EndoVLM: An Endoscopy Vision-Language Pre-training Model via Anatomy-Guided Sparsity and Progressive Alignment
Authors: Zhenyu Yi, Jianwei Xu, Yue Hu, Zhongwei Qiu, Sijing Li, Liang Huang, Bin Lv, Ling Zhang, +1 more
Organizations: 1DAMO Academy, Alibaba Group · 3Shanghai Jiao Tong University · 4Hupan Lab · Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University · 5Key Laboratory of Digestive Pathophysiology of Zhejiang Province, The First Affiliated Hospital of Zhejiang Chinese Medical University · 6Zhejiang University
Abstract
The development of foundation models (FMs) is crucial for advancing endoscopic image analysis. However, existing endoscopy FMs mainly rely on self-supervised learning from uni-modal images or videos, overlooking the rich semantic knowledge contained in clinical reports. Furthermore, effectively leveraging these records is hindered by a fundamental modality gap: structured anatomical descriptions are not naturally mapped to specific frames within the high-redundancy, uncurated visual streams. In this paper, we present EndoVLM, a novel vision-language FM pre-trained on over 348K endoscopic examinations, each pairing a clinical report with its corresponding image collection. An Anatomy-Guided Sparse Pooling mechanism utilizes textual descriptions as queries to drive sparse attention, efficiently aggregating semantically salient frames into anatomy-specific visual representations across redundant image-sets. Next, a Progressive Semantic-Aware Alignment strategy models clinical taxonomy (anatomy and pathological status) via structured soft targets, bridging the gap from global patient-level matching to fine-grained localized alignment. Finally, a Semantic-Concentrated Masked Autoencoder is applied exclusively to these semantic-rich frames, integrating low-level visual precision with robust high-level semantic representation. Extensive experiments across various downstream tasks demonstrate that EndoVLM outperforms existing foundation models and remains competitive with task-specific methods. Remarkably, EndoVLM also exhibits robust zero-shot generalization capabilities, highlighting its potential for broader clinical application.
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
Multimodal Large Language Models (MLLMs) have demonstrated remarkable potential in medical image analysis. However, their application in gastrointestinal endoscopy is currently hindered by two critical limitations: the misalignment between general model reasoning and standardized clinical cognitive pathways, and the lack of causal association between visual features and diagnostic outcomes. In this paper, we propose a novel Clinical-Cognitive-Aligned (CogAlign) framework to address these challenges. First, we endow the model with rigorous clinical analytical capabilities by constructing the hierarchical clinical cognition dataset and employing Supervised Fine-Tuning (SFT). Unlike conventional approaches, this strategy internalizes the hierarchical diagnostic logic of experts, ranging from anatomical localization and morphological evaluation to microvascular analysis, directly into the model. Second, to eliminate visual bias, we provide a theoretical analysis demonstrating that standard supervised tuning inevitably converges to spurious background correlations. Guided by this insight, we propose a counterfactual-driven reinforcement learning strategy to enforce causal rectification. By generating counterfactual normal samples via lesion masking and optimizing through clinical-cognition-centric rewards, we constrain the model to strictly ground its diagnosis in causal lesion features. Extensive experiments demonstrate that our approach achieves State-of-the-Art (SoTA) performance across multiple benchmarks, significantly enhancing diagnostic accuracy in complex clinical scenarios.
CT vision-language foundation models have demonstrated promising performance across downstream tasks, but are typically trained with whole-volume representations that dilute fine-grained anatomical signals. Fine-grained vision-language pre-training addresses this by aligning anatomy-level visual features with anatomy-specific text, but in doing so discards the global context that whole-volume models provide. Furthermore, existing fine-grained approaches train from scratch, making them computationally expensive. We introduce Anatomy Contextualized Adaptation (ACA), a lightweight framework that adapts frozen CT foundation model representations for anatomy-level vision-language alignment while enhancing global contextualization. ACA uses TotalSegmentator to decompose CT volumes into anatomy-level embeddings, which are refined via a transformer that captures cross-anatomy relationships, and aligned to both per-anatomy and scan-level text extracted from radiology reports. Evaluated on Merlin and CT-RATE, ACA consistently outperforms both the frozen foundation model baselines and existing fine-grained methods in zero-shot finding classification, while requiring less than one hour of training once embeddings are cached. The attention weights learned by ACA's inter-anatomy transformer additionally indicate plausible cross-anatomy context routing. Altogether, these results support ACA as a lightweight approach for adapting CT foundation models to anatomically grounded vision-language alignment while preserving and enhancing global anatomical context.
Roshan Kenia, Stephanie L McNamara, William Lotter