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01.
arXiv (math.PR) 2026-06-18

Kemeny's constant minimization for reversible Markov chains via structure-preserving perturbations

作者:
Fabio Durastante↗Miryam Gnazzo↗Beatrice Meini↗

arXiv:2510.24679v4 Announce Type: replace-cross Abstract: Kemeny's constant measures the efficiency of a Markov chain in traversing its states. We investigate whether structure-preserving perturbations to the transition probabilities of a reversible Markov chain can improve its connectivity while maintaining a fixed stationary distribution. Although the minimum achievable value for Kemeny's constant can be estimated, the required perturbations may be infeasible. We reformulate the problem as an optimization task, focusing on solution existence and efficient algorithms, with an emphasis on the problem of minimizing Kemeny's constant under sparsity constraints.

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02.
arXiv (CS.AI) 2026-06-24

Graph Alignment for Benchmarking Graph Neural Networks and Learning Positional Encodings

作者:
Adrien Lagesse↗Marc Lelarge↗

arXiv:2505.13087v2 Announce Type: replace-cross Abstract: We propose a novel benchmarking methodology for graph neural networks (GNNs) based on the graph alignment problem, a combinatorial optimization task that generalizes graph isomorphism by aligning two unlabeled graphs to maximize overlapping edges. We frame this problem as a self-supervised learning task and present several methods to generate graph alignment datasets using synthetic random graphs and real-world graph datasets from multiple domains. For a given graph dataset, we generate a family of graph alignment datasets with increasing difficulty, allowing us to rank the performance of various architectures. Our experiments prove that there is an optimal task difficulty for having a statistically relevant ranking of different models and that, even on a structure-only task, anisotropic models perform better compared to isotropic ones. To further prove that our synthetic task capture meaningful information, we show its effectiveness for self-supervised GNN pre-training: the learned node embeddings can be leveraged as positional encodings by transformers for graph regression or can be used to reconstruct the full structure of the graph with $98\%$ accuracy. To support reproducibility and further research, we provide an open-source Python package to generate graph alignment datasets and benchmark new GNN architectures. The source code is available at https://github.com/adrien-lagesse/graph-alignment-benchmark.

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03.
arXiv (math.PR) 2026-06-11

Percolation on hierarchical lattices

作者:
Caio Alves↗Rangel Baldasso↗Carlos Gustavo Moreira↗Augusto Teixeira↗

arXiv:2606.11503v1 Announce Type: new Abstract: We consider independent Bernoulli percolation on top of sequences of hierarchical graphs. Given a graph $G_{1}$ with two distinguished vertices $a_{1}$ and $b_{1}$, the hierarchical graph with seed $G_{1}$ is the sequence $\big( G_{k} \big)_{k \geq 1}$ resulting from the inductive procedure, where the graph $G_{k+1}$ is obtained from $G_{k}$ by replacing each of its edges with a copy of $G_{1}$, attached by the vertices $a_{1}$ and $b_{1}$. We prove that, under sharp hypotheses, percolation on these graphs presents a unique phase transition. Second, we establish the existence of several critical exponents in this context, such as the critical exponents for the correlation length $\nu$, the surface tension $\mu$, the one-arm exponent $\alpha_{1}$. Several results are also obtained for their infinite counterpart $G_\infty$, which is the Benjamini-Schramm limit of $G_k$: uniqueness of the infinite cluster, continuity of $\theta(p)$, existence of the percolation-probability exponent $\beta$ and scaling relations for the critical exponents $\alpha_1$, $\nu$ and $\beta$. Furthermore, we analyze noise sensitivity for crossing functions in $G_{k}$ and establish sharp noise sensitivity in this setting. Finally, we propose a setup where it is possible to verify the locality hypothesis, stating that the critical threshold for percolation is a local property, while critical exponents are determined by the global geometry of the graph. As a consequence of the techniques developed here, we also provide a necessary and sufficient condition for the existence of a unique fixed point for the map $p \mapsto \mathbb{E}_p[g]$ in $(0,1)$, where $g:\{0,1\}^n \to \{0,1\}$ is a nontrivial monotone Boolean function.

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

Sharp Transitions for Subsystem Complexity

作者:
Yale Fan↗Nicholas Hunter-Jones↗Andreas Karch↗Shivan Mittal↗

arXiv:2510.18832v2 Announce Type: replace-cross Abstract: The circuit complexity of time-evolved pure quantum states grows linearly in time for an exponentially long time. This behavior has been proven in certain models, is conjectured to hold for generic quantum many-body systems, and is believed to be dual to the long-time growth of black hole interiors in AdS/CFT. Achieving a similar understanding for mixed states remains an important problem. In this work, we study the circuit complexity of time-evolved subsystems of pure quantum states. We find that for greater-than-half subsystem sizes, the complexity grows linearly in time for an exponentially long time, similarly to that of the full state. However, for less-than-half subsystem sizes, the complexity rises and then falls, returning to low complexity as the subsystem equilibrates. Notably, the transition between these two regimes occurs sharply at half system size. We use holographic duality to map out this picture of subsystem complexity dynamics and rigorously prove the existence of the sharp transition in random quantum circuits. Furthermore, we use holography to predict features of complexity growth at finite temperature that lie beyond the reach of techniques based on random quantum circuits. In particular, at finite temperature, we argue for an additional sharp transition at a critical less-than-half subsystem size. Below this critical value, the subsystem complexity saturates nearly instantaneously rather than exhibiting a rise and fall. This novel phenomenon, as well as an analogous transition above half system size, provides a target for future studies based on rigorous methods.

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05.
arXiv (CS.CV) 2026-06-18

ProductConsistency: Improving Product Identity Preservation in Instruction-Based Image Editing via SFT and RL

作者:
Mukund Khanna↗Raj Singh Yadav↗Kunal Singh↗

Recent advances in instruction-based image editing have enabled models to perform complex visual edits from natural language instructions. However, in product-centric scenarios where preserving product features, branding, and textual elements are critical, current open and closed source models often struggle to maintain this fine-grained object identity. This issue is further compounded by the lack of datasets for instruction-based product image editing with text fidelity constraints, leaving it largely treated as an implicit capability of instruction-based image editing models. In this work, we introduce the ProductConsistency dataset which is designed to improve product-centric image editing. Our approach includes a supervised fine-tuning (SFT) dataset of 87k samples for product editing, a reinforcement learning (RL) dataset with 869 unique product images, and a new benchmark dataset, the ProductConsistency Benchmark, to allow rigorous and standardized evaluation of editing models. To guide RL training, we propose a Cyclic Consistency reward that enforces semantic preservation of product identity by using caption similarity between the original product description and captions generated from the edited image. We fine-tune both Qwen-Image-Edit-2511 and Flux.1-Kontext-dev using our dataset and demonstrate consistent improvements over baseline models in OCR and Perceptual metrics, and MLLM-based evaluations as well, indicating stronger product consistency, text rendering, and overall visual quality; with the Qwen-Image-Edit-2511 model achieving a 5x reduction in the character error rate. The code and pipeline is available at https://anonymous.4open.science/r/ProductConsistency-6FCC/README.md

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06.
PLOS Computational Biology 2026-06-01

Challenges and progress in RNA velocity: Comparative analysis across multiple biological contexts

作者:
Sarah Ancheta↗

by Sarah Ancheta, Leah Dorman, Guillaume Le Treut, Abel Gurung, Greg Huber, Loïc A. Royer, Alejandro Granados, Merlin Lange Single-cell RNA sequencing is revolutionizing our understanding of cell state dynamics, allowing researchers to capture and quantify the transcriptomic profile of a single cell at a specific timepoint. Among the computational techniques used to predict cellular trajectories, RNA velocity has emerged as a predominant tool for modeling transcriptional dynamics. RNA velocity leverages the mRNA maturation process to generate velocity vectors that predict the likely future state of a cell, offering insights into cellular differentiation, aging, and disease progression. Although this technique has shown promise across biological fields, the performance accuracy varies depending on the RNA velocity method and dataset. We established a comparative pipeline and analyzed the performance of five RNA velocity methods on three datasets based on local consistency, method agreement, identification of driver genes, and robustness to sequencing depth. This benchmark provides a resource for scientists to understand the strengths and limitations of different RNA velocity methods.

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

LLM-Based Visual Explanation Evaluation Framework for Assessing the Explainability of Facial Skin Disease Classification Models

作者:
Gyuyeon Na↗

This study proposes a domain-specific LLM-based Visual Explanation Evaluation Framework for assessing Grad-CAM explanations in facial skin disease diagnosis models. While previous studies have primarily focused on improving classification performance through data augmentation techniques, relatively few studies have systematically examined whether model explanations are grounded in clinically relevant lesion regions. In this study, geometric augmentation, color-based augmentation, and mixed augmentation strategies were applied to facial skin disease classification models based on EfficientNet-B0, MobileNetV3, and ResNet18. Grad-CAM was employed to generate visual explanations representing the models' decision-making processes. Furthermore, an LLM-as-a-Judge evaluation framework was designed using GPT-5.5, Gemini 3.5 Flash, and Claude Sonnet 4.6 to assess Grad-CAM explanations from the perspectives of lesion localization and explanation trustworthiness. To improve evaluation consistency and clinical grounding, a progressive prompt engineering strategy was introduced, incorporating evaluation rubrics, clinical knowledge, penalty rules, and structured output formats.

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

Detecting Explanatory Insufficiency in Learned Representations: A Framework for Representational Vigilance

作者:
Jacques Raynal↗Pierre Slangen↗Elsa Raynal↗Jacques Margerit↗

arXiv:2606.13172v1 Announce Type: new Abstract: Learned representations are central to modern machine learning and are commonly evaluated through predictive performance, robustness, uncertainty estimation, or generalization. However, a learned representation may remain operationally successful while progressively failing to organize persistent residual structures that are not fully captured by conventional evaluation metrics. This article introduces VER, the Vigilant Evaluator of Representations, a conceptual framework for monitoring representational adequacy in learned representations. VER does not propose a new learning algorithm, loss function, or model architecture. Instead, it formalizes a diagnostic process through which persistent residual structures may be identified, analyzed, and interpreted as potential indicators of explanatory insufficiency. The framework distinguishes representational inadequacy from ordinary prediction error, uncertainty, noise, and distribution shift. It introduces a monitoring sequence based on representation identification, explanatory-domain delimitation, residual-structure detection, explanatory-resistance evaluation, and vigilance signaling. VER is intended as a contribution to representation diagnostics in machine learning. Its objective is not to replace existing evaluation methods but to complement them by treating representational adequacy as an explicit object of inquiry. A path toward empirical evaluation through representational-vigilance benchmarks is also outlined.

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09.
arXiv (CS.CL) 2026-06-18

PatchWorld: Gradient-Free Optimization of Executable World Models

作者:
Jiaxin Bai↗Yue Guo↗Yifei Dong↗Jiaxuan Xiong↗Tianshi Zheng↗Yixia Li↗Tianqing Fang↗Yufei Li↗Yisen Gao↗Haoyu Huang↗Zhongwei Xie↗Hong Ting Tsang↗…

Text-agent environments are typically modeled as partially observable Markov decision processes (POMDPs), assuming that the simulator's latent state and transition dynamics are hidden from the agent. Yet little work has examined whether executable code can be induced to serve as a world model for prediction and planning under partial observability. We introduce PatchWorld, a gradient-free framework that turns offline trajectories into executable Python world models through counterexample-guided code repair. Instead of predicting the next observation with a black-box model, PatchWorld induces symbolic belief-state programs whose action updates can be inspected, replayed, and locally patched. Across seven AgentGym environments, PatchWorld-Simple achieves the highest code-based planning score among evaluated methods, reaching 76.4\% macro success in live one-step lookahead while invoking no LLM calls inside the world-model prediction module itself. We further find that a human-specified residual-memory bias improves surface observation fidelity but weakens decision utility. This exposes a tradeoff in executable world models, since improving observation fidelity can come at the expense of action-discriminative dynamics, and vice versa. Code is available at https://github.com/HKBU-KnowComp/PatchWorld.

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10.
arXiv (CS.CV) 2026-06-18

VGGHeads: 3D Multi Head Alignment with a Large-Scale Synthetic Dataset

作者:
Orest Kupyn↗Eugene Khvedchenia↗Christian Rupprecht↗

Human head detection, keypoint estimation, and 3D head model fitting are essential tasks with many applications. However, traditional real-world datasets often suffer from bias, privacy, and ethical concerns, and they have been recorded in laboratory environments, which makes it difficult for trained models to generalize. Here, we introduce \method – a large-scale synthetic dataset generated with diffusion models for human head detection and 3D mesh estimation. Our dataset comprises over 1 million high-resolution images, each annotated with detailed 3D head meshes, facial landmarks, and bounding boxes. Using this dataset, we introduce a new model architecture capable of simultaneous head detection and head mesh reconstruction from a single image in a single step. Through extensive experimental evaluations, we demonstrate that models trained on our synthetic data achieve strong performance on real images. Furthermore, the versatility of our dataset makes it applicable across a broad spectrum of tasks, offering a general and comprehensive representation of human heads.

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11.
arXiv (CS.LG) 2026-06-12

Reliability of Probabilistic Emulation of Physical Systems

作者:
Sam F. Greenbury↗Radka Jersakova↗Paolo Conti↗Marjan Famili↗Christopher Iliffe Sprague↗Edwin Brown↗Jason D. McEwen↗

arXiv:2606.12997v1 Announce Type: new Abstract: Two dominant approaches have emerged for generating probabilistic forecasts of physical systems: generative models, such as diffusion or flow matching; and ensembles of deterministic models with stochasticity injected, trained using the continuous ranked probability score (CRPS) loss. While both approaches have demonstrated strong predictive accuracy, the reliability of their uncertainties has not been systematically assessed. We address this gap by developing a framework to evaluate both approaches across diverse 2D spatiotemporal physical systems, under matched model size and computational budget. We assess the reliability of probabilistic emulation by inspecting the empirical coverage of predictive intervals, while also considering accuracy and computational efficiency metrics. CRPS-trained ensembles typically achieve more reliable uncertainties on both single-step prediction and autoregressive rollouts, demonstrating better coverage than the standard alternative of training generative models in a latent space. Moreover, the CRPS approach offers significantly faster inference. When generative models are trained in ambient rather than a compressed latent space, which is often infeasible for high-dimensional problems, they exhibit comparable coverage to CRPS-trained ensembles, though with substantially larger inference latency. In contrast, when CRPS-trained ensembles are trained in latent space they do not show a marked degradation in coverage with respect to ambient space. Both generative models and CRPS-trained ensembles demonstrate good predictive accuracy. To facilitate future research and application, we release AutoCast, a modular framework implementing both generative models and CRPS-trained ensembles, alongside AutoSim, a flexible dataset generation package for rapid prototyping.

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12.
arXiv (CS.LG) 2026-06-11

UniIntervene: Agentic Intervention for Efficient Real-World Reinforcement Learning

作者:
Haoyuan Deng↗Yitong Gao↗Yudong Lin↗Haichao Liu↗Zhenyu Wu↗Ziwei Wang↗

arXiv:2606.12372v1 Announce Type: cross Abstract: Human-in-the-loop reinforcement learning (HiL-RL) has emerged as an effective paradigm for real-world robotic manipulation, enabling online policy improvement with human guidance. However, current HiL-RL frameworks remain intervention-intensive, relying on frequent human corrections to redirect the policy out of unproductive exploration, which incurs high labor cost and limits real-world scalability. To address this, we propose UniIntervene, an agentic intervention model that detects unproductive exploration and autonomously recovers the policy toward high-value states, taking over the bulk of interventions from human operators. Specifically, UniIntervene first performs future-conditioned action-value estimation, predicting the latent consequence of the current action and evaluating its induced value, which provides a more stable progress signal. Building on this, a temporal value-risk critic aggregates recent value dynamics and triggers intervention when the estimated value exhibits sustained stagnation or degradation. When intervention is required, UniIntervene retrieves a high-value recovery target from a memory of past intervention episodes and produces executable corrective actions through a goal-conditioned recovery policy. In this way, UniIntervene turns intervention from passive human correction into a value-aware recovery process for efficient real-world RL. Extensive experiments on diverse real-world manipulation tasks demonstrate that UniIntervene improves the average success rate by 8.6% while reducing human interventions by 57% relative to state-of-the-art HiL-RL baselines.

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13.
arXiv (quant-ph) 2026-06-12

Quantum optical photoelectron interferometry

作者:
Jonathan Dubois↗Viviane Cotte↗Richard Ta\"ieb↗Camille L\'ev\^eque↗J\'er\'emie Caillat↗Pranshu Dave↗Pascal Sali\`eres↗David Bresteau↗Charles Bourassin-Bouchet↗Anne L'Huillier↗David Busto↗

arXiv:2606.13447v1 Announce Type: new Abstract: We present a general theoretical framework for multiphoton processes driven by quantum light fields, establishing a direct link between photon statistics and photoelectron observables. Our results show that the autocorrelation and cross-correlation functions, which quantify the underlying photon statistics, are directly mapped onto the resulting photoelectron spectra. Although our framework is broadly applicable, we demonstrate specifically in the example of reconstruction of attosecond beating by interference of two-photon transitions (RABBIT) the influence of the light statistical properties. In this approach, the amplitude, contrast and phase of the oscillations of the sideband signal as a function of pump-probe delay reveal the quantum nature of light. We analyze these observables across several quantum configurations, including correlated infrared and harmonic modes, as well as the uncorrelated case with non-classical harmonic statistics, thereby establishing a general framework for quantum-light RABBIT spectroscopy. We compare the analytical theory with numerical simulations for the case of classical harmonics and an infrared field in a squeezed coherent state, obtaining excellent agreement. Our results reveal how the interplay between classical and quantum correlations dictates the coherence of the photoemission process, providing a new window into the quantum-optical foundations of attosecond science.

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14.
arXiv (CS.AI) 2026-06-11

Position: Stop Anthropomorphizing Intermediate Tokens as Reasoning/Thinking Traces!

作者:
Subbarao Kambhampati↗Karthik Valmeekam↗Siddhant Bhambri↗Vardhan Palod↗Lucas Saldyt↗Kaya Stechly↗Soumya Rani Samineni↗Durgesh Kalwar↗Upasana Biswas↗

arXiv:2504.09762v4 Announce Type: replace Abstract: Intermediate token generation (ITG), where a model produces output before the solution, has become a standard method to improve the performance of language models on reasoning tasks. These intermediate tokens have been called \say{reasoning traces} or even \say{thinking traces} – implicitly anthropomorphizing the traces, and implying that these traces resemble steps a human might take when solving a challenging problem, and as such can provide an interpretable window into the operation of the model's thinking process to the end user. In this position paper, we present evidence that this anthropomorphization isn't a harmless metaphor, and instead is quite dangerous – it confuses the nature of these models and how to use them effectively, and leads to questionable research. We call on the community to avoid such anthropomorphization of intermediate tokens.

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

Towards One-for-All Anomaly Detection for Tabular Data

作者:
Shiyuan Li↗Yixin Liu↗Yu Zheng↗Xiaofeng Cao↗Shirui Pan↗Heng Tao Shen↗

arXiv:2603.14407v2 Announce Type: replace Abstract: Tabular anomaly detection (TAD) aims to identify samples that deviate from the majority in tabular data and is critical in many real-world applications. However, existing methods follow a ``one model for one dataset (OFO)'' paradigm, which relies on dataset-specific training and thus incurs high computational cost and yields limited generalization to unseen domains. To address these limitations, we propose OFA-TAD, a generalist one-for-all (OFA) TAD framework that only requires one-time training on multiple source datasets and can generalize to unseen datasets from diverse domains on-the-fly. To realize one-for-all tabular anomaly detection, OFA-TAD extracts neighbor-distance patterns as transferable cues, and introduces multi-view neighbor-distance representations from multiple transformation-induced metric spaces to mitigate the transformation sensitivity of distance profiles. To adaptively combine multi-view distance evidence, a Mixture-of-Experts (MoE) scoring network is employed for view-specific anomaly scoring and entropy-regularized gated fusion, with a multi-strategy anomaly synthesis mechanism to support training under the one-class constraint. Extensive experiments on 34 datasets from 14 domains demonstrate that OFA-TAD achieves superior anomaly detection performance and strong cross-domain generalizability under the strict OFA setting. The source code is available at https://github.com/Shiy-Li/OFA-TAD.

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

The Latent Color Subspace: Emergent Order in High-Dimensional Chaos

作者:
Mateusz Pach↗Jessica Bader↗Quentin Bouniot↗Serge Belongie↗Zeynep Akata↗

Text-to-image generation models have advanced rapidly, yet achieving fine-grained control over generated images remains difficult, largely due to limited understanding of how semantic information is encoded. We develop an interpretation of the color representation in the Variational Autoencoder latent space of FLUX.1 [Dev], revealing a structure reflecting Hue, Saturation, and Lightness. We verify our Latent Color Subspace (LCS) interpretation by demonstrating that it can both predict and explicitly control color, introducing a fully training-free method in FLUX based solely on closed-form latent-space manipulation. Code is available at https://github.com/ExplainableML/LCS.

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

OpenTie: Open-vocabulary Sequential Rebar Tying System

作者:
Sai Fan↗Mingze Liu↗Haozhen Li↗Haobo Liang↗Yixing Yuan↗Yanke Wang↗

Robotic practices on the construction site emerge as an attention-attracting manner owing to their capability of tackling complex challenges, especially in the rebar-involved scenarios. Most of existing products and research are mainly focused on the collection of large amounts of data with model training demands. To fulfill this gap, we propose OpenTie, a 3D training-free rebar tying framework utilizing a RGB-to-point-cloud generation and an open-vocabulary rebar detection on the real-world test. We implement the OpenTie via a robotic arm with a binocular camera and guarantee a high accuracy by applying the prompt-based object detection method on the image filtered by our proposed post-processing procedure for the image-to-point-cloud generation framework. Our pipeline requires no training efforts and outperforms the training-based object detection, i.e., YOLO-based method, with the verification on the real-world sequential rebar tying test. The system is flexible for horizontal and vertical rebar tying tasks and holds the potential application to the real construction site with possibility of commercialization.

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

Intelligent Automation for Embodied Benchmark Construction: Pipelines, Embodiments, Simulators, and Trends

作者:
Jinshan Lai↗Jianwei Hu↗Baoyang Jiang↗Fengchun Zhang↗Leyuan Wang↗Haotian Li↗Yida Wang↗Tingxuan Huang↗Xi Ren↗Qiang Ma↗

arXiv:2606.12207v1 Announce Type: cross Abstract: Embodied intelligence now spans navigation, household assistance, manipulation, autonomous driving, aerial agents, and multimodal large-model control. This expansion has made benchmark construction a central bottleneck for reliable evaluation. Unlike static datasets, embodied benchmarks combine task specifications, environments, robot data, demonstrations, annotations, metrics, evaluation scripts, and release policies into a single evaluation system. This survey reviews the literature through a five-stage construction pipeline: requirement and task construction, data acquisition, data cleaning and annotation, benchmark suite generation and metric definition, and evaluation execution with diagnostic feedback. For each stage, the survey analyzes the transition from manual curation to traditional automation, foundation-model assistance, and agentic closed-loop workflows. It also compares qualitative construction costs across human labor, data and asset acquisition, compute and simulation, validation and debugging, governance and maintenance, and rework risk. The main conclusion is that automation does not simply reduce benchmark cost. Instead, it often shifts cost toward validation, auditability, version control, and long-term governance. Progress in embodied evaluation will therefore depend not only on larger benchmark suites, but also on construction pipelines that are diagnosable, auditable, and responsibly refreshable.

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

BioPIE: A Biomedical Protocol Information Extraction Dataset for Experiment Understanding

作者:
Haofei Hou↗Shunyi Zhao↗Fanxu Meng↗Kairui Yang↗Lecheng Ruan↗Qining Wang↗

arXiv:2601.04524v2 Announce Type: replace Abstract: Understanding biomedical experiments provides a foundation for downstream tasks, e.g., laboratory automation, and facilitates effective cross-disciplinary communication. Two challenges, High Information Density (HID) and Multi-Step Reasoning (MSR), pose unique difficulties for precise experimental understanding. Extracting structured knowledge, e.g., Knowledge Graphs (KGs), is an effective approach to address the HID and MSR. However, existing biomedical datasets for structured knowledge information extraction are limited to a general or coarse-grained level, hindering fine-grained experimental understanding. To address this gap, we introduce Biomedical Protocol Information Extraction Dataset (BioPIE), a dataset providing procedure-centric KGs that capture entities, actions, and relations at a scale sufficient for reasoning across biomedical protocols. We evaluate information extraction methods on BioPIE and implement a question answering system leveraging the dataset for validation, demonstrating improved understanding performance on test sets as well as on the HID and MSR question sets.

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20.
arXiv (CS.CV) 2026-06-17

Geometry-Consistent Endoscopic Representations for Image-Guided Navigation via Structured Foundation Model Adaptation

作者:
Hongchao Shu↗Roger D. Soberanis-Mukul↗Hao Ding↗Morgan Ringel↗Mali Shen↗Saif Iftekar Sayed↗Hedyeh Rafii-Tari↗Mathias Unberath↗

Accurate vision-based navigation in monocular endoscopy is difficult due to limited depth cues, weak tissue texture, non-rigid deformation, and substantial appearance variation across domains, all of which complicate pose estimation, depth prediction, and image-to-anatomy alignment. Although recent vision foundation models have shown promise, their learned representations often remain insufficiently geometry-consistent, hindering stable feature correspondence and limiting their reliability for downstream navigation tasks. We propose a unified framework for learning geometry-consistent and domain-robust image representations for monocular endoscopy. The framework combines a synthetic data pipeline that provides accurate geometric supervision with Hierarchy-Aware Geometry-Semantic Adaptation, a structured alternative to standard LoRA that inserts low-rank adapters selectively across the transformer hierarchy and couples them with layer-wise training objectives to encourage geometric correspondence in intermediate features and semantic consistency in deeper features. Experiments on public and proprietary datasets show improved geometric and semantic representation quality, leading to better performance on downstream navigation tasks including pose estimation and monocular depth estimation. The learned representations show favorable synthetic-to-real transfer on clinical bronchoscopy and provide a useful initialization for adaptation to sinus endoscopy and colonoscopy under limited supervision. The framework also shows favorable scaling with model size and training data. These results support hierarchy-aware, geometry-guided adaptation as a practical approach for endoscopic representation learning.

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21.
medRxiv (Medicine) 2026-06-17

Deep learning for interactive and automated inner retinal layer segmentation in OCT images of patients with retinitis pigmentosa using limited training data

作者:
Laurence↗D. S↗Schilling↗Grimm↗N.-A↗Mace↗Bemme↗Pape↗

Purpose: New therapeutic strategies such as optogenetics have created a need for accurate tracking of inner retina degeneration in Retinitis pigmentosa (RP) patients. We introduce two tailored deep learning models to segment the RNFL (retinal nerve fibre layer), GCIPL (ganglion cell inner plexiform layer), INL (inner nuclear layer), CFT (central foveal thickness) and RPE (retinal pigment epithelium) in RP: The first is based on a Segment Anything Model (SAM), the second on nnU-Net. To our knowledge, SAM has not yet been applied to retinal layers in OCT data. Methods: SD-OCT images of a retrospective cohort of 37 RP patients were included. Data for four training cycles were prepared semi-automatically in MATLAB, then assessed and corrected by three expert graders. 1,700 segmented B-Scans from two open datasets were used for pretraining. For post-processing, semantic retinal boundary detection was developed. The final models, OCT-SAM and nnU-Net, were trained on 228 annotated RP scans. Detected layer thicknesses were validated against manual segmentation at 90 random points in 30 OCT B-Scans. Finally, OCT-SAM was tested on three RP cases with retrospective, longitudinal OCT data. Results: nnU-Net achieved a precision, recall and F-1 score of 0.96 while OCT-SAM performance resulted in slightly lower values of 0.93, 0.8 and 0.85, respectively. OCT-SAM measurements had low bias and good agreement with manual annotations, confirming reliability. Conclusions: OCT-SAM enabled fast data annotation and tool integration, whereas nnU-Net provided the best segmentation performance. OCT-SAM demonstrated longitudinal reproducibility and detected RP-characteristic pathologies and degenerative changes. Future work will extend OCT-SAM to 3D OCT segmentation.

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22.
bioRxiv (Bioinfo) 2026-06-14

FENNEC: Fine-Tuned Ensemble Neural Networks Accelerate Chemically Modified siRNA Design and Screening

作者:
Larsen↗A. W↗Butnaru↗Braun↗Rotrattanadumrong↗Berninger↗Yonchev↗Gagneur↗Marsico↗

Small interfering RNAs (siRNAs) are a clinically validated therapeutic modality, yet designing potent chemically modified siRNAs remains a costly and iterative process, limited by scarce public data. Computational prediction of siRNA efficacy is therefore essential for rational design and accelerated preclinical development. However, despite the critical role of chemical modifications in therapeutic performance, current state-of-the-art machine learning methods either are not designed to model the chemical diversity of therapeutic siRNAs, or exhibit poor generalization performance. Here, we present FENNEC (Fine-Tuned Ensemble of Neural Networks for siRNA Efficiency Characterization), a machine-learning framework for predicting siRNA activity across chemically diverse design spaces. To support this effort, we curated the largest patent-derived dataset to date of chemically modified siRNAs from 42 patents using OCR-based table extraction and stringent filtering. FENNEC combines temporal convolutional networks with thermodynamic descriptors, experimental covariates, and embeddings from RNA foundation models to capture both local chemical determinants and broader target-context information. Importantly, we show that language-model-derived embeddings provide meaningful higher-order representations of target transcripts, particularly in data-scarce settings. FENNEC achieved robust predictive performance across both gene-level and scaffold-level validation settings, with additional experimental validation on a novel AHSA1-targeting dataset further supporting its generalizability across chemically modified siRNAs. In benchmarking, FENNEC outperformed classical machine-learning and state-of-the-art deep learning models, demonstrating generalization to unseen chemistry. Model interpretation recovered established design principles, including position-specific effects of glycol nucleic acid, 2'-fluoro modifications, and phosphorothioate backbones. Furthermore, in silico perturbation analyses suggest that FENNEC can serve not only as a predictive model, but also as an oracle for the design and optimization of chemically modified siRNAs. Together, our work addresses a key gap in the field by enabling chemically aware deep learning for siRNA design, supported by a large and diverse collection of chemically modified siRNA measurements.

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23.
arXiv (CS.CV) 2026-06-16

Training-free sparse attention based on cumulative energy filtering

作者:
Chunlu Li↗Yixuan Pan↗Bai Du↗Zhenyuan Chen↗Yanzhao Li↗Hui Dong↗Hui Wang↗Zhiqiang Zou↗

Sparse attention accelerates Diffusion Transformers (DiTs) for video generation by computing only the important tokens while skipping the rest. The token selection strategy is key to balancing sparsity and accuracy. We formulate the token filtering process as a dual-goal optimization problem: maximizing sparsity and minimizing accuracy degradation. Existing algorithms cannot fulfill both objectives simultaneously. For example, Top-p only considers the accuracy constraint, while Top-k maintains a fixed computational budget but loosens the accuracy constraint. This paper demonstrates that maintaining a fixed recall rate is sufficient for ensuring accuracy, whereas a fixed threshold is suboptimal for reducing computational cost. Therefore, we propose a dynamic thresholding scheme to improve sparsity while maintaining the same level of accuracy. Furthermore, our algorithm is deeply integrated with Flash Attention (FA), eliminating the need for any additional masking computation overhead. Experimental results on Wan 2.2 validate that, compared to the BLASST algorithm which is also integrated with FA, our dynamic thresholding strategy enhances sparsity from 61.42\% to 82\% with a VBench metric drop of less than 5\%. This results in an approximate 15\% in attention computation and a $1.61\times$ increase in computational efficiency, which is 1.18x higher than that of BLASST.

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24.
arXiv (CS.CV) 2026-06-16

Hierarchical GRU with Input-Conditioned Slot Queries for Ball Action Anticipation

作者:
Parthsarthi Rawat↗

We present a hierarchical model for ball action anticipation in football broadcast video. Given a 30-second observation window, the system predicts actions occurring in the subsequent 5-second window across 10 classes. A shared local Transformer encodes clip-level features within each 5-second sub-window; a GRU then aggregates temporal context across all sub-windows; finally, a Transformer decoder with K input-conditioned event slots decodes the anticipation target via three decoupled heads (objectness, class, temporal offset). We introduce frequency-reweighted Hungarian matching that systematically favours rare action classes, and Gaussian soft targets for temporal bin supervision. On the SoccerNet Ball Action Anticipation benchmark, our method achieves 17.91% mAP on the test server.

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25.
arXiv (math.PR) 2026-06-18

Random Schrödinger operators on manifolds and abstract bounds for multiplier-type operators

作者:
Jean-Claude Cuenin↗Konstantin Merz↗Eduard Stefanescu↗

arXiv:2606.19075v1 Announce Type: cross Abstract: We study random Schrödinger operators on closed Riemannian manifolds with Anderson-type potentials. We prove high-probability spectral inclusion bounds showing that eigenvalues remain close to those of the Laplacian, with deviations controlled by a norm of the potential coefficients. Compared with deterministic bounds, this yields a square-root cancellation gain. The proof is based on a general principle showing that randomisation improves operator norm bounds for multiplier-type operators, which we formulate in both discrete and continuous settings.

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