Colon-Bench: An Agentic Workflow for Scalable Dense Lesion Annotation in Full-Procedure Colonoscopy Videos

Early screening via colonoscopy is critical for colon cancer prevention, yet developing robust AI systems for this domain is hindered by the lack of densely annotated, long-sequence video datasets. Existing datasets predominantly focus on single-class polyp detection and lack the rich spatial, temporal, and linguistic annotations required to evaluate modern Multimodal Large Language Models (MLLMs). To address this critical gap, we introduce Colon-Bench, generated via a novel multi-stage agentic workflow. Our pipeline seamlessly integrates temporal proposals, bounding-box tracking, AI-driven visual confirmation, and human-in-the-loop review to scalably annotate full-procedure videos. The resulting verified benchmark is unprecedented in scope, encompassing 528 videos, 14 distinct lesion categories (including polyps, ulcers, and bleeding), over 300,000 bounding boxes, 213,000 segmentation masks, and 133,000 words of clinical descriptions. We utilize Colon-Bench to rigorously evaluate state-of-the-art MLLMs across lesion classification, Open-Vocabulary Video Object Segmentation (OV-VOS), and video Visual Question Answering (VQA). The MLLM results demonstrate surprisingly high localization performance in medical domains compared to SAM-3. Finally, we analyze common VQA errors from MLLMs to introduce a novel "colon-skill" prompting strategy, improving zero-shot MLLM performance by up to 9.7% across most MLLMs. The dataset and the code are available at https://abdullahamdi.com/colon-bench .

Exemplar Diffusion: Improving Medical Object Detection with Opportunistic Labels

We present a framework to take advantage of existing labels at inference, called \textit{exemplars}, in order to improve the performance of object detection in medical images. The method, \textit{exemplar diffusion}, leverages existing diffusion methods for object detection to enable a training-free approach to adding information of known bounding boxes at test time. We demonstrate that for medical image datasets with clear spatial structure, the method yields an across-the-board increase in average precision and recall, and a robustness to exemplar quality, enabling non-expert annotation. Moreover, we demonstrate how our method may also be used to quantify predictive uncertainty in diffusion detection methods. Source code and data splits openly available online: https://github.com/waahlstrand/ExemplarDiffusion

Smart Operation Theatre: An AI-based System for Surgical Gauze Counting

During surgeries, there is a risk of medical gauzes being left inside patients' bodies, leading to "Gossypiboma" in patients and can cause serious complications in patients and also lead to legal problems for hospitals from malpractice lawsuits and regulatory penalties. Diagnosis depends on imaging methods such as X-rays or CT scans, and the usual treatment involves surgical excision. Prevention methods, such as manual counts and RFID-integrated gauzes, aim to minimize gossypiboma risks. However, manual tallying of 100s of gauzes by nurses is time-consuming and diverts resources from patient care. In partnership with Singapore General Hospital (SGH) we have developed a new prevention method, an AI-based system for gauze counting in surgical settings. Utilizing real-time video surveillance and object recognition technology powered by YOLOv5, a Deep Learning model was designed to monitor gauzes on two designated trays labelled "In" and "Out". Gauzes are tracked from the "In" tray, prior to their use in the patient's body & in the "Out" tray post-use, ensuring accurate counting and verifying that no gauze remains inside the patient at the end of the surgery. We have trained it using numerous images from Operation Theatres & augmented it to satisfy all possible scenarios. This study has also addressed the shortcomings of previous project iterations. Previously, the project employed two models: one for human detection and another for gauze detection, trained on a total of 2800 images. Now we have an integrated model capable of identifying both humans and gauzes, using a training set of 11,000 images. This has led to improvements in accuracy and increased the frame rate from 8 FPS to 15 FPS now. Incorporating doctor's feedback, the system now also supports manual count adjustments, enhancing its reliability in actual surgeries.

Deterministic Mode Proposals: An Efficient Alternative to Generative Sampling for Ambiguous Segmentation

Many segmentation tasks, such as medical image segmentation or future state prediction, are inherently ambiguous, meaning that multiple predictions are equally correct. Current methods typically rely on generative models to capture this uncertainty. However, identifying the underlying modes of the distribution with these methods is computationally expensive, requiring large numbers of samples and post-hoc clustering. In this paper, we shift the focus from stochastic sampling to the direct generation of likely outcomes. We introduce mode proposal models, a deterministic framework that efficiently produces a fixed-size set of proposal masks in a single forward pass. To handle superfluous proposals, we adapt a confidence mechanism, traditionally used in object detection, to the high-dimensional space of segmentation masks. Our approach significantly reduces inference time while achieving higher ground-truth coverage than existing generative models. Furthermore, we demonstrate that our model can be trained without knowing the full distribution of outcomes, making it applicable to real-world datasets. Finally, we show that by decomposing the velocity field of a pre-trained flow model, we can efficiently estimate prior mode probabilities for our proposals.

Medical Image Spatial Grounding with Semantic Sampling

Vision language models (VLMs) have shown significant promise in visual grounding for images as well as videos. In medical imaging research, VLMs represent a bridge between object detection and segmentation, and report understanding and generation. However, spatial grounding of anatomical structures in the three-dimensional space of medical images poses many unique challenges. In this study, we examine image modalities, slice directions, and coordinate systems as differentiating factors for vision components of VLMs, and the use of anatomical, directional, and relational terminology as factors for the language components. We then demonstrate that visual and textual prompting systems such as labels, bounding boxes, and mask overlays have varying effects on the spatial grounding ability of VLMs. To enable measurement and reproducibility, we introduce \textbf{MIS-Ground}, a benchmark that comprehensively tests a VLM for vulnerabilities against specific modes of \textbf{M}edical \textbf{I}mage \textbf{S}patial \textbf{Ground}ing. We release MIS-Ground to the public at \href{https://anonymous.4open.science/r/mis-ground}{\texttt{anonymous.4open.science/r/mis-ground}}. In addition, we present \textbf{MIS-SemSam}, a low-cost, inference-time, and model-agnostic optimization of VLMs that improve their spatial grounding ability with the use of \textbf{Sem}antic \textbf{Sam}pling. We find that MIS-SemSam improves the accuracy of Qwen3-VL-32B on MIS-Ground by 13.06\%.

Addressing Data Scarcity in 3D Trauma Detection through Self-Supervised and Semi-Supervised Learning with Vertex Relative Position Encoding

Accurate detection and localization of traumatic injuries in abdominal CT scans remains a critical challenge in emergency radiology, primarily due to severe scarcity of annotated medical data. This paper presents a label-efficient approach combining self-supervised pre-training with semi-supervised detection for 3D medical image analysis. We employ patch-based Masked Image Modeling (MIM) to pre-train a 3D U-Net encoder on 1,206 CT volumes without annotations, learning robust anatomical representations. The pretrained encoder enables two downstream clinical tasks: 3D injury detection using VDETR with Vertex Relative Position Encoding, and multi-label injury classification. For detection, semi-supervised learning with 2,000 unlabeled volumes and consistency regularization achieves 56.57% validation mAP@0.50 and 45.30% test mAP@0.50 with only 144 labeled training samples, representing a 115% improvement over supervised-only training. For classification, expanding to 2,244 labeled samples yields 94.07% test accuracy across seven injury categories using only a frozen encoder, demonstrating immediately transferable self-supervised features. Our results validate that self-supervised pre-training combined with semi-supervised learning effectively addresses label scarcity in medical imaging, enabling robust 3D object detection with limited annotations.

Toward Clinically Ready Foundation Models in Medical Image Analysis: Adaptation Mechanisms and Deployment Trade-offs

Foundation models (FMs) have demonstrated strong transferability across medical imaging tasks, yet their clinical utility depends critically on how pretrained representations are adapted to domain-specific data, supervision regimes, and deployment constraints. Prior surveys primarily emphasize architectural advances and application coverage, while the mechanisms of adaptation and their implications for robustness, calibration, and regulatory feasibility remain insufficiently structured. This review introduces a strategy-centric framework for FM adaptation in medical image analysis (MIA). We conceptualize adaptation as a post-pretraining intervention and organize existing approaches into five mechanisms: parameter-, representation-, objective-, data-centric, and architectural/sequence-level adaptation. For each mechanism, we analyze trade-offs in adaptation depth, label efficiency, domain robustness, computational cost, auditability, and regulatory burden. We synthesize evidence across classification, segmentation, and detection tasks, highlighting how adaptation strategies influence clinically relevant failure modes rather than only aggregate benchmark performance. Finally, we examine how adaptation choices interact with validation protocols, calibration stability, multi-institutional deployment, and regulatory oversight. By reframing adaptation as a process of controlled representational change under clinical constraints, this review provides practical guidance for designing FM-based systems that are robust, auditable, and compatible with clinical deployment.

Unleashing Video Language Models for Fine-grained HRCT Report Generation

Generating precise diagnostic reports from High-Resolution Computed Tomography (HRCT) is critical for clinical workflow, yet it remains a formidable challenge due to the high pathological diversity and spatial sparsity within 3D volumes. While Video Language Models (VideoLMs) have demonstrated remarkable spatio-temporal reasoning in general domains, their adaptability to domain-specific, high-volume medical interpretation remains underexplored. In this work, we present AbSteering, an abnormality-centric framework that steers VideoLMs toward precise HRCT report generation. Specifically, AbSteering introduces: (i) an abnormality-centric Chain-of-Thought scheme that enforces abnormality reasoning, and (ii) a Direct Preference Optimization objective that utilizes clinically confusable abnormalities as hard negatives to enhance fine-grained discrimination. Our results demonstrate that general-purpose VideoLMs possess strong transferability to high-volume medical imaging when guided by this paradigm. Notably, AbSteering outperforms state-of-the-art domain-specific CT foundation models, which are pretrained with large-scale CTs, achieving superior detection sensitivity while simultaneously mitigating hallucinations. Our data and model weights are released at https://anonymous.4open.science/r/hrct-report-generation-video-vlm-728C/

Evaluating Few-Shot Pill Recognition Under Visual Domain Shift

Adverse drug events are a significant source of preventable harm, which has led to the development of automated pill recognition systems to enhance medication safety. Real-world deployment of these systems is hindered by visually complex conditions, including cluttered scenes, overlapping pills, reflections, and diverse acquisition environments. This study investigates few-shot pill recognition from a deployment-oriented perspective, prioritizing generalization under realistic cross-dataset domain shifts over architectural innovation. A two-stage object detection framework is employed, involving base training followed by few-shot fine-tuning. Models are adapted to novel pill classes using one, five, or ten labeled examples per class and are evaluated on a separate deployment dataset featuring multi-object, cluttered scenes. The evaluation focuses on classification-centric and error-based metrics to address heterogeneous annotation strategies. Findings indicate that semantic pill recognition adapts rapidly with few-shot supervision, with classification performance reaching saturation even with a single labeled example. However, stress testing under overlapping and occluded conditions demonstrates a marked decline in localization and recall, despite robust semantic classification. Models trained on visually realistic, multi-pill data consistently exhibit greater robustness in low-shot scenarios, underscoring the importance of training data realism and the diagnostic utility of few-shot fine-tuning for deployment readiness.

Location-Aware Pretraining for Medical Difference Visual Question Answering

Unlike conventional single-image models, differential medical VQA frameworks process multiple images to identify differences, mirroring the comparative diagnostic workflow of radiologists. However, standard vision encoders trained on contrastive or classification objectives often fail to capture the subtle visual variations necessary for distinguishing disease progression from acquisition differences. To address this limitation, we introduce a pretraining framework that incorporates location-aware tasks, including automatic referring expressions (AREF), grounded captioning (GCAP), and conditional automatic referring expressions (CAREF). These specific tasks enable the vision encoder to learn fine-grained, spatially grounded visual representations that are often overlooked by traditional pre-training methods. We subsequently integrate this enhanced vision encoder with a language model to perform medical difference VQA. Experimental results demonstrate that our approach achieves state-of-the-art performance in detecting and reasoning about clinically relevant changes in chest X-ray images.