Yidong Zhao

Yidong Zhao, Changchun Yang, Artur Schweidtmann et al.

The self-configuring nnU-Net has achieved leading performance in a large range of medical image segmentation challenges. It is widely considered as the model of choice and a strong baseline for medical image segmentation. However, despite its extraordinary performance, nnU-Net does not supply a measure of uncertainty to indicate its possible failure. This can be problematic for large-scale image segmentation applications, where data are heterogeneous and nnU-Net may fail without notice. In this work, we introduce a novel method to estimate nnU-Net uncertainty for medical image segmentation. We propose a highly effective scheme for posterior sampling of weight space for Bayesian uncertainty estimation. Different from previous baseline methods such as Monte Carlo Dropout and mean-field Bayesian Neural Networks, our proposed method does not require a variational architecture and keeps the original nnU-Net architecture intact, thereby preserving its excellent performance and ease of use. Additionally, we boost the segmentation performance over the original nnU-Net via marginalizing multi-modal posterior models. We applied our method on the public ACDC and M&M datasets of cardiac MRI and demonstrated improved uncertainty estimation over a range of baseline methods. The proposed method further strengthens nnU-Net for medical image segmentation in terms of both segmentation accuracy and quality control.

Yi Zhang, Yidong Zhao, Qian Tao

Deformable image registration remains a central challenge in medical image analysis, particularly under multi-modal scenarios where intensity distributions vary significantly across scans. While deep learning methods provide efficient feed-forward predictions, they often fail to generalize robustly under distribution shifts at test time. A straightforward remedy is full network fine-tuning, yet for modern architectures such as Transformers or deep U-Nets, this adaptation is prohibitively expensive in both memory and runtime when operating in 3D. Meanwhile, the naive fine-tuning struggles more with potential degradation in performance in the existence of drastic domain shifts. In this work, we propose a registration framework that integrates a frozen pretrained \textbf{mono-modal} registration model with a lightweight adaptation pipeline for \textbf{multi-modal} image registration. Specifically, we employ style transfer based on contrast-agnostic representation generation and refinement modules to bridge modality and domain gaps with instance optimization at test time. This design is orthogonal to the choice of backbone mono-modal model, thus avoids the computational burden of full fine-tuning while retaining the flexibility to adapt to unseen domains. We evaluate our approach on the Learn2Reg 2025 LUMIR validation set and observe consistent improvements over the pretrained state-of-the-art mono-modal backbone. In particular, the method ranks second on the multi-modal subset, third on the out-of-domain subset, and achieves fourth place overall in Dice score. These results demonstrate that combining frozen mono-modal models with modality adaptation and lightweight instance optimization offers an effective and practical pathway toward robust multi-modal registration.

Yidong Zhao, Joao Tourais, Iain Pierce et al.

Deep learning (DL)-based methods have achieved state-of-the-art performance for many medical image segmentation tasks. Nevertheless, recent studies show that deep neural networks (DNNs) can be miscalibrated and overconfident, leading to "silent failures" that are risky for clinical applications. Bayesian DL provides an intuitive approach to DL failure detection, based on posterior probability estimation. However, the posterior is intractable for large medical image segmentation DNNs. To tackle this challenge, we propose a Bayesian learning framework using Hamiltonian Monte Carlo (HMC), tempered by cold posterior (CP) to accommodate medical data augmentation, named HMC-CP. For HMC computation, we further propose a cyclical annealing strategy, capturing both local and global geometries of the posterior distribution, enabling highly efficient Bayesian DNN training with the same computational budget as training a single DNN. The resulting Bayesian DNN outputs an ensemble segmentation along with the segmentation uncertainty. We evaluate the proposed HMC-CP extensively on cardiac magnetic resonance image (MRI) segmentation, using in-domain steady-state free precession (SSFP) cine images as well as out-of-domain datasets of quantitative T1 and T2 mapping. Our results show that the proposed method improves both segmentation accuracy and uncertainty estimation for in- and out-of-domain data, compared with well-established baseline methods such as Monte Carlo Dropout and Deep Ensembles. Additionally, we establish a conceptual link between HMC and the commonly known stochastic gradient descent (SGD) and provide general insight into the uncertainty of DL. This uncertainty is implicitly encoded in the training dynamics but often overlooked. With reliable uncertainty estimation, our method provides a promising direction toward trustworthy DL in clinical applications.

Yidong Zhao, Yi Zhang, Qian Tao

Deep learning-based methods have achieved prestigious performance for magnetic resonance imaging (MRI) reconstruction, enabling fast imaging for many clinical applications. Previous methods employ convolutional networks to learn the image prior as the regularization term. In quantitative MRI, the physical model of nuclear magnetic resonance relaxometry is known, providing additional prior knowledge for image reconstruction. However, traditional reconstruction networks are limited to learning the spatial domain prior knowledge, ignoring the relaxometry prior. Therefore, we propose a relaxometry-guided quantitative MRI reconstruction framework to learn the spatial prior from data and the relaxometry prior from MRI physics. Additionally, we also evaluated the performance of two popular reconstruction backbones, namely, recurrent variational networks (RVN) and variational networks (VN) with U- Net. Experiments demonstrate that the proposed method achieves highly promising results in quantitative MRI reconstruction.

Yi Zhang, Yidong Zhao, Qian Tao

Deformable image registration is inherently a multi-objective optimization (MOO) problem, requiring a delicate balance between image similarity and deformation regularity. These conflicting objectives often lead to poor optimization outcomes, such as being trapped in unsatisfactory local minima or experiencing slow convergence. Deep learning methods have recently gained popularity in this domain due to their efficiency in processing large datasets and achieving high accuracy. However, they often underperform during test time compared to traditional optimization techniques, which further explore iterative, instance-specific gradient-based optimization. This performance gap is more pronounced when a distribution shift between training and test data exists. To address this issue, we focus on the instance optimization (IO) paradigm, which involves additional optimization for test-time instances based on a pre-trained model. IO effectively combines the generalization capabilities of deep learning with the fine-tuning advantages of instance-specific optimization. Within this framework, we emphasize the use of gradient projection to mitigate conflicting updates in MOO. This technique projects conflicting gradients into a common space, better aligning the dual objectives and enhancing optimization stability. We validate our method using a state-of-the-art foundation model on the 3D Brain inter-subject registration task (LUMIR) from the Learn2Reg 2024 Challenge. Our results show significant improvements over standard gradient descent, leading to more accurate and reliable registration results.

Yi Zhang, Yidong Zhao, Hui Xue et al.

Image registration is essential for medical image applications where alignment of voxels across multiple images is needed for qualitative or quantitative analysis. With recent advancements in deep neural networks and parallel computing, deep learning-based medical image registration methods become competitive with their flexible modelling and fast inference capabilities. However, compared to traditional optimization-based registration methods, the speed advantage may come at the cost of registration performance at inference time. Besides, deep neural networks ideally demand large training datasets while optimization-based methods are training-free. To improve registration accuracy and data efficiency, we propose a novel image registration method, termed Recurrent Inference Image Registration (RIIR) network. RIIR is formulated as a meta-learning solver to the registration problem in an iterative manner. RIIR addresses the accuracy and data efficiency issues, by learning the update rule of optimization, with implicit regularization combined with explicit gradient input. We evaluated RIIR extensively on brain MRI and quantitative cardiac MRI datasets, in terms of both registration accuracy and training data efficiency. Our experiments showed that RIIR outperformed a range of deep learning-based methods, even with only $5\%$ of the training data, demonstrating high data efficiency. Key findings from our ablation studies highlighted the important added value of the hidden states introduced in the recurrent inference framework for meta-learning. Our proposed RIIR offers a highly data-efficient framework for deep learning-based medical image registration.