Reconstruction
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Continuous 3D Spatial Transcriptomics Reconstruction via Histology-Informed Implicit Neural Representations
2026-11-10 14:16:40Kaito Shiku, Ryoma Bise, Ahtisham Fazeel Abbasi, Yuichiro Iwashita, Shumpei Takezaki, Andreas Dengel, Muhammad Nabeel AsimAbstract
Three-dimensional spatial transcriptomics (3D ST) enables the analysis of gene-expression patterns across tissue depths. However, 3D ST measurements are acquired from discrete 2D tissue sections, which are often sparsely sampled due to high acquisition costs. To address this limitation, we propose a histology-informed multi-task implicit neural representation (HIM-INR) for continuous 3D gene-expression reconstruction from sparse ST observations. HIM-INR jointly reconstructs gene-expression profiles and histological representations using an INR with a shared backbone, leveraging densely sampled histological images as auxiliary spatial supervision. Once trained, HIM-INR predicts gene expression at arbitrary 3D coordinates without requiring histological images. Experiments on two 3D ST datasets demonstrate improved reconstruction over existing methods, particularly as the number of missing ST sections increases.
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URL
https://arxiv.org/abs/2611.14129
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Lipschitz-Controlled Flow Matching for Robust Image Restoration
2026-11-10 12:40:17Sedjro Salomon Hotegni, Konstantin Sonntag, Paul-Christian B\"urkner, Sebastian PeitzAbstract
Flow-matching models can produce high-quality image restorations, but their learned dynamics may amplify small input perturbations and make reconstructions unstable. We introduce LipsFlower to reduce this amplification. We derive stability bounds for Flow-from-$Y$, which initializes the ordinary differential equation from a noise-perturbed observation, as well as for observation-conditioned posterior sampling, which conditions the velocity field on the observation throughout integration. Based on this analysis, we develop LipHDiT, a Lipschitz-aware hourglass diffusion transformer that serves as the vector-field architecture of LipsFlower. LipHDiT incorporates stabilized approximate spectral normalization, bounded modulation, and convex residual mixing. We also use adversarial finite-radius gain regularization at sampled interpolation states to penalize excessive sensitivity to the state and, for conditional sampling, the observation. We test both formulations on blind face restoration, measuring adversarial robustness and the perceptual quality of the reconstructions. LipsFlower reduces perturbation amplification while keeping restoration quality competitive with the evaluated baselines. These results suggest that Lipschitz-aware flow matching can improve the stability of generative image restoration.
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URL
https://arxiv.org/abs/2611.13995
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TransGHOST: Real-Time, Synthesis-Free Reconstruction of Instrument-Occluded Regions in Ophthalmic Microsurgery
2026-11-10 12:08:36Niran Nataraj, Maina Sogabe, Masamichi Yamashita, Norihiko Ito, Kenji KawashimaAbstract
Intraoperative scene perception in ophthalmic microsurgery is limited by instrument occlusion: when a tool enters the high-magnification field, it conceals tissue from both the surgeon and the perception components of robot-assisted systems that process the video. Generative inpainting can remove the occluder but replaces the missing image content with synthesis, which is unsuitable when visual provenance matters. Many video inpainters also depend on future frames and cannot operate online. We present TransGHOST, a causal reference-guided reconstruction pipeline whose non-generative safe mode operates in real time. Every restored value is obtained by resampling a recorded frame using geometric transforms fitted only to visible regions. The system provides per-pixel confidence and provenance and marks unsupported pixels as abstentions. We evaluate TransGHOST on a new veterinary clinical corpus of canine cataract surgery with pixel-level instrument and anatomy labels. Only the occluded region is scored, and each scoring target is verified to differ from the reference supplied to the system. Safe mode reaches 31.89 dB masked PSNR and 0.915 masked SSIM at 51.7 ms median and 85.5 ms 95th-percentile latency. On a pre-declared held-out cohort using instrument cutouts excluded from segmentation training, it reaches 29.83 dB masked PSNR, while matched-mask evaluation on validation shows a 3.45 dB advantage over LaMa. Region-aware reference selection improves masked PSNR by 3.60 dB over recency when candidate references can themselves be occluded. Reference-age analysis further defines the operating interval for the brief, repeated occlusions targeted by TransGHOST.
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URL
https://arxiv.org/abs/2611.13971
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RB-LDC: Redundancy-Balanced Latent Coding for Noise-Robust Diffusion Latents
2026-11-10 11:41:05Hyunseok Jeong, Jaeho Jeon, Young-Sik KimAbstract
Latent diffusion models decode approximately correct latents, making decoder sensitivity to perturbations relevant to image quality. After whitening, forward diffusion corrupts every direction at the same signal-to-noise ratio (SNR), despite unequal decoder sensitivities. We study an invertible linear layer between the encoder and diffusion process that shifts each direction's log-SNR. Its linear minimum mean-square-error (LMMSE) recovery risk has an exact spectral expression for any whitened latent distribution. Under an energy budget and a floor ensuring invertibility, minimizing decoder-sensitivity-weighted LMMSE risk integrated over the diffusion schedule yields a unique optimal allocation. The layer aligns with the decoder's expected pullback metric and equalizes marginal risk reduction across directions, computed by a deterministic spectral solver. At large budgets, the allocation follows a power law in sensitivity whose exponent is determined by the low-SNR tail of the loss weighting: one half for noise prediction and two thirds for data prediction under the cosine schedule, with a crossover on truncated schedules. We instantiate this principle as RB-LDC using Jacobian-based sensitivity estimates. On ImageNet at 256 x 256 resolution with SD-VAE and VA-VAE, trained RB-LDC improves reconstruction from noisy latents over budget-matched isotropic coding in all four metrics and five coding configurations, averaged over 15 SNRs and three pipeline seeds. It reduces average perturbed FID by 17.1 for VA-VAE block-local coding while preserving clean reconstruction. We also report intermediate SNRs where perturbed FID worsens. With a frozen diffusion model, RB-LDC yields lower FID point estimates in all 12 tested combinations of sampling progress and channel SNR under corruption during sampling.
Abstract (translated)
URL
https://arxiv.org/abs/2611.13955
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Kierston & KierstonBench: Simulation of Allentown, PA and Evaluation of Language Models in Crime Investigation and Surveillance Tasks
2026-11-10 11:27:46Andrew Semenov, Svyatoslav DorofeevAbstract
Large language models are candidates for collecting and analyzing records in criminal investigations and mass surveillance. Their capability and accuracy in this work cannot currently be measured. Real deployments lack the ground truth needed to score a model's conclusions, and no benchmark evaluates these capabilities in a simulated environment. We present Kierston, a city-scale simulation engine, and KierstonBench, a benchmark that tests these capabilities against known simulated events. Kierston models approximately 125,000 residents of Allentown, Pennsylvania, generating their daily activities and the telecommunications, financial, administrative and license-plate records that surveillance and investigative systems collect about them. These records derive from a common behavioral timeline and are distributed across sources representing separate providers. Models investigate through a restricted records interface, linking observations across sources without access to the underlying simulation. The benchmark comprises 32 task families covering record linkage, routine reconstruction, incident investigation and assessment of deceptive accounts. In an evaluation of sixteen language models, most could not perform records investigation and submitted identifications the records did not support. A small number of frontier models solved most of the tasks and abstained when evidence was insufficient. In some cases these models still fell for common deceptions and assumptions, and none replaced an investigator.
Abstract (translated)
URL
https://arxiv.org/abs/2611.04785
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FastWild-GS: Minutes-Scale In-the-Wild Gaussian Splatting via Compact Per-Image Appearance Adaptation
2026-11-10 09:39:33Donghun Ryu, Seokhyun Kim, Minhyeok LeeAbstract
Internet photos of a scene differ in exposure, illumination and transient objects such as passers-by, so one set of Gaussian colours cannot explain all photos (the in-the-wild setting). Recent in-the-wild Gaussian Splatting methods mostly report hours of per-scene optimization. We present FastWild-GS, which describes each photo by a 128-dimensional Photo Appearance Token and a per-channel transform, a scale and an offset applied to the rendered image (six parameters); a small MLP predicts the colour of each Gaussian from this token and a per-Gaussian feature, replacing the spherical-harmonics colour. The same transform is applied to the renders that score Gaussians for densification and pruning, so appearance differences between photos are not counted as reconstruction error. On PhotoTourism, FastWild-GS trains in 8.8 minutes per scene with the lowest LPIPS among the compared methods, 23x faster than AsymGS, the next best in LPIPS. On NeRF-OSR, it has the best average PSNR, SSIM and LPIPS among the compared methods in 9.7 minutes per scene.
Abstract (translated)
URL
https://arxiv.org/abs/2611.13808
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CIALLO: Learning Shared Intent Representations for Cross-Embodiment Manipulation
2026-11-10 08:35:27Choo Sin Wai, Dake Zhong, Jingye Zhang, Zhifang Liu, Siyao Xiao, Zirong Ding, Yuhong Zhang, Kangjie Chen, Dongbin Zhang, Guorui Song, Guocun Wang, Peng Jiao, Haoqian WangAbstract
Robot demonstrations contain reusable manipulation knowledge, but transferring this knowledge across embodiments requires representations that bridge differences in control interfaces. Action reconstruction alone does not ensure that similar behaviors across robots share a representation. To address this gap, we introduce CIALLO, an action codec that aligns actions, visual changes, and observation-grounded language in a shared space of short-horizon behavioral intent. An embodiment-conditioned decoder maps this intent back to robot-specific actions, allowing a shared representation to support different control interfaces. After pretraining on eight embodiments, CIALLO adapts to a new robot from one recording of at most 10 seconds by updating only its embodiment embeddings. The calibrated codec then remains frozen while a policy learns to predict intent from observations and instructions. We instantiate this policy with Qwen3.5-4B to form Qwen-CIALLO, whose backbone requires no large-scale robot-action pretraining before policy finetuning. With 20 demonstrations per task, Qwen-CIALLO achieves 76.7\% average success across real SO-101 and single-arm Piper robots, compared with 70.0\% for fully finetuned $\pi_0$. In simulation, we additionally finetune the action decoder, achieving 97.3\% success on LIBERO and 52.7\% on RoboTwin 2.0. The LIBERO policy also achieves 80.8\% on LIBERO-Plus without further finetuning. Together, these results support a shared action codec as a transferable control interface that separates embodiment calibration from task learning.
Abstract (translated)
URL
https://arxiv.org/abs/2611.13732
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DepthGS: Depth-Guided Gaussian Splatting with Adaptive Regularization for High-Quality Surface Reconstruction
2026-11-10 06:16:16Xiao Ren, Yu Liu, Ning An, Jian Cheng, Xin Qiao, You-Fu Li, He KongAbstract
Recently, 3D Gaussian Splatting (3DGS) has emerged as an efficient representation for novel view synthesis, offering fast differentiable rendering and high visual fidelity, and has increasingly been extended to surface reconstruction. However, the relationship between depth information and reconstruction error remains insufficiently explored, limiting the principled design of geometric optimization strategies. To fill the above gap, we propose DepthGS, a depth-guided Gaussian splatting framework. We derive theoretical relations between depth discrepancies and reconstruction error under single-view and multi-view settings, and rigorously establish corresponding upper bounds on reconstruction error. The above analysis informs the design of adaptive regularization strategies in both single-view and multi-view optimization. More specifically, for single-view optimization, we propose a depth-difference-guided adaptive normal regularization strategy that modulates the normal constraint strength using a geometric reliability weight computed from local depth differences. For multi-view optimization, we introduce a cross-view depth consistency regularization strategy that promotes consistency between neighboring-view depth maps and the corresponding depth predictions obtained by transforming the current view's depth predictions into those neighboring views. Extensive experiments on DTU, Mip-NeRF360, and Tanks and Temples demonstrate that DepthGS achieves competitive performance in both surface reconstruction and novel view synthesis.
Abstract (translated)
URL
https://arxiv.org/abs/2611.13628
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When to Start Denoising? Adaptive Denoising Entry for Generative Video Compression
2026-11-10 06:02:13Zifu Zhang, Yuqiao Li, Ding Ding, Shengxi Li, Mai Xu, Daowen Li, Kai Li, Ying ChenAbstract
Generative video compression offers a promising solution for compressing and reconstructing videos under extremely low bitrate constraints, among which the diffusion-based solutions still achieve the best performance by providing the powerful generative latent prior. However, their effectiveness critically depends on when the compressed latent is introduced into the diffusion process, which directly governs the trade-off between reconstruction fidelity and perceptual realism. To address this limitation, we identify denoising start-timestep selection as a key factor governing this trade-off and formulate it as a geometric optimization problem. Based on this formulation, we propose a novel adaptive diffusion entry method for generative video compression (ADE-GVC), the first timestep-aware generative video compression framework, featuring a lightweight predictor that estimates an adaptive denoising start point from the compressed latent. A temporal adapter further extracts compression-aware conditions and injects them into a pretrained video diffusion model, enabling the reconstruction of videos with both high fidelity and realism. More importantly, we observe a strong quantitative relationship between the predicted timesteps and the distortion between the original and compressed latents, providing empirical support for our optimization formulation. Extensive experiments demonstrate that ADE-GVC achieves the state-of-the-art performance on perceptual metrics and substantially improves reconstruction realism over existing generative video compression methods. Notably, our ADE-GVC achieves an average bitrate savings of 40.99\% (on DISTS) and 95.24\% (on PSNR) compared to the latest open-source baseline GLC-Video.
Abstract (translated)
URL
https://arxiv.org/abs/2611.13620
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Lightweight Deep Learning Framework for Astrocyte-Centric 3D Reconstruction across Normal and Stress-associated Ultrastructural States
2026-11-10 04:54:30Bowen Deng, Gwang-Jin Jeong, Seulgi Noh, Ji Young Mun, Na Young KimAbstract
The morphology of astrocytes is closely associated with their ability to support and modulate neural circuit functions; however, its reconstruction from volume electron microscopy (vEM) data remains labor-intensive and computationally resource-intensive, placing substantial barriers on its broader adoption and scalability despite the high spatial resolution of vEM. We present AstroSeg-vEM, a lightweight, astrocyte-centric framework for morphology-preserving astrocyte segmentation, 3D reconstruction, and quantitative morphological analysis in vEM images. AstroSeg-vEM combines transformer-based 2D segmentation with dedicated post-processing methods and operates directly on high-resolution EM sections, making it well suited to anisotropic vEM data and downstream proofreading workflows while preserving the full in-plane resolution of the original EM data. Across four mouse hippocampal datasets representing normal and morphologically defined stress-associated astrocyte ultrastructural states, AstroSeg-vEM demonstrates robust performance and generalization, achieving average Dice and weighted Dice values of 0.92 and 0.95, respectively, on a held-out test dataset. Its lightweight architecture enables efficient, high-fidelity reconstruction on consumer-grade hardware, providing a scalable and accessible platform for large-scale astrocyte ultrastructure analysis and future astrocyte-neuron interaction studies.
Abstract (translated)
URL
https://arxiv.org/abs/2611.13581
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Massive Activations Confound Sparse Autoencoders
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Sparse autoencoders (SAEs) are commonly evaluated by variance explained and ablation damage. We show how massive activations undermine both evaluations, and propose a correction. Massive activations cause up to 99.9% of activation variance to lie along the first principal component (PC1). Because the PC1 component has no unique sparse decomposition, each SAE run rebuilds it from a different set of features. These features dominate importance rankings: an average of 47 of the 50 most important features are unmatched in a separate run, compared with about 27 of a random 50. A dictionary can also report 99.96% of variance explained while leaving 33% of the variance outside PC1 unexplained. We bypass PC1 by training the SAE on activations with PC1 removed, then adding PC1 to the reconstruction. In affected models, the top-50 feature sharing rate rises from 4-39.5% to 73-99.5%. At the same TopK sparsity, the resulting SAE degrades the model up to 44% less and reduces content reconstruction error by up to 33.9%.
Abstract (translated)
URL
https://arxiv.org/abs/2611.13548
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GEMOR-GS: Global Extrinsic-calibration-refined Mapping and Online Relocalization for 3D Gaussian-Splatting SLAM
2026-11-10 03:51:43Yuchen Yang, Ming Ding, Xinyu Wu, Hesheng WangAbstract
Photorealistic and metrically consistent world representations are a primary requirement for LiDAR--inertial--visual SLAM systems that serve robots over continuous operation. 3D Gaussian splatting makes such representations attainable by supplying an explicit, renderable, and queryable scene model. We present GEMOR-GS (Global Extrinsic-calibration-refined Mapping and Online Relocalization for 3D Gaussian-Splatting SLAM) to make the Gaussian map geometrically accurate, globally refined, and re-enterable, providing a better appearance for robot perception and decision-making. To improve the 3DGS map, the LiDAR--camera extrinsic is first estimated offline by direct-method alignment over dedicated calibration segments and reused by all following online and offline processes. Under the calibrated geometry, keyframe poses and Gaussian parameters are refined alternately under a gated differentiable-rendering and LiDAR--projection objective. The final global reconstruction is then rebuilt from the refined keyframe schema with all online constraints lifted. For the robot SLAM lifecycle, the method recovers the pose from the 3DGS map after tracking loss through an XFeat bypass map, RANSAC-PnP coarse localization, and Gaussian RGB-D warp refinement. Experiments on one self-collected and five public sequences quantify each element: the offline reconstruction wins all paired keyframes against the online map by 14.3--19.9 dB, improves PSNR by approximately 9 dB over Gaussian-LIC2, and achieves 86--100% held-out relocalization success tied to extrinsic quality. The results show that GEMOR-GS improves the geometric accuracy, appearance fidelity, and re-enterability of the 3DGS map, serving as a dependable robot world model for SLAM and downstream tasks.
Abstract (translated)
URL
https://arxiv.org/abs/2611.13528
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SciFigure2Code: An AI-Reconstructed Benchmark for Scientific Figure-to-Code
2026-11-10 03:25:51Wentao Li, Yibo Wu, Yizhe Chen, Ruixuan Chen, Jiangjie Qiu, Yijun Li, Zhao Leyi, Xiaonan WangAbstract
Scientific figures are the interface through which research claims are inspected and reused, but final published panels rarely expose the data or plotting code that produced them. Recovering this hidden provenance from pixels is therefore underdetermined. We introduce SciFigure2Code, an AI-reconstructed benchmark that evaluates presentation recovery: generating editable Python programs that preserve how a scientific panel is arranged and read. Role-specialized Codex agents generate, execute, visually refine, and audit silver-standard presentation programs that capture geometry, visual hierarchy, encodings, annotations, and typography. This reconstruction-and-audit protocol turns final published panels into auditable reference packages; the resulting resource contains 6,740 reviewed panels and SciFigureBench, a balanced 337-panel test set across 31 chart subtypes, five domains, and three complexity levels. Across 14 zero-shot models, execution and structural fidelity remain weak; a 328-panel full-figure study further exposes failures to locate and isolate requested panels. Claude Opus 4.7 leads image-only reconstruction, Claude Opus 4.6 leads caption-assisted reconstruction, and plan-then-code prompting improves all four tested models. SciFigure2Code provides an auditable testbed for constructing editable, visually faithful scientific figure presentations.
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URL
https://arxiv.org/abs/2609.08155
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Dark Matters: VAE-Aware HDR Encoding for SDR-to-HDR Video Reconstruction
2026-11-10 03:16:31Donghoon Cha, Bomseok Park, Hansl von Kwon, Ku DoHyung, Hanwool SulAbstract
SDR-to-HDR reconstruction is an ill-posed problem in which clipped highlights, crushed shadows, and quantization artifacts must be recovered while preserving the original content. Latent diffusion models provide powerful generative priors for restoring missing detail, but their effectiveness is constrained by how HDR signals pass through the pretrained VAE. We find that common log-like encodings suppress low-luminance chromatic differences before generation, producing a dark-side collapse in the frozen-VAE latent. We introduce EquivFlow, a compact, invertible exposure-equivariant encoding that maps exposure changes to additive shifts while retaining a scale-independent chromatic component, without modifying the VAE. Encoding-level tests across pretrained image and video VAEs show that its exposure structure and deep-dark chroma transport persist across the tested hosts. Integrated into SDR-to-HDR video diffusion, EquivFlow delivers consistent chromatic-fidelity gains across the tested settings while retaining competitive reconstruction fidelity.
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URL
https://arxiv.org/abs/2611.13504
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DeRep: Learning Depth Representations for End-to-End Navigation in Cluttered Environments
2026-11-10 03:11:47Hanyu Jin, Kenji ShimadaAbstract
End-to-end navigation in cluttered environments relies on compact visual representations to support collision avoidance and goal-directed motion. Existing methods typically learn these representations jointly with the policy or through observation reconstruction, which does not explicitly specify what information the representation should preserve. Moreover, they are usually evaluated with a single downstream policy learner, although the benefit of a representation may depend on how the policy is learned. It therefore remains unclear how different representation-learning objectives affect downstream navigation performance and robustness. This work proposes DeRep, a navigation-oriented representation-learning method that combines local bird's-eye-view reachability supervision with depth reconstruction. To compare representation objectives under controlled conditions, we pretrain encoders with a common architecture and freeze them during downstream learning. We evaluate the representations using a linear policy probe, flow-matching imitation learning, and reinforcement learning with PPO. DeRep achieves the lowest linear policy probe prediction error and outperforms reconstruction alone across all six tested PPO conditions. In imitation learning, both reachability-based objectives achieve higher mean success rates than reconstruction alone, with similar mean success rates between the reachability-only and joint objectives. These results demonstrate consistent benefits of incorporating reachability supervision into depth representation pretraining across different downstream learning methods and evaluation conditions. We further deploy the PPO policy with the frozen DeRep encoder in Gazebo and on a physical quadrotor without fine-tuning, demonstrating its capability for zero-shot sim-to-sim and sim-to-real transfer.
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URL
https://arxiv.org/abs/2611.13499
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When Reconstruction Helps Event-Camera Person Triggers
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Event cameras record asynchronous changes in brightness. To use a general visual model as a recording trigger, a system must represent these measurements in a form the model can interpret. We compare direct grayscale accumulation, two temporal encodings, and two intensity reconstructors on paired real event data. On 192 windows from four held-out DSEC recordings, thresholds calibrated only on development data yielded 40 of 52 person detections and 12 of 140 background positives with E2VID. The strongest direct temporal encoding at an admissible fixed cutoff yielded 14 detections and seven background positives. A retrospective comparison at a common 10% background-positive cap yielded 40 detections for E2VID and at most 19 for any direct encoding. FireNet+ had lower preparation cost and produced 21 detections with zero observed background positives at its frozen cutoff. On the same 192 windows, Qwen3-VL-4B yielded 33/52, 2/140 with E2VID and 9/52, 9/140 with the highest-recall direct rendering, the three-bin image (person detections, background positives). A 96-second exploratory replay illustrates the sensitivity of episode capture and recording starts to cutoff selection. The experiments identify a detection benefit from reconstruction under controlled input history and distinguish it from the cost and false starts of continuous triggering.
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URL
https://arxiv.org/abs/2611.13488
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Camera3R: Feed-Forward 3D Reconstruction from Heterogeneous Camera Models
2026-11-10 01:56:04Ruxiao Duan, Yunwen Zhou, Erin Hong, Dongxu Zhao, Eric Turner, Federico Tombari, Alex WongAbstract
Feed-forward 3D reconstruction (3R) from unconstrained multi-view images has recently emerged as a prominent research direction in 3D computer vision. Various foundational reconstruction models have been proposed with different architectures and reconstruction paradigms. Despite being trained on large-scale perspective datasets with substantial computational resources, these models generally struggle to generalize to non-perspective images. This limitation hinders their deployment in applications involving arbitrary, unknown, and potentially heterogeneous camera models. To build on the capabilities of existing reconstruction models with minimal retraining, we propose Camera3R, a low-rank adaptation framework that efficiently extends perspective-pretrained 3R networks to any other camera models. Extensive experiments demonstrate that, with only 0.5% additional parameters and less than a day of training, Camera3R adapts a foundational 3D reconstruction model to non-perspective cameras while fully preserving its original performance on perspective inputs. Code is available at this https URL.
Abstract (translated)
URL
https://arxiv.org/abs/2611.13453
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Multi-Stage Phase-Aware Self-Supervised Reconstruction for Multi-Echo Gradient-Echo MRI
2026-11-09 23:25:26Juan Liu, Nian WangAbstract
Purpose: To develop a phase-aware self-supervised framework for accelerated high-resolution multi-echo gradient-echo (mGRE) MRI that preserves anatomical detail and complex echo information for quantitative mapping. Methods: We developed multi-stage phase-aware self-supervised reconstruction (MSPR-GRE), integrating progressive k-space expansion with phase estimation and refinement. Sequential unrolled networks reconstruct complex multi-echo images and update echo-dependent phase priors. A relaxation-informed temporal subspace is used for acquisitions with at least four echoes, while shorter echo trains are reconstructed in the image domain. Training uses held-out acquired k-space samples without fully sampled targets. Evaluation included 9.4 T ex vivo mouse-brain data 30um eight-echo and 18um dual-echo) and retrospectively undersampled 7 T AHEAD human-brain data, with supervised ablations. Results:MSPR-GRE reduced artifacts in regions of rapid phase variation and preserved fine mouse-brain anatomy. Across five AHEAD test datasets at R = 4, 8, and 12, it generally improved magnitude-image, T2* map, and QSM metrics, particularly at higher acceleration. At R = 12, fourth-echo magnitude NRMSE was 12.09$\pm$0.60% versus 21.55$\pm$1.12% for SSDU. Ablations indicated benefits of phase refinement, while supervised experiments supported multi-stage phase-aware reconstruction. Conclusion: MSPR-GRE improves accelerated mGRE reconstruction and quantitative-map agreement without fully sampled training targets. Further validation of generalizability and phase-estimation accuracy is needed.
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URL
https://arxiv.org/abs/2611.13352
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PegasusAI Studio: Legible Cyberinfrastructure and Accountable AI Agents for Scientific Workflows
2026-11-09 22:22:25Komal Thareja, Mats Rynge, Berent Aldikacti, Angelina Ju, Ian Lumsden, Anirban Mandal, Rajiv Mayani, Kin Wai Ng, Hamza Safri, Michael Stealey, Sai Swaminathan, Michela Taufer, Karan Vahi, Michael Zink, Ewa DeelmanAbstract
AI coding agents can now construct scientific workflows, but operating them on shared cyberinfrastructure (CI) raises problems that code generation does not solve. Agents need current knowledge of the workflow system and its execution sites and access to the runtime state of distributed executions, while facilities need to attribute every agent action to a user and bound it by that user's privileges. We present PegasusAI Studio, an AI-assisted science gateway built on the Pegasus and HTCondor stack. Studio makes CI legible to agents by projecting one facility-curated knowledge base into the native configuration of several coding agents, by introspecting workflow interfaces and execution sites, and by grounding diagnosis in workflow and scheduler telemetry. Agent actions operate within a trust envelope that combines federated authentication, per-user execution environments and scheduler credentials, provider-neutral model access, observability, and approval controls for state-changing actions. The same application runs as a JupyterHub-based gateway on a research cloud and as an Open OnDemand application on HPC systems. We evaluate Studio through case studies of legacy CASA weather workflow modernization, a gravitational-wave reanalysis, an EEG analysis built with an open-weight model, and an Event Horizon Telescope (EHT) M87 image reconstruction that recovered from two failed runs to a zero-failure execution. The evaluation establishes that these mechanisms operate as designed.
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URL
https://arxiv.org/abs/2611.13309
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DUO: Dual Readouts of Diffusion Models for OOD Detection
2026-11-09 22:13:09Alireza Javid, Shirin Shoushtari, Nuria Gonz\'alez PrelcicAbstract
Diffusion models are powerful generative methods for learning and sampling from complex data distributions. Safely deploying these models requires detecting inputs that fall outside their training distribution. Because diffusion models recover clean samples from noisy inputs, reconstruction error is often used for out-of-distribution (OOD) detection. This approach assumes that in-distribution (ID) inputs are reconstructed more accurately than OOD inputs. However, OOD inputs may be reconstructed equally well or even better, making this score unreliable. We therefore propose the leading sensitivity spectrum of intermediate denoising features as a complementary OOD signal and demonstrate that it remains informative when reconstruction error is misleading. We introduce DUal-readout of diffusion models for OOD detection (DUO), a fully unsupervised, training-free OOD detector that combines reconstruction error and feature sensitivity. DUO improves average AUROC by approximately 6% points over the strongest baselines while substantially reducing inference cost, and achieves SOTA on near-OOD and high-resolution benchmarks.
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URL
https://arxiv.org/abs/2611.13304
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