Gaussian Process Prior Variational Autoencoder for Endoscopic Videos
Authors: Ivan De Boi, Xinxing Shi, Xiaoyu Jiang, Tim J. M. Jaspers, Francisco Caetano, Mauricio A. Alvarez, Fons van der Sommen, Sam Van der Jeught
Organizations: Department of Electromechanics, InViLab, University of Antwerp, Antwerp, Belgium · Department of Computer Science, University of Manchester, Manchester, United Kingdom · Department of Electrical Engineering, Eindhoven University of Technology, Eindhoven, the Netherlands
Abstract
Endoscopic video analysis is essential for gastrointestinal diagnosis and computer-assisted interventions, but video sequences are routinely degraded by specular reflections, motion artifacts, and missing frames. These transient corruptions can distract clinicians, reduce image interpretability, and disrupt downstream tasks such as 3D reconstruction and navigation. Effective restoration therefore requires methods that exploit temporal continuity rather than treating frames in isolation. We introduce a Gaussian Process Prior Variational Autoencoder (GPVAE) framework for endoscopic video restoration that replaces the standard factorized latent prior with a temporal Gaussian process prior, enabling interpolation of missing frames with uncertainty-aware reconstruction. The framework combines endoscopy-specific encoders, including a convolutional EndoVAE backbone and pretrained Vision Transformer encoders from GastroNet-5M, with two scalable GP approximations: Hierarchical Prior Approximation (HPA) and Sparse Precision Approximation (SPA). Specular reflections are handled using a DUCKNet-based masking pipeline that excludes corrupted pixels from the reconstruction objective. On the C3VDv2 colonoscopy dataset, the best GPVAE variants reduced image reconstruction RMSE by 21.9% on average, and by up to 26.1%, relative to matched VAE baselines. Downstream trajectory RMSE was reduced by 12.7% on average across classical visual odometry and a pretrained PoseNet, at an average increase of 27.3% in training time per epoch. Finally, the GP posterior provides per-frame uncertainty estimates that reflect temporal support and offer a confidence signal for restored frames.
Developing foundation generative models for endoscopy is limited by the gap between natural and clinical images and the computational cost of training large Diffusion Transformers. Although representation alignment has improved efficiency in general computer vision, its role within the highly specialized endoscopic image space remains unclear. We introduce REVEAL (Representation-driven Endoscopic Visual Embedding Alignment), the largest generative foundation model for endoscopy to date, trained on GastroNet-5M (GN-5M), a multicenter dataset of 5 million endoscopic frames. Instead of depending on out-of-domain priors, REVEAL employs encoders pretrained directly on the endoscopic distribution to align diffusion latents with domain-specific visual features, preserving fine textures and intricate anatomical structures. Beyond image generation, REVEAL also serves as a powerful feature extractor; in multiple benchmarks, it delivers performance that is competitive with, and in several cases exceeds, endoscopic foundation models such as EndoViT and Endo-FM, specifically tuned for classification tasks, while demonstrating strong representation robustness under realistic imaging corruptions. REVEAL produces high-fidelity images and maintains robust structural coherence in latent-space edits such as inpainting and outpainting. This high-capacity backbone lowers the computational threshold for building specialized clinical tools, offering an open, versatile foundation for conditional synthesis, segmentation, and out-of-distribution detection in future intelligent gastroenterology systems.
Francisco Caetano, Tim J. M. Jaspers, Haiko Middeljans +7
Robot-assisted minimally invasive surgery (MIS) critically depends on reliable endoscopic perception for navigation and safety. However, conventional endoscopes provide only a limited field of view, leaving large portions of the surrounding anatomy unobserved. Recent neural rendering approaches, such as Neural Radiance Fields and 3D Gaussian Splatting, enable novel view synthesis from endoscopic videos, but their reliance on sparse observations often leads to severe artifacts when extrapolating beyond the training trajectory. In this work, we propose ExtraGS, a framework for enhancing endoscopic view extrapolation through diffusion-guided 3D Gaussian Splatting. Starting from an initial reconstruction, we introduce an uncertainty-guided virtual camera sampling strategy to actively explore blind spots and maximize information gain. The rendered views from these sampled locations are refined using a diffusion model to recover plausible anatomical structures, producing pseudo-observations that guide further optimization. To prevent the generated content from degrading reliable regions, we adopt a confidence-weighted fine-tuning strategy when incorporating these pseudo-observations. Extensive experiments on multiple public endoscopic datasets demonstrate that ExtraGS significantly reduces extrapolation artifacts and achieves state-of-the-art performance in endoscopic novel view synthesis.
Video Capsule Endoscopy (VCE) poses a challenging multi-label temporal classification problem, requiring simultaneous localization of 8 anatomical regions and detection of 9 pathological findings across tens of thousands of frames. We present GALAR-TemporalNet v2, a hierarchical temporal model that addresses three core challenges: extreme class imbalance, long-range temporal dependencies, and pathology--anatomy entanglement. Our architecture combines windowed self-attention for local modeling, a Dual-Graph GCN for global frame relationships, and Bidirectional Mamba for selective boundary context encoding. A novel anatomy prototype residual pathway decouples pathological deviation signals from normal organ appearance, and a frame-level GCN skip connection stabilizes training of visually confusable rare classes. The competition version, GALAR-TemporalNet, achieved an overall mAP@0.5 of 0.2644 and mAP@0.95 of 0.2353 on the RARE-VISION test set. Following the competition, the redesigned GALAR-TemporalNet v2 -- incorporating a restructured pathology branch, refined loss functions, and extended post-processing -- improved these results to mAP@0.5 of 0.3409 and mAP@0.95 of 0.3333.