Jinming Duan

Shaokun Lan, Haoran Dou, Jinghan Huang et al.

In-silico trials of medical devices require the generation of virtual populations of anatomies. In cardiovascular applications, virtual anatomy is typically represented as a 3D+t mesh sampled from a generative model. However, most existing mesh generators focus on static anatomy, while sequence models often lack explicit periodicity. To this end, we propose 4D F-MeshLDM, a conditional generative framework comprising a convolutional mesh VAE to encode meshes, a structural latent space that parameterises motion using a truncated Fourier series, and a diffusion prior that learns the latent distribution over Fourier coefficient tokens. By conditioning the diffusion process on clinical covariates via affine modulation, we enable controllable synthesis. Sampling tokens and performing inverse Fourier synthesis yield cycle-consistent latent trajectories, which can be decoded into 3D+t cardiac mesh sequences. Experiments on 5,000 UK Biobank subjects demonstrate that 4D F-MeshLDM outperforms state-of-the-art baselines in anatomical fidelity and achieves near-zero cycle closure error. Furthermore, the generated cohorts accurately preserve clinical functional indices, highlighting the potential of our framework for reliable in-silico cardiac trials.

Xi Jia, Alexander Thorley, Alberto Gomez et al.

U-Net style networks are commonly utilized in unsupervised image registration to predict dense displacement fields, which for high-resolution volumetric image data is a resource-intensive and time-consuming task. To tackle this challenge, we first propose Fourier-Net, which replaces the costly U-Net style expansive path with a parameter-free model-driven decoder. Instead of directly predicting a full-resolution displacement field, our Fourier-Net learns a low-dimensional representation of the displacement field in the band-limited Fourier domain which our model-driven decoder converts to a full-resolution displacement field in the spatial domain. Expanding upon Fourier-Net, we then introduce Fourier-Net+, which additionally takes the band-limited spatial representation of the images as input and further reduces the number of convolutional layers in the U-Net style network's contracting path. Finally, to enhance the registration performance, we propose a cascaded version of Fourier-Net+. We evaluate our proposed methods on three datasets, on which our proposed Fourier-Net and its variants achieve comparable results with current state-of-the art methods, while exhibiting faster inference speeds, lower memory footprint, and fewer multiply-add operations. With such small computational cost, our Fourier-Net+ enables the efficient training of large-scale 3D registration on low-VRAM GPUs. Our code is publicly available at \url{https://github.com/xi-jia/Fourier-Net}.

Xi Jia, Joseph Bartlett, Tianyang Zhang et al.

Due to their extreme long-range modeling capability, vision transformer-based networks have become increasingly popular in deformable image registration. We believe, however, that the receptive field of a 5-layer convolutional U-Net is sufficient to capture accurate deformations without needing long-range dependencies. The purpose of this study is therefore to investigate whether U-Net-based methods are outdated compared to modern transformer-based approaches when applied to medical image registration. For this, we propose a large kernel U-Net (LKU-Net) by embedding a parallel convolutional block to a vanilla U-Net in order to enhance the effective receptive field. On the public 3D IXI brain dataset for atlas-based registration, we show that the performance of the vanilla U-Net is already comparable with that of state-of-the-art transformer-based networks (such as TransMorph), and that the proposed LKU-Net outperforms TransMorph by using only 1.12% of its parameters and 10.8% of its mult-adds operations. We further evaluate LKU-Net on a MICCAI Learn2Reg 2021 challenge dataset for inter-subject registration, our LKU-Net also outperforms TransMorph on this dataset and ranks first on the public leaderboard as of the submission of this work. With only modest modifications to the vanilla U-Net, we show that U-Net can outperform transformer-based architectures on inter-subject and atlas-based 3D medical image registration. Code is available at https://github.com/xi-jia/LKU-Net.

Xi Jia, Joseph Bartlett, Wei Chen et al.

Unsupervised image registration commonly adopts U-Net style networks to predict dense displacement fields in the full-resolution spatial domain. For high-resolution volumetric image data, this process is however resource-intensive and time-consuming. To tackle this problem, we propose the Fourier-Net, replacing the expansive path in a U-Net style network with a parameter-free model-driven decoder. Specifically, instead of our Fourier-Net learning to output a full-resolution displacement field in the spatial domain, we learn its low-dimensional representation in a band-limited Fourier domain. This representation is then decoded by our devised model-driven decoder (consisting of a zero padding layer and an inverse discrete Fourier transform layer) to the dense, full-resolution displacement field in the spatial domain. These changes allow our unsupervised Fourier-Net to contain fewer parameters and computational operations, resulting in faster inference speeds. Fourier-Net is then evaluated on two public 3D brain datasets against various state-of-the-art approaches. For example, when compared to a recent transformer-based method, named TransMorph, our Fourier-Net, which only uses 2.2\% of its parameters and 6.66\% of the multiply-add operations, achieves a 0.5\% higher Dice score and an 11.48 times faster inference speed. Code is available at \url{https://github.com/xi-jia/Fourier-Net}.

Qiufu Li, Xi Jia, Jiancan Zhou et al.

Sample-to-class-based face recognition models can not fully explore the cross-sample relationship among large amounts of facial images, while sample-to-sample-based models require sophisticated pairing processes for training. Furthermore, neither method satisfies the requirements of real-world face verification applications, which expect a unified threshold separating positive from negative facial pairs. In this paper, we propose a unified threshold integrated sample-to-sample based loss (USS loss), which features an explicit unified threshold for distinguishing positive from negative pairs. Inspired by our USS loss, we also derive the sample-to-sample based softmax and BCE losses, and discuss their relationship. Extensive evaluation on multiple benchmark datasets, including MFR, IJB-C, LFW, CFP-FP, AgeDB, and MegaFace, demonstrates that the proposed USS loss is highly efficient and can work seamlessly with sample-to-class-based losses. The embedded loss (USS and sample-to-class Softmax loss) overcomes the pitfalls of previous approaches and the trained facial model UniTSFace exhibits exceptional performance, outperforming state-of-the-art methods, such as CosFace, ArcFace, VPL, AnchorFace, and UNPG. Our code is available.

Xinxing Cheng, Xi Jia, Wenqi Lu et al.

Deep image registration has demonstrated exceptional accuracy and fast inference. Recent advances have adopted either multiple cascades or pyramid architectures to estimate dense deformation fields in a coarse-to-fine manner. However, due to the cascaded nature and repeated composition/warping operations on feature maps, these methods negatively increase memory usage during training and testing. Moreover, such approaches lack explicit constraints on the learning process of small deformations at different scales, thus lacking explainability. In this study, we introduce a model-driven WiNet that incrementally estimates scale-wise wavelet coefficients for the displacement/velocity field across various scales, utilizing the wavelet coefficients derived from the original input image pair. By exploiting the properties of the wavelet transform, these estimated coefficients facilitate the seamless reconstruction of a full-resolution displacement/velocity field via our devised inverse discrete wavelet transform (IDWT) layer. This approach avoids the complexities of cascading networks or composition operations, making our WiNet an explainable and efficient competitor with other coarse-to-fine methods. Extensive experimental results from two 3D datasets show that our WiNet is accurate and GPU efficient. The code is available at https://github.com/x-xc/WiNet .

Tiantian Geng, Teng Wang, Jinming Duan et al.

Existing audio-visual event localization (AVE) handles manually trimmed videos with only a single instance in each of them. However, this setting is unrealistic as natural videos often contain numerous audio-visual events with different categories. To better adapt to real-life applications, in this paper we focus on the task of dense-localizing audio-visual events, which aims to jointly localize and recognize all audio-visual events occurring in an untrimmed video. The problem is challenging as it requires fine-grained audio-visual scene and context understanding. To tackle this problem, we introduce the first Untrimmed Audio-Visual (UnAV-100) dataset, which contains 10K untrimmed videos with over 30K audio-visual events. Each video has 2.8 audio-visual events on average, and the events are usually related to each other and might co-occur as in real-life scenes. Next, we formulate the task using a new learning-based framework, which is capable of fully integrating audio and visual modalities to localize audio-visual events with various lengths and capture dependencies between them in a single pass. Extensive experiments demonstrate the effectiveness of our method as well as the significance of multi-scale cross-modal perception and dependency modeling for this task.

Wei Chen, Xi Jia, Zhongqun Zhang et al.

In this paper, we propose a novel 3D graph convolution based pipeline for category-level 6D pose and size estimation from monocular RGB-D images. The proposed method leverages an efficient 3D data augmentation and a novel vector-based decoupled rotation representation. Specifically, we first design an orientation-aware autoencoder with 3D graph convolution for latent feature learning. The learned latent feature is insensitive to point shift and size thanks to the shift and scale-invariance properties of the 3D graph convolution. Then, to efficiently decode the rotation information from the latent feature, we design a novel flexible vector-based decomposable rotation representation that employs two decoders to complementarily access the rotation information. The proposed rotation representation has two major advantages: 1) decoupled characteristic that makes the rotation estimation easier; 2) flexible length and rotated angle of the vectors allow us to find a more suitable vector representation for specific pose estimation task. Finally, we propose a 3D deformation mechanism to increase the generalization ability of the pipeline. Extensive experiments show that the proposed pipeline achieves state-of-the-art performance on category-level tasks. Further, the experiments demonstrate that the proposed rotation representation is more suitable for the pose estimation tasks than other rotation representations.

Yuting Zhang, Boyang Liu, Karina V. Bunting et al.

The echocardiographic measurement of left ventricular ejection fraction (LVEF) is fundamental to the diagnosis and classification of patients with heart failure (HF). In order to quantify LVEF automatically and accurately, this paper proposes a new pipeline method based on deep neural networks and ensemble learning. Within the pipeline, an Atrous Convolutional Neural Network (ACNN) was first trained to segment the left ventricle (LV), before employing the area-length formulation based on the ellipsoid single-plane model to calculate LVEF values. This formulation required inputs of LV area, derived from segmentation using an improved Jeffrey's method, as well as LV length, derived from a novel ensemble learning model. To further improve the pipeline's accuracy, an automated peak detection algorithm was used to identify end-diastolic and end-systolic frames, avoiding issues with human error. Subsequently, single-beat LVEF values were averaged across all cardiac cycles to obtain the final LVEF. This method was developed and internally validated in an open-source dataset containing 10,030 echocardiograms. The Pearson's correlation coefficient was 0.83 for LVEF prediction compared to expert human analysis (p<0.001), with a subsequent area under the receiver operator curve (AUROC) of 0.98 (95% confidence interval 0.97 to 0.99) for categorisation of HF with reduced ejection (HFrEF; LVEF<40%). In an external dataset with 200 echocardiograms, this method achieved an AUC of 0.90 (95% confidence interval 0.88 to 0.91) for HFrEF assessment. This study demonstrates that an automated neural network-based calculation of LVEF is comparable to expert clinicians performing time-consuming, frame-by-frame manual evaluation of cardiac systolic function.

Alexander Thorley, Agis Chartsias, Jordan Strom et al.

Video transformers have recently demonstrated strong potential for echocardiogram (echo) analysis, leveraging self-supervised pre-training and flexible adaptation across diverse tasks. However, like other models operating on videos, they are prone to learning spurious correlations from non-diagnostic regions such as image backgrounds. To overcome this limitation, we propose the Video Anatomically Constrained Transformer (ViACT), a novel framework that integrates anatomical priors directly into the transformer architecture. ViACT represents a deforming anatomical structure as a point set and encodes both its spatial geometry and corresponding image patches into transformer tokens. During pre-training, ViACT follows a masked autoencoding strategy that masks and reconstructs only anatomical patches, enforcing that representation learning is focused on the anatomical region. The pre-trained model can then be fine-tuned for tasks localized to this region. In this work we focus on the myocardium, demonstrating the framework on echo analysis tasks such as left ventricular ejection fraction (EF) regression and cardiac amyloidosis (CA) detection. The anatomical constraint focuses transformer attention within the myocardium, yielding interpretable attention maps aligned with regions of known CA pathology. Moreover, ViACT generalizes to myocardium point tracking without requiring task-specific components such as correlation volumes used in specialized tracking networks.

Luoying Hao, Yan Hu, Wenjun Lin et al.

Recognition and localization of surgical detailed actions is an essential component of developing a context-aware decision support system. However, most existing detection algorithms fail to provide high-accuracy action classes even having their locations, as they do not consider the surgery procedure's regularity in the whole video. This limitation hinders their application. Moreover, implementing the predictions in clinical applications seriously needs to convey model confidence to earn entrustment, which is unexplored in surgical action prediction. In this paper, to accurately detect fine-grained actions that happen at every moment, we propose an anchor-context action detection network (ACTNet), including an anchor-context detection (ACD) module and a class conditional diffusion (CCD) module, to answer the following questions: 1) where the actions happen; 2) what actions are; 3) how confidence predictions are. Specifically, the proposed ACD module spatially and temporally highlights the regions interacting with the extracted anchor in surgery video, which outputs action location and its class distribution based on anchor-context interactions. Considering the full distribution of action classes in videos, the CCD module adopts a denoising diffusion-based generative model conditioned on our ACD estimator to further reconstruct accurately the action predictions. Moreover, we utilize the stochastic nature of the diffusion model outputs to access model confidence for each prediction. Our method reports the state-of-the-art performance, with improvements of 4.0% mAP against baseline on the surgical video dataset.

Hang Zhang, Xiang Chen, Renjiu Hu et al.

Learning-based deformable image registration (DIR) accelerates alignment by amortizing traditional optimization via neural networks. Label supervision further enhances accuracy, enabling efficient and precise nonlinear alignment of unseen scans. However, images with sparse features amid large smooth regions, such as retinal vessels, introduce aperture and large-displacement challenges that unsupervised DIR methods struggle to address. This limitation occurs because neural networks predict deformation fields in a single forward pass, leaving fields unconstrained post-training and shifting the regularization burden entirely to network weights. To address these issues, we introduce SmoothProper, a plug-and-play neural module enforcing smoothness and promoting message passing within the network's forward pass. By integrating a duality-based optimization layer with tailored interaction terms, SmoothProper efficiently propagates flow signals across spatial locations, enforces smoothness, and preserves structural consistency. It is model-agnostic, seamlessly integrates into existing registration frameworks with minimal parameter overhead, and eliminates regularizer hyperparameter tuning. Preliminary results on a retinal vessel dataset exhibiting aperture and large-displacement challenges demonstrate our method reduces registration error to 1.88 pixels on 2912x2912 images, marking the first unsupervised DIR approach to effectively address both challenges. The source code will be available at https://github.com/tinymilky/SmoothProper.

Xi Jia, Wenqi Lu, Xinxing Cheng et al.

In unsupervised medical image registration, the predominant approaches involve the utilization of a encoder-decoder network architecture, allowing for precise prediction of dense, full-resolution displacement fields from given paired images. Despite its widespread use in the literature, we argue for the necessity of making both the encoder and decoder learnable in such an architecture. For this, we propose a novel network architecture, termed LessNet in this paper, which contains only a learnable decoder, while entirely omitting the utilization of a learnable encoder. LessNet substitutes the learnable encoder with simple, handcrafted features, eliminating the need to learn (optimize) network parameters in the encoder altogether. Consequently, this leads to a compact, efficient, and decoder-only architecture for 3D medical image registration. Evaluated on two publicly available brain MRI datasets, we demonstrate that our decoder-only LessNet can effectively and efficiently learn both dense displacement and diffeomorphic deformation fields in 3D. Furthermore, our decoder-only LessNet can achieve comparable registration performance to state-of-the-art methods such as VoxelMorph and TransMorph, while requiring significantly fewer computational resources. Our code and pre-trained models are available at https://github.com/xi-jia/LessNet.

Luoying Hao, Yan Hu, Yang Yue et al.

A comprehensive and explicit understanding of surgical scenes plays a vital role in developing context-aware computer-assisted systems in the operating theatre. However, few works provide systematical analysis to enable hierarchical surgical scene understanding. In this work, we propose to represent the tasks set [phase recognition --> step recognition --> action and instrument detection] as multi-level semantic scene understanding (MSSU). For this target, we propose a novel hierarchical context transformer (HCT) network and thoroughly explore the relations across the different level tasks. Specifically, a hierarchical relation aggregation module (HRAM) is designed to concurrently relate entries inside multi-level interaction information and then augment task-specific features. To further boost the representation learning of the different tasks, inter-task contrastive learning (ICL) is presented to guide the model to learn task-wise features via absorbing complementary information from other tasks. Furthermore, considering the computational costs of the transformer, we propose HCT+ to integrate the spatial and temporal adapter to access competitive performance on substantially fewer tunable parameters. Extensive experiments on our cataract dataset and a publicly available endoscopic PSI-AVA dataset demonstrate the outstanding performance of our method, consistently exceeding the state-of-the-art methods by a large margin. The code is available at https://github.com/Aurora-hao/HCT.

Tianyang Zhang, Shaoming Zheng, Jun Cheng et al.

Generative models have been widely proposed in image recognition to generate more images where the distribution is similar to that of the real ones. It often introduces a discriminator network to differentiate the real data from the generated ones. Such models utilise a discriminator network tasked with differentiating style transferred data from data contained in the target dataset. However in doing so the network focuses on discrepancies in the intensity distribution and may overlook structural differences between the datasets. In this paper we formulate a new image-to-image translation problem to ensure that the structure of the generated images is similar to that in the target dataset. We propose a simple, yet powerful Structure-Unbiased Adversarial (SUA) network which accounts for both intensity and structural differences between the training and test sets when performing image segmentation. It consists of a spatial transformation block followed by an intensity distribution rendering module. The spatial transformation block is proposed to reduce the structure gap between the two images, and also produce an inverse deformation field to warp the final segmented image back. The intensity distribution rendering module then renders the deformed structure to an image with the target intensity distribution. Experimental results show that the proposed SUA method has the capability to transfer both intensity distribution and structural content between multiple datasets.

Jiahui Yin, Xinxing Cheng, Jinming Duan et al.

Myocardial motion tracking is important for assessing cardiac function and diagnosing cardiovascular diseases, for which cine cardiac magnetic resonance (CMR) has been established as the gold standard imaging modality. Many existing methods learn motion from single image pairs consisting of a reference frame and a randomly selected target frame from the cardiac cycle. However, these methods overlook the continuous nature of cardiac motion and often yield inconsistent and non-smooth motion estimations. In this work, we propose a novel Mamba-based cardiac motion tracking network (MCM) that explicitly incorporates target image sequence from the cardiac cycle to achieve smooth and temporally consistent motion tracking. By developing a bi-directional Mamba block equipped with a bi-directional scanning mechanism, our method facilitates the estimation of plausible deformation fields. With our proposed motion decoder that integrates motion information from frames adjacent to the target frame, our method further enhances temporal coherence. Moreover, by taking advantage of Mamba's structured state-space formulation, the proposed method learns the continuous dynamics of the myocardium from sequential images without increasing computational complexity. We evaluate the proposed method on two public datasets. The experimental results demonstrate that the proposed method quantitatively and qualitatively outperforms both conventional and state-of-the-art learning-based cardiac motion tracking methods. The code is available at https://github.com/yjh-0104/MCM.

Xinxing Cheng, Tianyang Zhang, Wenqi Lu et al.

Deep learning-based image registration methods have shown state-of-the-art performance and rapid inference speeds. Despite these advances, many existing approaches fall short in capturing spatially varying information in non-local regions of feature maps due to the reliance on spatially-shared convolution kernels. This limitation leads to suboptimal estimation of deformation fields. In this paper, we propose a 3D Spatial-Awareness Convolution Block (SACB) to enhance the spatial information within feature representations. Our SACB estimates the spatial clusters within feature maps by leveraging feature similarity and subsequently parameterizes the adaptive convolution kernels across diverse regions. This adaptive mechanism generates the convolution kernels (weights and biases) tailored to spatial variations, thereby enabling the network to effectively capture spatially varying information. Building on SACB, we introduce a pyramid flow estimator (named SACB-Net) that integrates SACBs to facilitate multi-scale flow composition, particularly addressing large deformations. Experimental results on the brain IXI and LPBA datasets as well as Abdomen CT datasets demonstrate the effectiveness of SACB and the superiority of SACB-Net over the state-of-the-art learning-based registration methods. The code is available at https://github.com/x-xc/SACB_Net .

Joseph Bartlett, Jinming Duan

In this thesis, we offer a thorough investigation of different regularisation terms used in variational imaging problems, together with detailed optimisation processes of these problems. We begin by studying smooth problems and partially non-smooth problems in the form of Tikhonov denoising and Total Variation (TV) denoising, respectively. For Tikhonov denoising, we study an accelerated gradient method with adaptive restart, which shows a very rapid convergence rate. However, it is not straightforward to apply this fast algorithm to TV denoising, due to the non-smoothness of its built-in regularisation. To tackle this issue, we propose to utilise duality to convert such a non-smooth problem into a smooth one so that the accelerated gradient method with restart applies naturally. However, we notice that both Tikhonov and TV regularisations have drawbacks, in the form of blurred image edges and staircase artefacts, respectively. To overcome these drawbacks, we propose a novel adaption to Total Generalised Variation (TGV) regularisation called Total Smooth Variation (TSV), which retains edges and meanwhile does not produce results which contain staircase artefacts. To optimise TSV effectively, we then propose the Accelerated Proximal Gradient Algorithm (APGA) which also utilises adaptive restart techniques. Compared to existing state-of-the-art regularisations (e.g. TV), TSV is shown to obtain more effective results on denoising problems as well as advanced imaging applications such as magnetic resonance imaging (MRI) reconstruction and optical flow. TSV removes the staircase artefacts observed when using TV regularisation, but has the added advantage over TGV that it can be efficiently optimised using gradient based methods with Nesterov acceleration and adaptive restart. Code is available at https://github.com/Jbartlett6/Accelerated-First-Order-Method-for-Variational-Imaging.

Weizeng Lu, Xi Jia, Weicheng Xie et al.

We propose a geometry constrained network, termed GC-Net, for weakly supervised object localization (WSOL). GC-Net consists of three modules: a detector, a generator and a classifier. The detector predicts the object location defined by a set of coefficients describing a geometric shape (i.e. ellipse or rectangle), which is geometrically constrained by the mask produced by the generator. The classifier takes the resulting masked images as input and performs two complementary classification tasks for the object and background. To make the mask more compact and more complete, we propose a novel multi-task loss function that takes into account area of the geometric shape, the categorical cross-entropy and the negative entropy. In contrast to previous approaches, GC-Net is trained end-to-end and predict object location without any post-processing (e.g. thresholding) that may require additional tuning. Extensive experiments on the CUB-200-2011 and ILSVRC2012 datasets show that GC-Net outperforms state-of-the-art methods by a large margin. Our source code is available at https://github.com/lwzeng/GC-Net.

Kerstin Hammernik, Jo Schlemper, Chen Qin et al.

Purpose: To systematically investigate the influence of various data consistency layers, (semi-)supervised learning and ensembling strategies, defined in a $Σ$-net, for accelerated parallel MR image reconstruction using deep learning. Theory and Methods: MR image reconstruction is formulated as learned unrolled optimization scheme with a Down-Up network as regularization and varying data consistency layers. The different architectures are split into sensitivity networks, which rely on explicit coil sensitivity maps, and parallel coil networks, which learn the combination of coils implicitly. Different content and adversarial losses, a semi-supervised fine-tuning scheme and model ensembling are investigated. Results: Evaluated on the fastMRI multicoil validation set, architectures involving raw k-space data outperform image enhancement methods significantly. Semi-supervised fine-tuning adapts to new k-space data and provides, together with reconstructions based on adversarial training, the visually most appealing results although quantitative quality metrics are reduced. The $Σ$-net ensembles the benefits from different models and achieves similar scores compared to the single state-of-the-art approaches. Conclusion: This work provides an open-source framework to perform a systematic wide-range comparison of state-of-the-art reconstruction approaches for parallel MR image reconstruction on the fastMRI knee dataset and explores the importance of data consistency. A suitable trade-off between perceptual image quality and quantitative scores are achieved with the ensembled $Σ$-net.

Jinming Duan, Jo Schlemper, Chen Qin et al.

In this work, we propose a deep learning approach for parallel magnetic resonance imaging (MRI) reconstruction, termed a variable splitting network (VS-Net), for an efficient, high-quality reconstruction of undersampled multi-coil MR data. We formulate the generalized parallel compressed sensing reconstruction as an energy minimization problem, for which a variable splitting optimization method is derived. Based on this formulation we propose a novel, end-to-end trainable deep neural network architecture by unrolling the resulting iterative process of such variable splitting scheme. VS-Net is evaluated on complex valued multi-coil knee images for 4-fold and 6-fold acceleration factors. We show that VS-Net outperforms state-of-the-art deep learning reconstruction algorithms, in terms of reconstruction accuracy and perceptual quality. Our code is publicly available at https://github.com/j-duan/VS-Net.

Tiantian Geng, Jinrui Zhang, Qingni Wang et al.

Despite impressive advancements in video understanding, most efforts remain limited to coarse-grained or visual-only video tasks. However, real-world videos encompass omni-modal information (vision, audio, and speech) with a series of events forming a cohesive storyline. The lack of multi-modal video data with fine-grained event annotations and the high cost of manual labeling are major obstacles to comprehensive omni-modality video perception. To address this gap, we propose an automatic pipeline consisting of high-quality multi-modal video filtering, semantically coherent omni-modal event boundary detection, and cross-modal correlation-aware event captioning. In this way, we present LongVALE, the first-ever Vision-Audio-Language Event understanding benchmark comprising 105K omni-modal events with precise temporal boundaries and detailed relation-aware captions within 8.4K high-quality long videos. Further, we build a baseline that leverages LongVALE to enable video large language models (LLMs) for omni-modality fine-grained temporal video understanding for the first time. Extensive experiments demonstrate the effectiveness and great potential of LongVALE in advancing comprehensive multi-modal video understanding.

Qiufu Li, Xi Jia, Jiancan Zhou et al.

This paper introduces the concept of uniform classification, which employs a unified threshold to classify all samples rather than adaptive threshold classifying each individual sample. We also propose the uniform classification accuracy as a metric to measure the model's performance in uniform classification. Furthermore, begin with a naive loss, we mathematically derive a loss function suitable for the uniform classification, which is the BCE function integrated with a unified bias. We demonstrate the unified threshold could be learned via the bias. The extensive experiments on six classification datasets and three feature extraction models show that, compared to the SoftMax loss, the models trained with the BCE loss not only exhibit higher uniform classification accuracy but also higher sample-wise classification accuracy. In addition, the learned bias from BCE loss is very close to the unified threshold used in the uniform classification. The features extracted by the models trained with BCE loss not only possess uniformity but also demonstrate better intra-class compactness and inter-class distinctiveness, yielding superior performance on open-set tasks such as face recognition.

Jintao Song, Wenqi Lu, Yunwen Lei et al.

The Alternating Direction Method of Multipliers (ADMM) has gained significant attention across a broad spectrum of machine learning applications. Incorporating the over-relaxation technique shows potential for enhancing the convergence rate of ADMM. However, determining optimal algorithmic parameters, including both the associated penalty and relaxation parameters, often relies on empirical approaches tailored to specific problem domains and contextual scenarios. Incorrect parameter selection can significantly hinder ADMM's convergence rate. To address this challenge, in this paper we first propose a general approach to optimize the value of penalty parameter, followed by a novel closed-form formula to compute the optimal relaxation parameter in the context of linear quadratic problems (LQPs). We then experimentally validate our parameter selection methods through random instantiations and diverse imaging applications, encompassing diffeomorphic image registration, image deblurring, and MRI reconstruction.

Fengming Lin, Arezoo Zakeri, Yidan Xue et al.

Deep learning-based medical image-to-mesh reconstruction has rapidly evolved, enabling the transformation of medical imaging data into three-dimensional mesh models that are critical in computational medicine and in silico trials for advancing our understanding of disease mechanisms, and diagnostic and therapeutic techniques in modern medicine. This survey systematically categorizes existing approaches into four main categories: template models, statistical models, generative models, and implicit models. Each category is analysed in detail, examining their methodological foundations, strengths, limitations, and applicability to different anatomical structures and imaging modalities. We provide an extensive evaluation of these methods across various anatomical applications, from cardiac imaging to neurological studies, supported by quantitative comparisons using standard metrics. Additionally, we compile and analyze major public datasets available for medical mesh reconstruction tasks and discuss commonly used evaluation metrics and loss functions. The survey identifies current challenges in the field, including requirements for topological correctness, geometric accuracy, and multi-modality integration. Finally, we present promising future research directions in this domain. This systematic review aims to serve as a comprehensive reference for researchers and practitioners in medical image analysis and computational medicine.

Alexander Thorley, Agis Chartsias, Jordan Strom et al.

Cardiac amyloidosis (CA) is a rare cardiomyopathy, with typical abnormalities in clinical measurements from echocardiograms such as reduced global longitudinal strain of the myocardium. An alternative approach for detecting CA is via neural networks, using video classification models such as convolutional neural networks. These models process entire video clips, but provide no assurance that classification is based on clinically relevant features known to be associated with CA. An alternative paradigm for disease classification is to apply models to quantitative features such as strain, ensuring that the classification relates to clinically relevant features. Drawing inspiration from this approach, we explicitly constrain a transformer model to the anatomical region where many known CA abnormalities occur -- the myocardium, which we embed as a set of deforming points and corresponding sampled image patches into input tokens. We show that our anatomical constraint can also be applied to the popular self-supervised learning masked autoencoder pre-training, where we propose to mask and reconstruct only anatomical patches. We show that by constraining both the transformer and pre-training task to the myocardium where CA imaging features are localized, we achieve increased performance on a CA classification task compared to full video transformers. Our model provides an explicit guarantee that the classification is focused on only anatomical regions of the echo, and enables us to visualize transformer attention scores over the deforming myocardium.

Yuting Zhang, Karina V. Bunting, Asgher Champsi et al.

Cardiovascular diseases (CVDs) remain the foremost cause of mortality worldwide, a burden worsened by a severe deficit of healthcare workers. Artificial intelligence (AI) agents have shown potential to alleviate this gap via automated early detection and proactive screening, yet their clinical application remains limited by: 1) prompt-based clinical role assignment that relies on intrinsic model capabilities without domain-specific tool support; or 2) rigid sequential workflows, whereas clinical care often requires adaptive reasoning that orders specific tests and, based on their results, guides personalised next steps; 3) general and static knowledge bases without continuous learning capability; and 4) fixed unimodal or bimodal inputs and lack of on-demand visual outputs when further clarification is needed. In response, a multimodal framework, CardAIc-Agents, was proposed to augment models with external tools and adaptively support diverse cardiac tasks. Specifically, a CardiacRAG agent generated general plans from updatable cardiac knowledge, while the chief agent integrated tools to autonomously execute these plans and deliver decisions. To enable adaptive and case-specific customization, a stepwise update strategy was proposed to dynamically refine plans based on preceding execution results, once the task was assessed as complex. In addition, a multidisciplinary discussion tool was introduced to interpret challenging cases, thereby supporting further adaptation. When clinicians raised concerns, visual review panels were provided to assist final validation. Experiments across three datasets showed the efficiency of CardAIc-Agents compared to mainstream Vision-Language Models (VLMs), state-of-the-art agentic systems, and fine-tuned VLMs.

Tiantian Geng, Teng Wang, Jinming Duan et al.

Video event localization tasks include temporal action localization (TAL), sound event detection (SED) and audio-visual event localization (AVEL). Existing methods tend to over-specialize on individual tasks, neglecting the equal importance of these different events for a complete understanding of video content. In this work, we aim to develop a unified framework to solve TAL, SED and AVEL tasks together to facilitate holistic video understanding. However, it is challenging since different tasks emphasize distinct event characteristics and there are substantial disparities in existing task-specific datasets (size/domain/duration). It leads to unsatisfactory results when applying a naive multi-task strategy. To tackle the problem, we introduce UniAV, a Unified Audio-Visual perception network to effectively learn and share mutually beneficial knowledge across tasks and modalities. Concretely, we propose a unified audio-visual encoder to derive generic representations from multiple temporal scales for videos from all tasks. Meanwhile, task-specific experts are designed to capture the unique knowledge specific to each task. Besides, instead of using separate prediction heads, we develop a novel unified language-aware classifier by utilizing semantic-aligned task prompts, enabling our model to flexibly localize various instances across tasks with an impressive open-set ability to localize novel categories. Extensive experiments demonstrate that UniAV, with its unified architecture, significantly outperforms both single-task models and the naive multi-task baseline across all three tasks. It achieves superior or on-par performances compared to the state-of-the-art task-specific methods on ActivityNet 1.3, DESED and UnAV-100 benchmarks.

Lasse Hansen, Wiebke Heyer, Christoph Großbröhmer et al.

Medical image registration is critical for clinical applications, and fair benchmarking of different methods is essential for monitoring ongoing progress. To date, the Learn2Reg 2020-2023 challenges have released several complementary datasets and established metrics for evaluations. However, these editions did not capture all aspects of the registration problem, particularly in terms of modality diversity and task complexity. To address these limitations, the 2024 edition introduces three new tasks, including large-scale multi-modal registration and unsupervised inter-subject brain registration, as well as the first microscopy-focused benchmark within Learn2Reg. The new datasets also inspired new method developments, including invertibility constraints, pyramid features, keypoints alignment and instance optimisation.

Yuting Zhang, Tiantian Geng, Luoying Hao et al.

Contemporary cardiovascular management involves complex consideration and integration of multimodal cardiac datasets, where each modality provides distinct but complementary physiological characteristics. While the effective integration of multiple modalities could yield a holistic clinical profile that accurately models the true clinical situation with respect to data modalities and their relatives weightings, current methodologies remain limited by: 1) the scarcity of patient- and time-aligned multimodal data; 2) reliance on isolated single-modality or rigid multimodal input combinations; 3) alignment strategies that prioritize cross-modal similarity over complementarity; and 4) a narrow single-task focus. In response to these limitations, a comprehensive multimodal dataset was curated for immediate application, integrating laboratory test results, electrocardiograms, and echocardiograms with clinical outcomes. Subsequently, a unified framework, Textual Guidance Multimodal fusion for Multiple cardiac tasks (TGMM), was proposed. TGMM incorporated three key components: 1) a MedFlexFusion module designed to capture the unique and complementary characteristics of medical modalities and dynamically integrate data from diverse cardiac sources and their combinations; 2) a textual guidance module to derive task-relevant representations tailored to diverse clinical objectives, including heart disease diagnosis, risk stratification and information retrieval; and 3) a response module to produce final decisions for all these tasks. Furthermore, this study systematically explored key features across multiple modalities and elucidated their synergistic contributions in clinical decision-making. Extensive experiments showed that TGMM outperformed state-of-the-art methods across multiple clinical tasks, with additional validation confirming its robustness on another public dataset.

Ziwei Zou, Bei Zou, Xiaoyan Kui et al.

Atlas construction is fundamental to medical image analysis, offering a standardized spatial reference for tasks such as population-level anatomical modeling. While data-driven registration methods have recently shown promise in pairwise settings, their reliance on large training datasets, limited generalizability, and lack of true inference phases in groupwise contexts hinder their practical use. In contrast, model-driven methods offer training-free, theoretically grounded, and data-efficient alternatives, though they often face scalability and optimization challenges when applied to large 3D datasets. In this work, we introduce DARC (Diffeomorphic Atlas Registration via Coordinate descent), a novel model-driven groupwise registration framework for atlas construction. DARC supports a broad range of image dissimilarity metrics and efficiently handles arbitrary numbers of 3D images without incurring GPU memory issues. Through a coordinate descent strategy and a centrality-enforcing activation function, DARC produces unbiased, diffeomorphic atlases with high anatomical fidelity. Beyond atlas construction, we demonstrate two key applications: (1) One-shot segmentation, where labels annotated only on the atlas are propagated to subjects via inverse deformations, outperforming state-of-the-art few-shot methods; and (2) shape synthesis, where new anatomical variants are generated by warping the atlas mesh using synthesized diffeomorphic deformation fields. Overall, DARC offers a flexible, generalizable, and resource-efficient framework for atlas construction and applications.

Wiebke Heyer, Yannic Elser, Lennart Berkel et al.

In modern cancer research, the vast volume of medical data generated is often underutilised due to challenges related to patient privacy. The OncoReg Challenge addresses this issue by enabling researchers to develop and validate image registration methods through a two-phase framework that ensures patient privacy while fostering the development of more generalisable AI models. Phase one involves working with a publicly available dataset, while phase two focuses on training models on a private dataset within secure hospital networks. OncoReg builds upon the foundation established by the Learn2Reg Challenge by incorporating the registration of interventional cone-beam computed tomography (CBCT) with standard planning fan-beam CT (FBCT) images in radiotherapy. Accurate image registration is crucial in oncology, particularly for dynamic treatment adjustments in image-guided radiotherapy, where precise alignment is necessary to minimise radiation exposure to healthy tissues while effectively targeting tumours. This work details the methodology and data behind the OncoReg Challenge and provides a comprehensive analysis of the competition entries and results. Findings reveal that feature extraction plays a pivotal role in this registration task. A new method emerging from this challenge demonstrated its versatility, while established approaches continue to perform comparably to newer techniques. Both deep learning and classical approaches still play significant roles in image registration, with the combination of methods, particularly in feature extraction, proving most effective.

Sean Rendell, Jinming Duan

Diffeomorphic image registration is a commonly used method to deform one image to resemble another. While warping a single image to another is useful, it can be advantageous to warp multiple images simultaneously, such as in tracking the motion of the heart across a sequence of images. In this paper, our objective is to propose a novel method capable of registering a group or sequence of images to a target image, resulting in registered images that appear identical and therefore have a low rank. Moreover, we aim for these registered images to closely resemble the target image. Through experimental evidence, we will demonstrate our method's superior efficacy in producing low-rank groupwise deformations compared to other state-of-the-art approaches.

Alessa Hering, Lasse Hansen, Tony C. W. Mok et al.

Image registration is a fundamental medical image analysis task, and a wide variety of approaches have been proposed. However, only a few studies have comprehensively compared medical image registration approaches on a wide range of clinically relevant tasks. This limits the development of registration methods, the adoption of research advances into practice, and a fair benchmark across competing approaches. The Learn2Reg challenge addresses these limitations by providing a multi-task medical image registration data set for comprehensive characterisation of deformable registration algorithms. A continuous evaluation will be possible at https://learn2reg.grand-challenge.org. Learn2Reg covers a wide range of anatomies (brain, abdomen, and thorax), modalities (ultrasound, CT, MR), availability of annotations, as well as intra- and inter-patient registration evaluation. We established an easily accessible framework for training and validation of 3D registration methods, which enabled the compilation of results of over 65 individual method submissions from more than 20 unique teams. We used a complementary set of metrics, including robustness, accuracy, plausibility, and runtime, enabling unique insight into the current state-of-the-art of medical image registration. This paper describes datasets, tasks, evaluation methods and results of the challenge, as well as results of further analysis of transferability to new datasets, the importance of label supervision, and resulting bias. While no single approach worked best across all tasks, many methodological aspects could be identified that push the performance of medical image registration to new state-of-the-art performance. Furthermore, we demystified the common belief that conventional registration methods have to be much slower than deep-learning-based methods.

Alexander Thorley, Xi Jia, Hyung Jin Chang et al.

Deterministic approaches using iterative optimisation have been historically successful in diffeomorphic image registration (DiffIR). Although these approaches are highly accurate, they typically carry a significant computational burden. Recent developments in stochastic approaches based on deep learning have achieved sub-second runtimes for DiffIR with competitive registration accuracy, offering a fast alternative to conventional iterative methods. In this paper, we attempt to reduce this difference in speed whilst retaining the performance advantage of iterative approaches in DiffIR. We first propose a simple iterative scheme that functionally composes intermediate non-stationary velocity fields to handle large deformations in images whilst guaranteeing diffeomorphisms in the resultant deformation. We then propose a convex optimisation model that uses a regularisation term of arbitrary order to impose smoothness on these velocity fields and solve this model with a fast algorithm that combines Nesterov gradient descent and the alternating direction method of multipliers (ADMM). Finally, we leverage the computational power of GPU to implement this accelerated ADMM solver on a 3D cardiac MRI dataset, further reducing runtime to less than 2 seconds. In addition to producing strictly diffeomorphic deformations, our methods outperform both state-of-the-art deep learning-based and iterative DiffIR approaches in terms of dice and Hausdorff scores, with speed approaching the inference time of deep learning-based methods.

Xi Jia, Alexander Thorley, Wei Chen et al.

Data-driven deep learning approaches to image registration can be less accurate than conventional iterative approaches, especially when training data is limited. To address this whilst retaining the fast inference speed of deep learning, we propose VR-Net, a novel cascaded variational network for unsupervised deformable image registration. Using the variable splitting optimization scheme, we first convert the image registration problem, established in a generic variational framework, into two sub-problems, one with a point-wise, closed-form solution while the other one is a denoising problem. We then propose two neural layers (i.e. warping layer and intensity consistency layer) to model the analytical solution and a residual U-Net to formulate the denoising problem (i.e. generalized denoising layer). Finally, we cascade the warping layer, intensity consistency layer, and generalized denoising layer to form the VR-Net. Extensive experiments on three (two 2D and one 3D) cardiac magnetic resonance imaging datasets show that VR-Net outperforms state-of-the-art deep learning methods on registration accuracy, while maintains the fast inference speed of deep learning and the data-efficiency of variational model.

Wei Chen, Xi Jia, Hyung Jin Chang et al.

In this paper, we focus on category-level 6D pose and size estimation from monocular RGB-D image. Previous methods suffer from inefficient category-level pose feature extraction which leads to low accuracy and inference speed. To tackle this problem, we propose a fast shape-based network (FS-Net) with efficient category-level feature extraction for 6D pose estimation. First, we design an orientation aware autoencoder with 3D graph convolution for latent feature extraction. The learned latent feature is insensitive to point shift and object size thanks to the shift and scale-invariance properties of the 3D graph convolution. Then, to efficiently decode category-level rotation information from the latent feature, we propose a novel decoupled rotation mechanism that employs two decoders to complementarily access the rotation information. Meanwhile, we estimate translation and size by two residuals, which are the difference between the mean of object points and ground truth translation, and the difference between the mean size of the category and ground truth size, respectively. Finally, to increase the generalization ability of FS-Net, we propose an online box-cage based 3D deformation mechanism to augment the training data. Extensive experiments on two benchmark datasets show that the proposed method achieves state-of-the-art performance in both category- and instance-level 6D object pose estimation. Especially in category-level pose estimation, without extra synthetic data, our method outperforms existing methods by 6.3% on the NOCS-REAL dataset.

Chen Qin, Jo Schlemper, Kerstin Hammernik et al.

We present a deep network interpolation strategy for accelerated parallel MR image reconstruction. In particular, we examine the network interpolation in parameter space between a source model that is formulated in an unrolled scheme with L1 and SSIM losses and its counterpart that is trained with an adversarial loss. We show that by interpolating between the two different models of the same network structure, the new interpolated network can model a trade-off between perceptual quality and fidelity.

Wei Chen, Xi Jia, Hyung Jin Chang et al.

In this paper, we propose a novel real-time 6D object pose estimation framework, named G2L-Net. Our network operates on point clouds from RGB-D detection in a divide-and-conquer fashion. Specifically, our network consists of three steps. First, we extract the coarse object point cloud from the RGB-D image by 2D detection. Second, we feed the coarse object point cloud to a translation localization network to perform 3D segmentation and object translation prediction. Third, via the predicted segmentation and translation, we transfer the fine object point cloud into a local canonical coordinate, in which we train a rotation localization network to estimate initial object rotation. In the third step, we define point-wise embedding vector features to capture viewpoint-aware information. To calculate more accurate rotation, we adopt a rotation residual estimator to estimate the residual between initial rotation and ground truth, which can boost initial pose estimation performance. Our proposed G2L-Net is real-time despite the fact multiple steps are stacked via the proposed coarse-to-fine framework. Extensive experiments on two benchmark datasets show that G2L-Net achieves state-of-the-art performance in terms of both accuracy and speed.

Jo Schlemper, Chen Qin, Jinming Duan et al.

We explore an ensembled $Σ$-net for fast parallel MR imaging, including parallel coil networks, which perform implicit coil weighting, and sensitivity networks, involving explicit sensitivity maps. The networks in $Σ$-net are trained in a supervised way, including content and GAN losses, and with various ways of data consistency, i.e., proximal mappings, gradient descent and variable splitting. A semi-supervised finetuning scheme allows us to adapt to the k-space data at test time, which, however, decreases the quantitative metrics, although generating the visually most textured and sharp images. For this challenge, we focused on robust and high SSIM scores, which we achieved by ensembling all models to a $Σ$-net.

Chen Chen, Chen Qin, Huaqi Qiu et al.

Deep learning has become the most widely used approach for cardiac image segmentation in recent years. In this paper, we provide a review of over 100 cardiac image segmentation papers using deep learning, which covers common imaging modalities including magnetic resonance imaging (MRI), computed tomography (CT), and ultrasound (US) and major anatomical structures of interest (ventricles, atria and vessels). In addition, a summary of publicly available cardiac image datasets and code repositories are included to provide a base for encouraging reproducible research. Finally, we discuss the challenges and limitations with current deep learning-based approaches (scarcity of labels, model generalizability across different domains, interpretability) and suggest potential directions for future research.

Jo Schlemper, Jinming Duan, Cheng Ouyang et al.

We present simple reconstruction networks for multi-coil data by extending deep cascade of CNN's and exploiting the data consistency layer. In particular, we propose two variants, where one is inspired by POCSENSE and the other is calibration-less. We show that the proposed approaches are competitive relative to the state of the art both quantitatively and qualitatively.

Jo Schlemper, Ilkay Oksuz, James R. Clough et al.

AUTOMAP is a promising generalized reconstruction approach, however, it is not scalable and hence the practicality is limited. We present dAUTOMAP, a novel way for decomposing the domain transformation of AUTOMAP, making the model scale linearly. We show dAUTOMAP outperforms AUTOMAP with significantly fewer parameters.

Chen Qin, Jo Schlemper, Jinming Duan et al.

Dynamic magnetic resonance imaging (MRI) exhibits high correlations in k-space and time. In order to accelerate the dynamic MR imaging and to exploit k-t correlations from highly undersampled data, here we propose a novel deep learning based approach for dynamic MR image reconstruction, termed k-t NEXT (k-t NEtwork with X-f Transform). In particular, inspired by traditional methods such as k-t BLAST and k-t FOCUSS, we propose to reconstruct the true signals from aliased signals in x-f domain to exploit the spatio-temporal redundancies. Building on that, the proposed method then learns to recover the signals by alternating the reconstruction process between the x-f space and image space in an iterative fashion. This enables the network to effectively capture useful information and jointly exploit spatio-temporal correlations from both complementary domains. Experiments conducted on highly undersampled short-axis cardiac cine MRI scans demonstrate that our proposed method outperforms the current state-of-the-art dynamic MR reconstruction approaches both quantitatively and qualitatively.

Cheng Ouyang, Konstantinos Kamnitsas, Carlo Biffi et al.

Deep learning models trained on medical images from a source domain (e.g. imaging modality) often fail when deployed on images from a different target domain, despite imaging common anatomical structures. Deep unsupervised domain adaptation (UDA) aims to improve the performance of a deep neural network model on a target domain, using solely unlabelled target domain data and labelled source domain data. However, current state-of-the-art methods exhibit reduced performance when target data is scarce. In this work, we introduce a new data efficient UDA method for multi-domain medical image segmentation. The proposed method combines a novel VAE-based feature prior matching, which is data-efficient, and domain adversarial training to learn a shared domain-invariant latent space which is exploited during segmentation. Our method is evaluated on a public multi-modality cardiac image segmentation dataset by adapting from the labelled source domain (3D MRI) to the unlabelled target domain (3D CT). We show that by using only one single unlabelled 3D CT scan, the proposed architecture outperforms the state-of-the-art in the same setting. Finally, we perform ablation studies on prior matching and domain adversarial training to shed light on the theoretical grounding of the proposed method.

Wenjia Bai, Chen Chen, Giacomo Tarroni et al.

In the recent years, convolutional neural networks have transformed the field of medical image analysis due to their capacity to learn discriminative image features for a variety of classification and regression tasks. However, successfully learning these features requires a large amount of manually annotated data, which is expensive to acquire and limited by the available resources of expert image analysts. Therefore, unsupervised, weakly-supervised and self-supervised feature learning techniques receive a lot of attention, which aim to utilise the vast amount of available data, while at the same time avoid or substantially reduce the effort of manual annotation. In this paper, we propose a novel way for training a cardiac MR image segmentation network, in which features are learnt in a self-supervised manner by predicting anatomical positions. The anatomical positions serve as a supervisory signal and do not require extra manual annotation. We demonstrate that this seemingly simple task provides a strong signal for feature learning and with self-supervised learning, we achieve a high segmentation accuracy that is better than or comparable to a U-net trained from scratch, especially at a small data setting. When only five annotated subjects are available, the proposed method improves the mean Dice metric from 0.811 to 0.852 for short-axis image segmentation, compared to the baseline U-net.

Carlo Biffi, Juan J. Cerrolaza, Giacomo Tarroni et al.

Quantification of anatomical shape changes currently relies on scalar global indexes which are largely insensitive to regional or asymmetric modifications. Accurate assessment of pathology-driven anatomical remodeling is a crucial step for the diagnosis and treatment of many conditions. Deep learning approaches have recently achieved wide success in the analysis of medical images, but they lack interpretability in the feature extraction and decision processes. In this work, we propose a new interpretable deep learning model for shape analysis. In particular, we exploit deep generative networks to model a population of anatomical segmentations through a hierarchy of conditional latent variables. At the highest level of this hierarchy, a two-dimensional latent space is simultaneously optimised to discriminate distinct clinical conditions, enabling the direct visualisation of the classification space. Moreover, the anatomical variability encoded by this discriminative latent space can be visualised in the segmentation space thanks to the generative properties of the model, making the classification task transparent. This approach yielded high accuracy in the categorisation of healthy and remodelled left ventricles when tested on unseen segmentations from our own multi-centre dataset as well as in an external validation set, and on hippocampi from healthy controls and patients with Alzheimer's disease when tested on ADNI data. More importantly, it enabled the visualisation in three-dimensions of both global and regional anatomical features which better discriminate between the conditions under exam. The proposed approach scales effectively to large populations, facilitating high-throughput analysis of normal anatomy and pathology in large-scale studies of volumetric imaging.

Wenqi Lu, Jinming Duan, Joshua Deepak Veesa et al.

The forward model in diffuse optical tomography (DOT) describes how light propagates through a turbid medium. It is often approximated by a diffusion equation (DE) that is numerically discretized by the classical finite element method (FEM). We propose a nonlocal diffusion equation (NDE) as a new forward model for DOT, the discretization of which is carried out with an efficient graph-based numerical method (GNM). To quantitatively evaluate the new forward model, we first conduct experiments on a homogeneous slab, where the numerical accuracy of both NDE and DE is compared against the existing analytical solution. We further evaluate NDE by comparing its image reconstruction performance (inverse problem) to that of DE. Our experiments show that NDE is quantitatively comparable to DE and is up to 64% faster due to the efficient graph-based representation that can be implemented identically for geometries in different dimensions.

Wenqi Lu, Jinming Duan, David Orive-Miguel et al.

Total variation (TV) is a powerful regularization method that has been widely applied in different imaging applications, but is difficult to apply to diffuse optical tomography (DOT) image reconstruction (inverse problem) due to complex and unstructured geometries, non-linearity of the data fitting and regularization terms, and non-differentiability of the regularization term. We develop several approaches to overcome these difficulties by: i) defining discrete differential operators for unstructured geometries using both finite element and graph representations; ii) developing an optimization algorithm based on the alternating direction method of multipliers (ADMM) for the non-differentiable and non-linear minimization problem; iii) investigating isotropic and anisotropic variants of TV regularization, and comparing their finite element- and graph-based implementations. These approaches are evaluated on experiments on simulated data and real data acquired from a tissue phantom. Our results show that both FEM and graph-based TV regularization is able to accurately reconstruct both sparse and non-sparse distributions without the over-smoothing effect of Tikhonov regularization and the over-sparsifying effect of L$_1$ regularization. The graph representation was found to out-perform the FEM method for low-resolution meshes, and the FEM method was found to be more accurate for high-resolution meshes.

Ghalib A. Bello, Timothy J. W. Dawes, Jinming Duan et al.

Motion analysis is used in computer vision to understand the behaviour of moving objects in sequences of images. Optimising the interpretation of dynamic biological systems requires accurate and precise motion tracking as well as efficient representations of high-dimensional motion trajectories so that these can be used for prediction tasks. Here we use image sequences of the heart, acquired using cardiac magnetic resonance imaging, to create time-resolved three-dimensional segmentations using a fully convolutional network trained on anatomical shape priors. This dense motion model formed the input to a supervised denoising autoencoder (4Dsurvival), which is a hybrid network consisting of an autoencoder that learns a task-specific latent code representation trained on observed outcome data, yielding a latent representation optimised for survival prediction. To handle right-censored survival outcomes, our network used a Cox partial likelihood loss function. In a study of 302 patients the predictive accuracy (quantified by Harrell's C-index) was significantly higher (p < .0001) for our model C=0.73 (95$\%$ CI: 0.68 - 0.78) than the human benchmark of C=0.59 (95$\%$ CI: 0.53 - 0.65). This work demonstrates how a complex computer vision task using high-dimensional medical image data can efficiently predict human survival.