Vivien van Veldhuizen

Tim Veenboer, George Yiasemis, Eric Marcus et al.

Existing foundation models (FMs) in the medical domain often require extensive fine-tuning or rely on training resource-intensive decoders, while many existing encoders are pretrained with objectives biased toward specific tasks. This illustrates a need for a strong, task-agnostic foundation model that requires minimal fine-tuning beyond feature extraction. In this work, we introduce a suite of task-agnostic pretraining of CT foundation models (TAP-CT): a simple yet effective adaptation of Vision Transformers (ViTs) and DINOv2 for volumetric data, enabling scalable self-supervised pretraining directly on 3D CT volumes. Our approach incorporates targeted modifications to patch embeddings, positional encodings, and volumetric augmentations, making the architecture depth-aware while preserving the simplicity of the underlying architectures. We show that large-scale 3D pretraining on an extensive in-house CT dataset (105K volumes) yields stable, robust frozen representations that generalize strongly across downstream tasks. To promote transparency and reproducibility, and to establish a powerful, low-resource baseline for future research in medical imaging, we will release all pretrained models, experimental configurations, and downstream benchmark code at https://huggingface.co/fomofo/tap-ct-b-3d.

Vivien van Veldhuizen, Sharvaree Vadgama, Onno J. de Boer et al.

Early detection of Barrett's Esophagus (BE), the only known precursor to Esophageal adenocarcinoma (EAC), is crucial for effectively preventing and treating esophageal cancer. In this work, we investigate the potential of geometric Variational Autoencoders (VAEs) to learn a meaningful latent representation that captures the progression of BE. We show that hyperspherical VAE (S-VAE) and Kendall Shape VAE show improved classification accuracy, reconstruction loss, and generative capacity. Additionally, we present a novel autoencoder architecture that can generate qualitative images without the need for a variational framework while retaining the benefits of an autoencoder, such as improved stability and reconstruction quality.

Xin Wang, Yuan Gao, George Yiasemis et al.

Efficient and explainable breast cancer (BC) risk prediction is critical for large-scale population-based screening. Breast MRI provides functional information for personalized risk assessment. Yet effective modeling remains challenging as fully 3D CNNs capture volumetric context at high computational cost, whereas lightweight 2D CNNs fail to model inter-slice continuity. Importantly, breast MRI modeling for shor- and long-term BC risk stratification remains underexplored. In this study, we propose LoGo-MR, a 2.5D local-global structural modeling framework for five-year BC risk prediction. Aligned with clinical interpretation, our framework first employs neighbor-slice encoding to capture subtle local cues linked to short-term risk. It then integrates transformer-enhanced multiple-instance learning (MIL) to model distributed global patterns related to long-term risk and provide interpretable slice importance. We further apply this framework across axial, sagittal, and coronal planes as LoGo3-MR to capture complementary volumetric information. This multi-plane formulation enables voxel-level risk saliency mapping, which may assist radiologists in localizing risk-relevant regions during breast MRI interpretation. Evaluated on a large breast MRI screening cohort (~7.5K), our method outperforms 2D/3D baselines and existing SOTA MIL methods, achieving AUCs of 0.77-0.69 for 1- to 5-year prediction and improving C-index by ~6% over 3D CNNs. LoGo3-MR further improves overall performance with interpretable localization across three planes, and validation across seven backbones shows consistent gains. These results highlight the clinical potential of efficient MRI-based BC risk stratification for large-scale screening. Code will be released publicly.

Vivien van Veldhuizen

This work is an exploratory research concerned with determining in what way reinforcement learning can be used to predict optimal PID parameters for a robot designed for apple harvest. To study this, an algorithm called Advantage Actor Critic (A2C) is implemented on a simulated robot arm. The simulation primarily relies on the ROS framework. Experiments for tuning one actuator at a time and two actuators a a time are run, which both show that the model is able to predict PID gains that perform better than the set baseline. In addition, it is studied if the model is able to predict PID parameters based on where an apple is located. Initial tests show that the model is indeed able to adapt its predictions to apple locations, making it an adaptive controller.

Vivien van Veldhuizen, Vanessa Botha, Chunyao Lu et al.

Foundation models (FMs) are changing the way medical images are analyzed by learning from large collections of unlabeled data. Instead of relying on manually annotated examples, FMs are pre-trained to learn general-purpose visual features that can later be adapted to specific clinical tasks with little additional supervision. In this review, we examine how FMs are being developed and applied in pathology, radiology, and ophthalmology, drawing on evidence from over 150 studies. We explain the core components of FM pipelines, including model architectures, self-supervised learning methods, and strategies for downstream adaptation. We also review how FMs are being used in each imaging domain and compare design choices across applications. Finally, we discuss key challenges and open questions to guide future research.