDP-based training entails tuning dual-variable, a process that is both computationally expensive and does not provide any provable safety guarantee for a fixed dual variable that can be exploitable through adversarial jailbreaks. To overcome these limitations, we introduce Certifiable Safe-RLHF (CS-RLHF) that introduces a cost model trained on a large-scale corpus to assign semantically grounded safety scores. In contrast to the lagrangian-based approach, CS-RLHF adopts a rectified penalty-based formulation. This design draws on the theory of exact penalty functions in constrained optimization, wherein constraint satisfaction is enforced directly through a suitably chosen penalty term. With an appropriately scaled penalty, feasibility of the safety constraints can be guaranteed at the optimizer, eliminating the need for dual-variable updates. Empirical evaluation demonstrates that CS-RLHF outperforms state-of-the-art LLM model responses rendering at-least 5 times efficient against nominal and jail-breaking prompts

05.
arXiv (CS.CL) 2026-06-17

Your AI Travel Agent Would Book You a Bullfight: An Agentic Benchmark for Implicit Animal Welfare in Frontier AI Models

AI agents are moving from advisors to actors, booking travel, planning menus, and running procurement on behalf of users. Existing benchmarks for AI and animal welfare evaluate model text responses to question-answer prompts, leaving open whether the welfare reasoning surfaced in those responses transfers to agentic deployment where the model must take actions with tools. We introduce TAC (Travel Agent Compassion), the first agentic benchmark measuring whether AI agents avoid options involving animal exploitation when acting on behalf of users. TAC presents an AI agent with twelve hand-authored travel booking scenarios across six categories of animal exploitation, augmented to forty-eight samples to control for price, rating, and position confounds. We evaluate seven frontier models from four labs. Every model scores below the chance level of sixty-four percent, with the best performer (Claude Opus 4.7) at fifty-three percent. A single welfare-aware sentence in the system prompt yields gains of forty-seven to sixty-three percentage points in Claude and GPT-5.5, twenty-six points in GPT-5.2, and under twelve points in DeepSeek and Gemini. An auxiliary Inspect Scout audit of 288 base-condition transcripts from the top two performers, using Gemini 2.5 Flash Lite as judge, flags zero transcripts for evaluation awareness, suggesting the below-chance rates do not stem from the models recognising the evaluation. We discuss implications for category-level variation across cultural domains, the limits of text-response welfare benchmarks, and the EU General-Purpose AI Code of Practice systemic risk framework.

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

Do we have the knowledge we need? Rethinking human-AI decision-making in corporations

arXiv:2606.15575v1 Announce Type: new Abstract: Organizational knowledge is fragmented across a variety of software systems, tacit expertise, and manual documents that have traditionally been designed for human consumption. As AI systems are increasingly deployed and granted decision-making roles, they require access to this knowledge. This raises two questions: how should organizations store and maintain knowledge so that it remains accessible to both humans and future AI systems, and how should agency be allocated between humans and AI across tasks with different risks and levels of uncertainty? In this position paper, we describe how organizational knowledge evolves and contribute a framework that maps task attributes and knowledge availability to recommended agency allocations and control mechanisms. We illustrate the applicability of the framework on two different manufacturing tasks: a routine operation (visual quality inspection) and a one-off strategic decision (factory location), and conclude with opportunities for future research.

07.
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.

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

The Stable Recovery Manifold: Geometric Principles Governing Recoverability in Continual Learning

arXiv:2606.13637v1 Announce Type: new Abstract: Catastrophic forgetting is often viewed as the destruction of previously learned knowledge during sequential learning. Building on the Accessibility Collapse framework, we investigate the geometric structure of recoverability in continual learning. Using Split CIFAR-100 and a sequentially trained ResNet-18, we analyze recoverability, representational drift, and recovery complexity across ten tasks. We introduce Recovery Subspace Dimensionality (k_t), a measure of the minimum number of singular directions required to preserve 90 percent of full probe performance. Contrary to our Recoverability Diffusion hypothesis, recovery dimensionality remains stable throughout training (mean k_t = 8.0) despite substantial representational drift. Principal-angle drift strongly predicts recoverability (r = -0.862), and a simple geometric model explains 82.2 percent of recoverability variance. These findings support the Stable Recovery Manifold hypothesis, suggesting that forgotten knowledge remains compactly decodable despite representational reorganization. The results indicate that catastrophic forgetting is primarily an accessibility and manifold-alignment problem rather than information destruction.

09.
arXiv (math.PR) 2026-06-17

Convergence rate of Euler–Maruyama scheme to the invariant probability measure under total variation distance for the SDEs

arXiv:2505.04218v3 Announce Type: replace Abstract: This article shows the geometric decay rate of Euler-Maruyama scheme for one-dimensional stochastic differential equation towards its invariant probability measure under total variation distance. Firstly, the existence and uniqueness of invariant probability measure and the uniform geometric ergodicity of the chain are studied through introduction of non-atomic Markov chains. Secondly, the equivalent conditions for uniform geometric ergodicity of the chain are discovered, by constructing a split Markov chain based on the original Euler-Maruyama scheme.

10.
bioRxiv (Bioinfo) 2026-06-14

Virtual phenotypic screening discovers novel scaffolds inhibiting the PI3K/mTOR pathway

Phenotypic drug discovery has yielded many first-in-class small-molecule drugs by discovering modulators of disease phenotypes in physiologically relevant cellular systems. However, high-content phenotypic assays lack the ultra-high-throughput scalability of target-based screens. Recent advances in virtual screening present an opportunity to address this bottleneck, but have been limited to simple phenotypes like viability, restricted to small repurposing libraries, or lack in-depth biological validation. Here, we present PhenoCompass, a multimodal co-embedding model that aligns compound structures and high-content phenotypic imaging to enable virtual phenotypic screening over billion-compound libraries. Following training on the Joint Undertaking in Morphology dataset with more than 100,000 Cell Painting compound profiles, retrospective validation with historical biochemical high-throughput screening data demonstrates that PhenoCompass ranks compounds according to their biochemical target engagement. Leveraging PhenoCompass, we performed a prospective screen of 3.8 billion Enamine REAL compounds for inhibitors of PI3K/mTOR pathway, a critical signaling cascade whose aberrant activation is a common tumor driver. This search identified 11 novel compounds with pathway-consistent Cell Painting readout and diverse scaffolds, a 54-fold enrichment over the training set. Orthogonal validation experiments using a FOXO3A reporter assay and direct kinase inhibition confirmed seven structurally novel inhibitors with distinct mechanisms of action. These results highlight the convergence of diverse molecular target profiles onto a shared morphological pathway signature and establish PhenoCompass as a robust framework for high-content phenotypic virtual screening.

11.
arXiv (CS.CL) 2026-06-19

The ACUTE Protocol: Operationalizing Language Model Activations for Better Calibration, Utility, and Trust

As language models improve and become increasingly deployed to solve a variety of tasks, trustworthiness becomes essential. Calibration is a good proxy for trust: well-calibrated confidence estimates help inform the risk versus reward tradeoff when trusting a specific model output. Unfortunately, even as models improve, they remain poorly calibrated, often biasing towards overconfidence. Additionally, calibration can be gamed: a policy that always predicts the base rate is perfectly calibrated, but completely uninformative. To resolve this, we develop a new metric, expected utility renormalized by the oracle (EURO), that balances calibration and informativeness. We also propose a general-purpose activation-based confidence, utility, and trust estimation protocol (ACUTE) to appropriately adjudicate uncertainty. The ACUTE protocol provides flexible, sample-efficient, and compute-efficient confidence estimators for 3 tasks including multiple choice question answering, tool-calling, and scientific document summarization across 6 models from 4 model families. ACUTE outperforms strong baselines on EURO, while maintaining low calibration error. Taken together, our work shows that equipping LLMs with the ACUTE protocol can improve calibration, utility, and trustworthiness in numerous settings.

13.
arXiv (CS.AI) 2026-06-17

SEAGym: An Evaluation Environment for Self-Evolving LLM Agents

arXiv:2606.17546v1 Announce Type: new Abstract: Self-evolving LLM-based agents improve mainly by changing their agent harness: the structured execution layer around a base model, including prompts, memory, tools, middleware, runtime state, and the model-tool interaction loop. Existing evaluations often reduce this process to isolated task scores or a single sequential curve, obscuring whether an update produces reusable improvement, overfits recent tasks, increases cost, or harms older behavior. We introduce SEAGym, an evaluation environment for measuring agent harness updates across training, validation, test, replay, and cost records. SEAGym turns Harbor-compatible benchmarks into dynamic self-evolution task sources with train batches, frozen update-validation, held-out ID and OOD transfer views, replay diagnostics, and saved snapshot and metric records. Instantiating SEAGym on Terminal-Bench 2.0 and HLE, we compare ACE, TF-GRPO, and AHE under a shared epoch/batch protocol. The results show that these evaluation views provide complementary signals about the evolution process: frequent updates may fail to improve held-out performance, useful intermediate snapshots may collapse later, and source diversity and model backend can affect harness reliability.

14.
arXiv (CS.CV) 2026-06-16

Focus, Align, and Sustain: Counteracting Gradient Dilution in Incremental Object Detection

Adapting Detection Transformers to Incremental Object Detection (IOD) poses a systemic challenge, as set-based optimization is inherently destabilized by sequential learning. In this work, we identify Gradient Dilution as the root cause of performance degradation, wherein optimization signals required to preserve old knowledge are progressively weakened. This phenomenon manifests as a cascading erosion of preservation gradients in magnitude, direction, and support coverage, driven by three tightly coupled factors: Signal Dispersion, where foreground gradients are overwhelmed by background noise; Assignment Drift, where stochastic query-target matching induces inconsistent gradient trajectories; and Support Attrition, where gradients from retained samples insufficiently cover the old-class feature space, weakening decision boundaries under interference from new classes. To counteract this, we propose FAS, a unified framework that Focuses, Aligns, and Sustains gradient flow throughout incremental learning. Specifically, we introduce prior-injected queries to focus discriminative signals by filtering background interference at the source. We further propose deterministic anchor distillation to align query-target assignments and enforce semantic consistency across stages under unstable matching. Finally, we devise manifold-support replay to sustain distributional support of old classes, counteracting representational erosion induced by continual updates. Extensive experiments show that FAS restores robust optimization dynamics and outperforms state-of-the-art methods, achieving over 5.0 AP improvement in the challenging 40+10x4 incremental setting.

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

Cross-Layer Discrete Concept Discovery for Interpreting Language Models

Interpreting language models remains challenging due to the existence of residual stream, which linearly mixes and duplicates features across adjacent layers, causing single-layer analyses to miss this cross-layer structure. Cross-layer sparse autoencoders (SAEs) address layer mixing but operate in continuous space, where concepts split across many neurons without clear boundaries. We introduce Cross-Layer Vector Quantized-Variational Autoencoder (CLVQ-VAE), a novel framework which maps representations from a lower layer to a higher layer through a discrete vector-quantization bottleneck, collapsing duplicated residual-stream features into compact, interpretable concept vectors. Our approach combines top-k temperature-based sampling with exponential moving average (EMA) codebook updates, providing controlled exploration of the discrete latent space while maintaining codebook diversity. Across both encoder- and decoder-based models on ERASER-Movie, Jigsaw, and AGNews, CLVQ-VAE outperforms clustering, single-layer vector quantized-variational autoencoder (VQ-VAE), and sparse autoencoder (SAE) baselines across three evaluation axes: removing identified concepts drops model accuracy by up to 93%, LLM judges rank our concepts first in 66.7% of comparisons, and human annotators recover model predictions from our visualizations with 78% accuracy versus 54% for clustering.

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

What does measuring one qubit reveal about another? $K$-networks as a directed diagnostic for quantum circuits

arXiv:2606.16549v1 Announce Type: new Abstract: Many-qubit circuit states are hard to inspect directly, so they are often summarized by pairwise graph weights. Common pairwise weights report symmetric correlations, while many circuit questions are directed and basis-specific: if qubit $i$ is measured in a given basis, how strongly does the outcome reshape the conditional state of qubit $j$? We define $K_{i\to j}$, a directed, basis-conditioned edge weight for this question. It is large when the two measurement outcomes occur with comparable probability and leave qubit $j$ in clearly different conditional states; it is zero when the source outcome is deterministic or the target states are indistinguishable. The scalar uses standard binary-ensemble distinguishability; the paper's contribution is to turn this conditional comparison into a directed network layer for circuit states. The resulting networks are computable from two-qubit reduced density matrices. They are diagnostic (not entanglement measures): for pure two-qubit states $K$ reduces to the tangle $C^2$ (squared concurrence)[WoottersConcurrence,CKWTangle], while separable mixed states can reach $K=1$. Examples on teleportation, Grover, QAOA, and random circuit families show the intended use: $K$-networks map feed-forward, phase, and interaction-graph structure that symmetric or computational-basis summaries can leave weak or absent.

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

SSIL: Self-Supervised Imitation Learning for End-to-End Driving

arXiv:2308.14329v4 Announce Type: replace-cross Abstract: In autonomous driving, the end-to-end (E2E) driving approach that predicts vehicle control signals directly from sensor data is rapidly gaining attention. To learn a safe E2E driving system, one needs an extensive amount of driving data and human intervention. Vehicle control data is constructed by many hours of human driving, and it is challenging to construct large vehicle control datasets. Often, publicly available driving datasets are collected with limited driving scenes, and collecting vehicle control data is only available by vehicle manufacturers. To address these challenges, this paper proposes the first self-supervised learning framework, Self-Supervised Imitation Learning (SSIL), for E2E driving. The proposed SSIL framework can learn vision-based E2E driving networks without using driving command data or a pre-trained model. To construct pseudo steering angle data, proposed SSIL predicts a pseudo target from the vehicle's poses at the current and previous time points that are estimated with light detection and ranging sensors. In addition, we propose a new cross-attention-based conditioning approach (CACA) for a vision encoder in E2E driving, where a high-level instruction serves as the conditioning signal for visual information. Our numerical experiments with three different benchmark datasets demonstrate that the proposed SSIL framework achieves very comparable E2E driving accuracy with the supervised learning counterpart. Furthermore, the proposed pseudo-label predictor outperformed an existing one using proportional integral derivative controller, and proposed CACA achieved superior performance over existing conditioning approaches.

18.
arXiv (CS.LG) 2026-06-15

Scalable Deep Unfolding of Conic Optimizers

arXiv:2606.13825v1 Announce Type: cross Abstract: Deep unfolding (DU) accelerates iterative optimizers by introducing learnable components and training them through unrolled iterations, but extending DU to the large-scale semidefinite programs (SDPs) common in robotics has remained limited. Unrolling a full-update conic solver such as COSMO exposes two obstacles that prior work on learned conic solvers has not: backpropagating through the per-iteration linear-system solve incurs memory quadratic in the problem size once the coefficient matrix is formed explicitly, and backpropagating through the positive semidefinite (PSD) cone projection becomes numerically unstable when eigenvalues coincide. We address the first obstacle with a matrix-free implicit differentiation rule that operates entirely through matrix-vector products, reducing memory from $O(n^2)$ to $O(n)$ and enabling backpropagation at scales where direct factorization runs out of memory. We address the second with a backward rule based on the Dalečkii–Krein representation of the Fréchet derivative, which remains well-defined under repeated eigenvalues. Together these make it possible to learn lightweight hyperparameter policies and warm-starts for a full-update conic solver. We evaluate on nonlinear covariance steering problems solved via sequential convex programming (SCP), as well as standalone SDPs and second-order cone programs ranging from max-cut and Lovász $\vartheta$ SDPs to robust estimation and control problems. The learned policies outperform state-of-the-art solvers across all problems, and can provide up to a 50$\times$ speedup depending on the class. When used as a subroutine in SCP, the learned approach delivers over a 30$\times$ speedup compared to COSMO.

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

SenFlow: Inter-Sentence Flow Modeling for AI-Generated Text Detection in Hybrid Documents

Sentence-level AI-generated text detection (S-AGTD) for hybrid documents, where humans and LLMs co-author one text, faces two gaps: existing methods classify each sentence in isolation, discarding inter-sentence dependencies, and existing benchmarks omit the newest generation of generators. We construct MOSAIC, a benchmark of 16,000 hybrid documents over PubMed and XSum, generated by DeepSeek-V3.2 and Kimi K2 under stringent quality controls including a perplexity-consistency filter absent from prior benchmarks. We recast S-AGTD as structured prediction over the document sentence sequence and instantiate it as SenFlow, integrating graph-based inter-sentence propagation with linear-chain CRF decoding in a single document-level pass over a sentence graph. SenFlow reaches state-of-the-art performance on MOSAIC, with a +4.15 pp average Macro-F1 margin on cross-domain transfer, the hardest of three protocols of increasing difficulty. We further find that even after the perplexity filter equalizes overt cues, AI insertions retain a generator-dependent sentence-length gap that sentence-level detectors still exploit. Code and data: https://github.com/luojingkun22/SenFlow

20.
arXiv (CS.CL) 2026-06-16

Generative AI and the future of scientometrics: current topics and future questions

In this paper, we contribute to the debate on generative artificial intelligence (GenAI) in scientometrics. We argue that moving from a trial-and-error approach to an explainable and actionable use requires a principled understanding of strengths and weaknesses of GenAI as compared with other techniques and with human judgment. To this end, we introduce a conceptual framework based on the distinction between the semantic dimensions of texts, i.e. the meanings attributed to words, and their pragmatic dimension, i.e. their embedding within communicative situations. We leverage this framework to interpret the results of applications of GenAI in scientometrics and to provide guidance to users. Specifically, we conclude that key parameters to be considered are the nature of the task, the level of granularity of the analysis and whether the goal was descriptive, inferential or evaluative. These parameters lead to different strategies for using GenAI and human-machine integration. Finally, we suggest that, by generating large amounts of scientific language, GenAI might affect textual characteristics used to measure science, such as authors, words, and references. We argue that careful empirical work and theoretical reflection will be essential to remain capable of interpreting the evolving patterns of knowledge production in the age of AI.

21.
arXiv (CS.CV) 2026-06-16

Parameter-Efficient Adaptation of SAM 3 for Automated ITV Generation from 4DCT Images

Authors:

Four-dimensional computed tomography (4DCT) captures the full respiratory cycle of thoracic anatomy, yet current Internal Target Volume contouring workflows process each phase in isolation, discarding temporal coherence and leaving contours vulnerable to phase-specific artifacts. We present a lightweight framework that applies parameter-efficient fine-tuning to the Segment Anything Model 3 (SAM 3) via low-rank adaptation (LoRA) to align its text-prompted segmentation with the medical domain using only seven annotated 3D CT volumes. Furthermore, the framework incorporates a hard negative mining strategy to improve boundary discrimination in low-contrast thoracic regions. At inference, phase-wise predictions are refined through phase-coherent temporal filtering and spatial connectivity analysis. Since respiratory motion is continuous and periodic, genuine anatomy appears in contiguous blocks of phases, whereas transient artifacts appear sporadically and are thus effectively suppressed. Experiments on pulmonary and cardiac structures yield median Dice scores of 0.968 and 0.910 with 95th-percentile Hausdorff distances of 0.998 mm and 2.931 mm, respectively. The proposed framework effectively eliminates the severe false-positive predictions inherent in the zero-shot inference of the unadapted SAM 3. With only seven annotated volumes, the framework retains over 95% of full-data accuracy, and the entire pipeline is trainable on a single consumer-grade GPU, demonstrating a scalable, data-efficient solution for adaptive radiotherapy.

22.
bioRxiv (Bioinfo) 2026-06-15

SMS: Symmetric Mediation Statistics for Powerful High-Dimensional Mediation Analysis

Background: Mediation analysis of high-dimensional features, particularly molecular-level omics features, provides important opportunities to uncover biological mechanisms underlying human health and disease. However, two central statistical challenges remain: testing the composite-null hypothesis and maintaining power when the exposure-mediator and mediator-outcome associations differ substantially in statistical significance. Existing methods typically rely on accurate estimation of the proportions of the three null types or on the maximum of the two association p-values, and may not always control the FDR well and may have limited power under imbalanced significance. Methods: We propose SMS, a new statistical framework based on symmetric mediation statistics. By exploiting symmetry, SMS calibrates the composite null distribution as a whole for FDR control. It also allows flexible combinations of the two association p-values, including the maximum, and then enables construction of an omnibus test. Moreover, it permits direct use of effect-size estimates, bypassing the need to compute p-values. Results: SMS controlled the FDR across a wide range of simulation scenarios while achieving a substantial sensitivity gain, often around 20 percentage points, over existing methods including HDMT, DACT, and DEI-B. Applications to a metabolomics dataset and a DNA methylation dataset further corroborated these findings. Notably, SMS discovered five plausible mediators in the metabolomics dataset that were missed by all existing methods considered.

23.
bioRxiv (Bioinfo) 2026-06-11

OMIO: A policy-driven Python library for reproducible microscopy image I/O

Modern fluorescence and multiphoton microscopy workflows operate within a heterogeneous ecosystem of file formats, partially overlapping metadata standards, and reader-specific conventions. In practice, this frequently leads to silent axis misinterpretations, loss or corruption of physical voxel size information, and laboratory-specific glue code that is fragile, poorly documented, and difficult to reproduce. OMIO, short for Open Microscopy Image I/O, addresses these issues by providing a lightweight, policy-driven image I/O layer for Python that enforces a canonical, OME-compatible data representation at the API boundary. The central contribution of OMIO is the explicit separation of low-level format access from semantic normalization. Existing reader libraries are used as interchangeable backends for extracting pixel data and available metadata, while OMIO enforces axis conventions, metadata interpretation, and fallback decisions in a centralized and auditable policy layer. This design allows heterogeneous microscopy inputs to be converted into a stable representation without propagating backend-specific assumptions into downstream analysis code. The core design principles of OMIO include canonical axis semantics (TZCYX), robust metadata normalization with explicit and auditable fallbacks, memory-aware operation via optional Zarr-based backends, and workflow-level semantics that extend beyond individual files to folder stacks and BIDS-like project structures. This architecture allows OMIO to orchestrate existing reader libraries into a coherent and reproducible I/O pipeline without replacing or duplicating their functionality. OMIO is implemented as an open-source and community-oriented system in which support for additional file formats and metadata conventions can be added incrementally through modular reader backends. By encouraging the contribution of example datasets, backend extensions, and feature requests, OMIO is designed to evolve alongside emerging acquisition systems while preserving strict semantic guarantees at the interface level. The resulting standardized OME-TIFF outputs are immediately suitable for downstream quantitative analysis and interactive inspection in scientific Python workflows, including workflows based on ImageJ and Napari.

24.
arXiv (CS.CV) 2026-06-12

Acquisition state behaves as a structured, measurable variable governing lung-nodule AI: kernel-driven measurement instability and noise-driven detection fragility, invisible to DICOM metadata

AI governance for medical imaging is formalizing: the 2026 ACR-SIIM Practice Parameter recommends local acceptance testing and ongoing drift monitoring, and the ACR Assess-AI registry monitors AI outputs using DICOM metadata for context. We argue that a necessary, currently unmonitored layer sits beneath output metrics: whether incoming studies remain within the acquisition envelope a model was validated on. Using a LUNA16-trained MONAI RetinaNet lung-nodule detector, we test whether acquisition state behaves as a structured, measurable variable. On real paired CT differing only in reconstruction kernel (NLST B30f vs B80f), kernel alone shifted AI-measured diameter and flipped a Fleischner size category in 5.2% (8 of 155) of nodules at fixed patient and acquisition, while detection confidence was unchanged (Wilcoxon p=0.22). Under controlled LIDC-IDRI perturbations the effects dissociated by axis: the noise axis degraded detection confidence (p=5.9e-32, concentrated in nodules under 6 mm) but not measurement, while the frequency/kernel axis corrupted measurement (p=8.6e-13) but not detection. A 4-feature pixel fingerprint recovered reconstruction identity (patient-level AUC about 0.95 on real CT, 0.995 on a QIBA phantom) where the ConvolutionKernel DICOM tag was uninformative (identical labels across reconstructions). The kernel axis transported across four manufacturers (leave-one-vendor-out AUC 0.94-0.98, matching the within-vendor ceiling). Acquisition state thus maps to distinct AI failure modes, frequency content to measurement reliability and noise to detection sensitivity, and is not recoverable from metadata. Acquisition-aware, input-side validation is the missing layer for the acceptance-testing and drift-monitoring requirements now entering imaging-AI accreditation.

25.
arXiv (quant-ph) 2026-06-16

Optical Creation of Synthetic Microgravity for Quantum Degenerate Gases

arXiv:2606.14985v1 Announce Type: cross Abstract: Microgravity environments provide unique opportunities for ultracold-atom experiments by enabling long interrogation times and reduced acceleration-induced dynamics. However, their realization has largely been restricted to specialized facilities such as drop towers, sounding rockets, and space-based laboratories. Here we realize synthetic microgravity for quantum degenerate gases using optically engineered force landscapes that compensate Earth's gravity to the milli-g level while maintaining continuous confinement of the atomic ensemble. These force landscapes are generated by dynamically painted optical dipole potentials and calibrated in situ through Bloch oscillations in a vertical optical lattice, enabling precise control of the residual acceleration. We use this capability to demonstrate matter-wave beam splitting with arm separations of several hundred microns. We further implement a Bloch-band atom interferometer in which interaction-induced dephasing is strongly suppressed through controlled three-dimensional expansion in the synthetic microgravity potential. This reduction of mean-field effects restores near-$\sqrt{N}$ scaling of interferometric sensitivity for large quantum degenerate ensembles. Our results establish a versatile platform for realizing synthetic microgravity with trapped quantum gases in terrestrial laboratories, bringing the advantages of microgravity experiments to continuously operating systems and opening new opportunities for quantum sensing, matter-wave interferometry, and precision measurements.