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Cross-Scale MAE: A Tale of Multi-Scale Exploitation in Remote Sensing

arXiv:2401.15855v1 Announce Type: cross Abstract: Remote sensing images present unique challenges to image analysis due to the extensive geographic coverage, hardware limitations, and misaligned multi-scale images. This paper revisits the classical multi-scale representation learning problem but under the general framework of self-supervised learning for remote sensing image understanding. We present Cross-Scale MAE, a self-supervised model built upon the Masked Auto-Encoder (MAE).During pre-training, Cross-Scale MAE employs scale augmentation techniques and enforces cross-scale consistency constraints through both contrastive and generative losses to ensure consistent and meaningful representations well-suited for a wide range of downstream tasks. Further, our implementation leverages the xFormers library to accelerate network pre-training on a single GPU while maintaining the quality of learned representations. Experimental evaluations demonstrate that Cross-Scale MAE exhibits superior performance compared to standard MAE and other state-of-the-art remote sensing MAE methods.
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CLPIPS: A Personalized Metric for AI-Generated Image Similarity

arXiv:2604.01234v1 Announce Type: cross Abstract: Iterative prompt refinement is central to reproducing target images with text to image generative models. Previous studies have incorporated image similarity metrics (ISMs) as additional feedback to human users. Existing ISMs such as LPIPS and CLIP provide objective measures of image likeness but often fail to align with human judgments, particularly in context specific or user driven tasks. In this paper, we introduce Customized Learned Perceptual Image Patch Similarity (CLPIPS), a customized extension of LPIPS that adapts a metric's notion of similarity directly to human judgments. We aim to explore whether lightweight, human augmented fine tuning can meaningfully improve perceptual alignment, positioning similarity metrics as adaptive components for human in the loop workflows with text to image tools. We evaluate CLPIPS on a human subject dataset in which participants iteratively regenerate target images and rank generated outputs by perceived similarity. Using margin ranking loss on human ranked image pairs, we fine tune only the LPIPS layer combination weights and assess alignment via Spearman rank correlation and Intraclass Correlation Coefficient. Our results show that CLPIPS achieves stronger correlation and agreement with human judgments than baseline LPIPS. Rather than optimizing absolute metric performance, our work emphasizes improving alignment consistency between metric predictions and human ranks, demonstrating that even limited human specific fine tuning can meaningfully enhance perceptual alignment in human in the loop text to image workflows.
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OkanNet: A Lightweight Deep Learning Architecture for Classification of Brain Tumor from MRI Images

arXiv:2604.01264v1 Announce Type: cross Abstract: Medical imaging techniques, especially Magnetic Resonance Imaging (MRI), are accepted as the gold standard in the diagnosis and treatment planning of neurological diseases. However, the manual analysis of MRI images is a time-consuming process for radiologists and is prone to human error due to fatigue. In this study, two different Deep Learning approaches were developed and analyzed comparatively for the automatic detection and classification of brain tumors (Glioma, Meningioma, Pituitary, and No Tumor). In the first approach, a custom Convolutional Neural Network (CNN) architecture named "OkanNet", which has a low computational cost and fast training time, was designed from scratch. In the second approach, the Transfer Learning method was applied using the 50-layer ResNet-50 [1] architecture, pre-trained on the ImageNet dataset. In experiments conducted on an extended dataset compiled by Masoud Nickparvar containing a total of $7,023$ MRI images, the Transfer Learning-based ResNet-50 model exhibited superior classification performance, achieving $96.49\%$ Accuracy and $0.963$ Precision. In contrast, the custom OkanNet architecture reached an accuracy rate of $88.10\%$; however, it proved to be a strong alternative for mobile and embedded systems with limited computational power by yielding results approximately $3.2$ times faster ($311$ seconds) than ResNet-50 in terms of training time. This study demonstrates the trade-off between model depth and computational efficiency in medical image analysis through experimental data.
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AffordTissue: Dense Affordance Prediction for Tool-Action Specific Tissue Interaction

arXiv:2604.01371v1 Announce Type: cross Abstract: Surgical action automation has progressed rapidly toward achieving surgeon-like dexterous control, driven primarily by advances in learning from demonstration and vision-language-action models. While these have demonstrated success in table-top experiments, translating them to clinical deployment remains challenging: current methods offer limited predictability on where instruments will interact on tissue surfaces and lack explicit conditioning inputs to enforce tool-action-specific safe interaction regions. Addressing this gap, we introduce AffordTissue, a multimodal framework for predicting tool-action specific tissue affordance regions as dense heatmaps during cholecystectomy. Our approach combines a temporal vision encoder capturing tool motion and tissue dynamics across multiple viewpoints, language conditioning enabling generalization across diverse instrument-action pairs, and a DiT-style decoder for dense affordance prediction. We establish the first tissue affordance benchmark by curating and annotating 15,638 video clips across 103 cholecystectomy procedures, covering six unique tool-action pairs involving four instruments (hook, grasper, scissors, clipper) and their associated tasks: dissection, grasping, clipping, and cutting. Experiments demonstrate substantial improvement over vision-language model baselines (20.6 px ASSD vs. 60.2 px for Molmo-VLM), showing that our task-specific architecture outperforms large-scale foundation models for dense surgical affordance prediction. By predicting tool-action specific tissue affordance regions, AffordTissue provides explicit spatial reasoning for safe surgical automation, potentially unlocking explicit policy guidance toward appropriate tissue regions and early safe stop when instruments deviate outside predicted safe zones.
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DeDelayed: Deleting Remote Inference Delay via On-Device Correction

arXiv:2510.13714v3 Announce Type: replace-cross Abstract: Video comprises the vast majority of bits that are generated daily, and is the primary signal driving current innovations in robotics, remote sensing, and wearable technology. Yet, the most powerful video understanding models are too expensive for the resource-constrained platforms used in these applications. One approach is to offload inference to the cloud; this gives access to GPUs capable of processing high-resolution videos in real time. But even with reliable, high-bandwidth communication channels, the combined latency of video encoding, model inference, and round-trip communication prohibits use for certain real-time applications. The alternative is to use fully local inference; but this places extreme constraints on computational and power costs, requiring smaller models and lower resolution, leading to degraded accuracy. To address these challenges, we propose Dedelayed, a real-time inference system that divides computation between a remote model operating on delayed video frames and a local model with access to the current frame. The remote model is trained to make predictions on anticipated future frames, which the local model incorporates into its prediction for the current frame. The local and remote models are jointly optimized with an autoencoder that limits the transmission bitrate required by the available downlink communication channel. We evaluate Dedelayed on the task of real-time streaming video segmentation using the BDD100k driving dataset. For a round trip delay of 100 ms, Dedelayed improves performance by 6.4 mIoU compared to fully local inference and 9.8 mIoU compared to remote inference -- an equivalent improvement to using a model ten times larger. We release our training code, pretrained models, and python library at https://github.com/InterDigitalInc/dedelayed .
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Modeling Spatiotemporal Neural Frames for High Resolution Brain Dynamic

arXiv:2603.24176v2 Announce Type: replace-cross Abstract: Capturing dynamic spatiotemporal neural activity is essential for understanding large-scale brain mechanisms. Functional magnetic resonance imaging (fMRI) provides high-resolution cortical representations that form a strong basis for characterizing fine-grained brain activity patterns. The high acquisition cost of fMRI limits large-scale applications, therefore making high-quality fMRI reconstruction a crucial task. Electroencephalography (EEG) offers millisecond-level temporal cues that complement fMRI. Leveraging this complementarity, we present an EEG-conditioned framework for reconstructing dynamic fMRI as continuous neural sequences with high spatial fidelity and strong temporal coherence at the cortical-vertex level. To address sampling irregularities common in real fMRI acquisitions, we incorporate a null-space intermediate-frame reconstruction, enabling measurement-consistent completion of arbitrary intermediate frames and improving sequence continuity and practical applicability. Experiments on the CineBrain dataset demonstrate superior voxel-wise reconstruction quality and robust temporal consistency across whole-brain and functionally specific regions. The reconstructed fMRI also preserves essential functional information, supporting downstream visual decoding tasks. This work provides a new pathway for estimating high-resolution fMRI dynamics from EEG and advances multimodal neuroimaging toward more dynamic brain activity modeling.
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Abnormalities and Disease Detection in Gastro-Intestinal Tract Images

arXiv:2603.22378v1 Announce Type: cross Abstract: Gastrointestinal (GI) tract image analysis plays a crucial role in medical diagnosis. This research addresses the challenge of accurately classifying and segmenting GI images for real-time applications, where traditional methods often struggle due to the diversity and complexity of abnormalities. The high computational demands of this domain require efficient and adaptable solutions. This PhD thesis presents a multifaceted approach to GI image analysis. Initially, texture-based feature extraction and classification methods were explored, achieving high processing speed (over 4000 FPS) and strong performance (F1-score: 0.76, Accuracy: 0.98) on the Kvasir V2 dataset. The study then transitions to deep learning, where an optimized model combined with data bagging techniques improved performance, reaching an accuracy of 0.92 and an F1-score of 0.60 on the HyperKvasir dataset, and an F1-score of 0.88 on Kvasir V2. To support real-time detection, a streamlined neural network integrating texture and local binary patterns was developed. By addressing inter-class similarity and intra-class variation through a learned threshold, the system achieved 41 FPS with high accuracy (0.99) and an F1-score of 0.91 on HyperKvasir. Additionally, two segmentation tools are proposed to enhance usability, leveraging Depth-Wise Separable Convolution and neural network ensembles for improved detection, particularly in low-FPS scenarios. Overall, this research introduces novel and adaptable methodologies, progressing from traditional texture-based techniques to deep learning and ensemble approaches, providing a comprehensive framework for advancing GI image analysis.
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Unmasking Biases and Reliability Concerns in Convolutional Neural Networks Analysis of Cancer Pathology Images

arXiv:2603.12445v1 Announce Type: cross Abstract: Convolutional Neural Networks have shown promising effectiveness in identifying different types of cancer from radiographs. However, the opaque nature of CNNs makes it difficult to fully understand the way they operate, limiting their assessment to empirical evaluation. Here we study the soundness of the standard practices by which CNNs are evaluated for the purpose of cancer pathology. Thirteen highly used cancer benchmark datasets were analyzed, using four common CNN architectures and different types of cancer, such as melanoma, carcinoma, colorectal cancer, and lung cancer. We compared the accuracy of each model with that of datasets made of cropped segments from the background of the original images that do not contain clinically relevant content. Because the rendered datasets contain no clinical information, the null hypothesis is that the CNNs should provide mere chance-based accuracy when classifying these datasets. The results show that the CNN models provided high accuracy when using the cropped segments, sometimes as high as 93\%, even though they lacked biomedical information. These results show that some CNN architectures are more sensitive to bias than others. The analysis shows that the common practices of machine learning evaluation might lead to unreliable results when applied to cancer pathology. These biases are very difficult to identify, and might mislead researchers as they use available benchmark datasets to test the efficacy of CNN methods.
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Multiscale Structure-Guided Latent Diffusion for Multimodal MRI Translation

arXiv:2603.12581v1 Announce Type: cross Abstract: Although diffusion models have achieved remarkable progress in multi-modal magnetic resonance imaging (MRI) translation tasks, existing methods still tend to suffer from anatomical inconsistencies or degraded texture details when handling arbitrary missing-modality scenarios. To address these issues, we propose a latent diffusion-based multi-modal MRI translation framework, termed MSG-LDM. By leveraging the available modalities, the proposed method infers complete structural information, which preserves reliable boundary details. Specifically, we introduce a style--structure disentanglement mechanism in the latent space, which explicitly separates modality-specific style features from shared structural representations, and jointly models low-frequency anatomical layouts and high-frequency boundary details in a multi-scale feature space. During the structure disentanglement stage, high-frequency structural information is explicitly incorporated to enhance feature representations, guiding the model to focus on fine-grained structural cues while learning modality-invariant low-frequency anatomical representations. Furthermore, to reduce interference from modality-specific styles and improve the stability of structure representations, we design a style consistency loss and a structure-aware loss. Extensive experiments on the BraTS2020 and WMH datasets demonstrate that the proposed method outperforms existing MRI synthesis approaches, particularly in reconstructing complete structures. The source code is publicly available at https://github.com/ziyi-start/MSG-LDM.
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Marker-Based 3D Reconstruction of Aggregates with a Comparative Analysis of 2D and 3D Morphologies

arXiv:2603.12667v1 Announce Type: cross Abstract: Aggregates, serving as the main skeleton in assemblies of construction materials, are important functional components in various building and transportation infrastructures. They can be used in unbound layer applications, e.g. pavement base and railroad ballast, bound applications of cement concrete and asphalt concrete, and as riprap and large-sized primary crushed rocks. Information on the size and shape or morphology of aggregates can greatly facilitate the Quality Assurance/Quality Control (QA/QC) process by providing insights of aggregate behavior during composition and packing. A full 3D characterization of aggregate particle morphology is difficult both during production in a quarry and at a construction site. Many aggregate imaging approaches have been developed to quantify the particle morphology by computer vision, including 2D image-based approaches that analyze particle silhouettes and 3D scanning-based methods that require expensive devices such as 3D laser scanners or X-Ray Computed Tomography (CT) equipment. This paper presents a flexible and cost-effective photogrammetry-based approach for the 3D reconstruction of aggregate particles. The proposed approach follows a marker-based design that enables background suppression, point cloud stitching, and scale referencing to obtain high-quality aggregate models. The accuracy of the reconstruction results was validated against ground-truth for selected aggregate samples. Comparative analyses were conducted on 2D and 3D morphological properties of the selected samples. Significant differences were found between the 2D and 3D statistics. Based on the presented approach, 3D shape information of aggregates can be obtained easily and at a low cost, thus allowing convenient aggregate inspection, data collection, and 3D morphological analysis.
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Empowering Semantic-Sensitive Underwater Image Enhancement with VLM

arXiv:2603.12773v1 Announce Type: cross Abstract: In recent years, learning-based underwater image enhancement (UIE) techniques have rapidly evolved. However, distribution shifts between high-quality enhanced outputs and natural images can hinder semantic cue extraction for downstream vision tasks, thereby limiting the adaptability of existing enhancement models. To address this challenge, this work proposes a new learning mechanism that leverages Vision-Language Models (VLMs) to empower UIE models with semantic-sensitive capabilities. To be concrete, our strategy first generates textual descriptions of key objects from a degraded image via VLMs. Subsequently, a text-image alignment model remaps these relevant descriptions back onto the image to produce a spatial semantic guidance map. This map then steers the UIE network through a dual-guidance mechanism, which combines cross-attention and an explicit alignment loss. This forces the network to focus its restorative power on semantic-sensitive regions during image reconstruction, rather than pursuing a globally uniform improvement, thereby ensuring the faithful restoration of key object features. Experiments confirm that when our strategy is applied to different UIE baselines, significantly boosts their performance on perceptual quality metrics as well as enhances their performance on detection and segmentation tasks, validating its effectiveness and adaptability.
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SAW: Toward a Surgical Action World Model via Controllable and Scalable Video Generation

arXiv:2603.13024v1 Announce Type: cross Abstract: A surgical world model capable of generating realistic surgical action videos with precise control over tool-tissue interactions can address fundamental challenges in surgical AI and simulation -- from data scarcity and rare event synthesis to bridging the sim-to-real gap for surgical automation. However, current video generation methods, the very core of such surgical world models, require expensive annotations or complex structured intermediates as conditioning signals at inference, limiting their scalability. Other approaches exhibit limited temporal consistency across complex laparoscopic scenes and do not possess sufficient realism. We propose Surgical Action World (SAW) -- a step toward surgical action world modeling through video diffusion conditioned on four lightweight signals: language prompts encoding tool-action context, a reference surgical scene, tissue affordance mask, and 2D tool-tip trajectories. We design a conditional video diffusion approach that reformulates video-to-video diffusion into trajectory-conditioned surgical action synthesis. The backbone diffusion model is fine-tuned on a custom-curated dataset of 12,044 laparoscopic clips with lightweight spatiotemporal conditioning signals, leveraging a depth consistency loss to enforce geometric plausibility without requiring depth at inference. SAW achieves state-of-the-art temporal consistency (CD-FVD: 199.19 vs. 546.82) and strong visual quality on held-out test data. Furthermore, we demonstrate its downstream utility for (a) surgical AI, where augmenting rare actions with SAW-generated videos improves action recognition (clipping F1-score: 20.93% to 43.14%; cutting: 0.00% to 8.33%) on real test data, and (b) surgical simulation, where rendering tool-tissue interaction videos from simulator-derived trajectory points toward a visually faithful simulation engine.
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OpenVision 3: A Family of Unified Visual Encoder for Both Understanding and Generation

arXiv:2601.15369v2 Announce Type: replace-cross Abstract: This paper presents a family of advanced vision encoder, named OpenVision 3, that learns a single, unified visual representation that can serve both image understanding and image generation. Our core architecture is simple: we feed VAE-compressed image latents to a ViT encoder and train its output to support two complementary roles. First, the encoder output is passed to the ViT-VAE decoder to reconstruct the original image, encouraging the representation to capture generative structure. Second, the same representation is optimized with contrastive learning and image-captioning objectives, strengthening semantic features. By jointly optimizing reconstruction- and semantics-driven signals in a shared latent space, the encoder learns representations that synergize and generalize well across both regimes. We validate this unified design through extensive downstream evaluations with the encoder frozen. For generation, we test it under the RAE framework: ours substantially surpasses the standard CLIP-based encoder (e.g., gFID: 1.87 vs. 2.54 on ImageNet). For multimodal understanding, we plug the encoder into the LLaVA-1.5 and LLaVA-NeXT framework: it performs comparably with a standard CLIP vision encoder (e.g., 63.3 vs. 61.2 on SeedBench, and 59.2 vs. 58.1 on GQA). We provide empirical evidence that generation and understanding are mutually beneficial in our architecture, while further underscoring the critical role of the VAE latent space. We hope this work can spur future research on unified modeling.
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Subclass Classification of Gliomas Using MRI Fusion Technique

arXiv:2502.18775v1 Announce Type: cross Abstract: Glioma, the prevalent primary brain tumor, exhibits diverse aggressiveness levels and prognoses. Precise classification of glioma is paramount for treatment planning and predicting prognosis. This study aims to develop an algorithm to fuse the MRI images from T1, T2, T1ce, and fluid-attenuated inversion recovery (FLAIR) sequences to enhance the efficacy of glioma subclass classification as no tumor, necrotic core, peritumoral edema, and enhancing tumor. The MRI images from BraTS datasets were used in this work. The images were pre-processed using max-min normalization to ensure consistency in pixel intensity values across different images. The segmentation of the necrotic core, peritumoral edema, and enhancing tumor was performed on 2D and 3D images separately using UNET architecture. Further, the segmented regions from multimodal MRI images were fused using the weighted averaging technique. Integrating 2D and 3D segmented outputs enhances classification accuracy by capturing detailed features like tumor shape, boundaries, and intensity distribution in slices, while also providing a comprehensive view of spatial extent, shape, texture, and localization within the brain volume. The fused images were used as input to the pre-trained ResNet50 model for glioma subclass classification. The network is trained on 80% and validated on 20% of the data. The proposed method achieved a classification of accuracy of 99.25%, precision of 99.30%, recall of 99.10, F1 score of 99.19%, Intersection Over Union of 84.49%, and specificity of 99.76, which showed a significantly higher performance than existing techniques. These findings emphasize the significance of glioma segmentation and classification in aiding accurate diagnosis.
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Deep Learning-Based Approach for Automatic 2D and 3D MRI Segmentation of Gliomas

arXiv:2502.19760v1 Announce Type: cross Abstract: Brain tumor diagnosis is a challenging task for clinicians in the modern world. Among the major reasons for cancer-related death is the brain tumor. Gliomas, a category of central nervous system (CNS) tumors, encompass diverse subregions. For accurate diagnosis of brain tumors, precise segmentation of brain images and quantitative analysis are required. A fully automatic approach to glioma segmentation is required because the manual segmentation process is laborious, prone to mistakes, as well as time-consuming. Modern techniques for segmenting gliomas are based on fully convolutional neural networks (FCNs), which can either use two-dimensional (2D) or three-dimensional (3D) convolutions. Nevertheless, 3D convolutions suffer from computational costs and memory demand, while 2D convolutions cannot fully utilize the spatial insights of volumetric clinical imaging data. To obtain an optimal solution, it is vital to balance the computational efficiency of 2D convolutions along with the spatial accuracy of 3D convolutions. This balance can potentially be realized by developing an advanced model to overcome these challenges. The 2D and 3D models implemented here are based on UNET architecture, Inception, and ResNet models. The research work has been implemented on the BraTS 2018, 2019, and 2020 datasets. The best performer of all the models' evaluations metrics for proposed methodologies offer superior potential in terms of the effective segmentation of gliomas. The ResNet model has resulted in 98.91% accuracy for 3D segmentation and 99.77 for 2D segmentations. The dice scores for 2D and 3D segmentations are 0.8312 and 0.9888, respectively. This model can be applied to various other medical applications with fine-tuning, thereby aiding clinicians in brain tumor analysis and improving the diagnosis process effectively.
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Improving Visual Object Tracking through Visual Prompting

arXiv:2409.18901v2 Announce Type: replace-cross Abstract: Learning a discriminative model that distinguishes the specified target from surrounding distractors across frames is essential for generic object tracking (GOT). Dynamic adaptation of target representation against distractors remains challenging because prevailing trackers exhibit limited discriminative capability. To address this issue, we present a new visual prompting mechanism for generic object tracking, termed PiVOT. PiVOT introduces mechanisms that leverage the pretrained foundation model (CLIP) to automatically generate and refine visual prompts online, thereby enabling the tracker to suppress distractors through contrastive guidance. To transfer contrastive knowledge from the foundation model to the tracker, PiVOT automatically propagates this knowledge online and dynamically generates and updates visual prompts. Specifically, it proposes a prompt initialization mechanism that produces an initial visual prompt highlighting potential target locations. The foundation model is then used to refine the prompt based on appearance similarities between candidate objects and reference templates across potential targets. After refinement, the visual prompt better highlights potential target locations and reduces irrelevant prompt information. With the proposed prompting mechanism, the tracker can generate instance-aware feature maps guided by the visual prompts, which are incrementally and automatically updated during tracking, thereby effectively suppressing distractors. Extensive experiments across multiple benchmarks indicate that PiVOT, with the proposed prompting mechanism, can suppress distracting objects and improve tracking performance.
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Enhancing Alzheimer's Diagnosis: Leveraging Anatomical Landmarks in Graph Convolutional Neural Networks on Tetrahedral Meshes

arXiv:2503.05031v2 Announce Type: replace-cross Abstract: Alzheimer's disease (AD) is a major neurodegenerative condition that affects millions around the world. As one of the main biomarkers in the AD diagnosis procedure, brain amyloid positivity is typically identified by positron emission tomography (PET), which is costly and invasive. Brain structural magnetic resonance imaging (sMRI) may provide a safer and more convenient solution for the AD diagnosis. Recent advances in geometric deep learning have facilitated sMRI analysis and early diagnosis of AD. However, determining AD pathology, such as brain amyloid deposition, in preclinical stage remains challenging, as less significant morphological changes can be observed. As a result, few AD classification models are generalizable to the brain amyloid positivity classification task. Blood-based biomarkers (BBBMs), on the other hand, have recently achieved remarkable success in predicting brain amyloid positivity and identifying individuals with high risk of being brain amyloid positive. However, individuals in medium risk group still require gold standard tests such as Amyloid PET for further evaluation. Inspired by the recent success of transformer architectures, we propose a geometric deep learning model based on transformer that is both scalable and robust to variations in input volumetric mesh size. Our work introduced a novel tokenization scheme for tetrahedral meshes, incorporating anatomical landmarks generated by a pre-trained Gaussian process model. Our model achieved superior classification performance in AD classification task. In addition, we showed that the model was also generalizable to the brain amyloid positivity prediction with individuals in the medium risk class, where BM alone cannot achieve a clear classification. Our work may enrich geometric deep learning research and improve AD diagnosis accuracy without using expensive and invasive PET scans.
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CryoNet.Refine: A One-step Diffusion Model for Rapid Refinement of Structural Models with Cryo-EM Density Map Restraints

arXiv:2602.22263v2 Announce Type: replace-cross Abstract: High-resolution structure determination by cryo-electron microscopy (cryo-EM) requires the accurate fitting of an atomic model into an experimental density map. Traditional refinement pipelines such as Phenix.real_space_refine and Rosetta are computationally expensive, demand extensive manual tuning, and present a significant bottleneck for researchers. We present CryoNet.Refine, an end-to-end deep learning framework that automates and accelerates molecular structure refinement. Our approach utilizes a one-step diffusion model that integrates a density-aware loss function with robust stereochemical restraints, enabling rapid optimization of a structure against experimental data. CryoNet.Refine provides a unified and versatile solution capable of refining protein complexes as well as DNA/RNA-protein complexes. In benchmarks against Phenix.real_space_refine, CryoNet.Refine consistently achieves substantial improvements in both model-map correlation and overall geometric quality metrics. By offering a scalable, automated, and powerful alternative, CryoNet.Refine aims to serve as an essential tool for next-generation cryo-EM structure refinement. Web server: https://cryonet.ai/refine; Source code: https://github.com/kuixu/cryonet.refine.
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Cryo-SWAN: the Multi-Scale Wavelet-decomposition-inspired Autoencoder Network for molecular density representation of molecular volumes

arXiv:2603.03342v1 Announce Type: cross Abstract: Learning robust representations of 3D shapes from voxelized data is essential for advancing AI methods in biomedical imaging. However, most contemporary 3D computer vision approaches operate on point clouds, meshes, or octrees, while volumetric density maps, the native format of structural biology and cryo-EM, remain comparatively underexplored. We present Cryo-SWAN, a voxel-based variational autoencoder inspired by multi-scale wavelet decomposition. The model performs conditional coarse-to-fine latent encoding and recursive residual quantization across perception scales, enabling accurate capture of both global geometry and high-frequency structural detail in molecular density volumes. Evaluated on ModelNet40, BuildingNet, and a newly curated dataset of cryo-EM volumes, ProteinNet3D, Cryo-SWAN consistently improves reconstruction quality over state-of-the-art 3D autoencoders. We demonstrate that the molecular densities organize in learned latent space according to shared geometric features, while integration with diffusion models enables denoising and conditional shape generation. Together, Cryo-SWAN is a practical framework for data-driven structural biology and volumetric imaging.
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Field imaging framework for morphological characterization of aggregates with computer vision: Algorithms and applications

arXiv:2603.03654v1 Announce Type: cross Abstract: Construction aggregates, including sand and gravel, crushed stone and riprap, are the core building blocks of the construction industry. State-of-the-practice characterization methods mainly relies on visual inspection and manual measurement. State-of-the-art aggregate imaging methods have limitations that are only applicable to regular-sized aggregates under well-controlled conditions. This dissertation addresses these major challenges by developing a field imaging framework for the morphological characterization of aggregates as a multi-scenario solution. For individual and non-overlapping aggregates, a field imaging system was designed and the associated segmentation and volume estimation algorithms were developed. For 2D image analyses of aggregates in stockpiles, an automated 2D instance segmentation and morphological analysis approach was established. For 3D point cloud analyses of aggregate stockpiles, an integrated 3D Reconstruction-Segmentation-Completion (RSC-3D) approach was established: 3D reconstruction procedures from multi-view images, 3D stockpile instance segmentation, and 3D shape completion to predict the unseen sides. First, a 3D reconstruction procedure was developed to obtain high-fidelity 3D models of collected aggregate samples, based on which a 3D aggregate particle library was constructed. Next, two datasets were derived from the 3D particle library for 3D learning: a synthetic dataset of aggregate stockpiles with ground-truth instance labels, and a dataset of partial-complete shape pairs, developed with varying-view raycasting schemes. A state-of-the-art 3D instance segmentation network and a 3D shape completion network were trained on the datasets, respectively. The application of the integrated approach was demonstrated on real stockpiles and validated with ground-truth, showing good performance in capturing and predicting the unseen sides of aggregates.
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