Homeomorphic Image Registration via Conformal-Invariant Hyperelastic Regularisation

Deformable image registration is a fundamental task in medical image analysis and plays a crucial role in a wide range of clinical applications. Recently, deep learning-based approaches have been widely studied for deformable medical image registration and achieved promising results. However, existing deep learning image registration techniques do not theoretically guarantee topology-preserving transformations. This is a key property to preserve anatomical structures and achieve plausible transformations that can be used in real clinical settings. We propose a novel framework for deformable image registration. Firstly, we introduce a novel regulariser based on conformal-invariant properties in a nonlinear elasticity setting. Our regulariser enforces the deformation field to be smooth, invertible and orientation-preserving. More importantly, we strictly guarantee topology preservation yielding to a clinical meaningful registration. Secondly, we boost the performance of our regulariser through coordinate MLPs, where one can view the to-be-registered images as continuously differentiable entities. We demonstrate, through numerical and visual experiments, that our framework is able to outperform current techniques for image registration.

CoNIC Challenge: Pushing the Frontiers of Nuclear Detection, Segmentation, Classification and Counting

Nuclear detection, segmentation and morphometric profiling are essential in helping us further understand the relationship between histology and patient outcome. To drive innovation in this area, we setup a community-wide challenge using the largest available dataset of its kind to assess nuclear segmentation and cellular composition. Our challenge, named CoNIC, stimulated the development of reproducible algorithms for cellular recognition with real-time result inspection on public leaderboards. We conducted an extensive post-challenge analysis based on the top-performing models using 1,658 whole-slide images of colon tissue. With around 700 million detected nuclei per model, associated features were used for dysplasia grading and survival analysis, where we demonstrated that the challenge's improvement over the previous state-of-the-art led to significant boosts in downstream performance. Our findings also suggest that eosinophils and neutrophils play an important role in the tumour microevironment. We release challenge models and WSI-level results to foster the development of further methods for biomarker discovery.

Provably Convergent Plug-and-Play Quasi-Newton Methods

Plug-and-Play (PnP) methods are a class of efficient iterative methods that aim to combine data fidelity terms and deep denoisers using classical optimization algorithms, such as ISTA or ADMM. Existing provable PnP methods impose heavy restrictions on the denoiser or fidelity function, such as nonexpansiveness or strict convexity. In this work, we propose a provable PnP method that imposes relatively light conditions based on proximal denoisers, and introduce a quasi-Newton step to greatly accelerate convergence. By specially parameterizing the deep denoiser as a gradient step, we further characterize the fixed-points of the quasi-Newton PnP algorithm.

Hidden Knowledge: Mathematical Methods for the Extraction of the Fingerprint of Medieval Paper from Digital Images

Medieval paper, a handmade product, is made with a mould which leaves an indelible imprint on the sheet of paper. This imprint includes chain lines, laid lines and watermarks which are often visible on the sheet. Extracting these features allows the identification of paper stock and gives information about chronology, localisation and movement of books and people. Most computational work for feature extraction of paper analysis has so far focused on radiography or transmitted light images. While these imaging methods provide clear visualisation for the features of interest, they are expensive and time consuming in their acquisition and not feasible for smaller institutions. However, reflected light images of medieval paper manuscripts are abundant and possibly cheaper in their acquisition. In this paper, we propose algorithms to detect and extract the laid and chain lines from reflected light images. We tackle the main drawback of reflected light images, that is, the low contrast attenuation of lines and intensity jumps due to noise and degradation, by employing the spectral total variation decomposition and develop methods for subsequent line extraction. Our results clearly demonstrate the feasibility of using reflected light images in paper analysis. This work enables the feature extraction for paper manuscripts that have otherwise not been analysed due to a lack of appropriate images. We also open the door for paper stock identification at scale.

Implicit neural representations for unsupervised super-resolution and denoising of 4D flow MRI

4D flow MRI is a non-invasive imaging method that can measure blood flow velocities over time. However, the velocity fields detected by this technique have limitations due to low resolution and measurement noise. Coordinate-based neural networks have been researched to improve accuracy, with SIRENs being suitable for super-resolution tasks. Our study investigates SIRENs for time-varying 3-directional velocity fields measured in the aorta by 4D flow MRI, achieving denoising and super-resolution. We trained our method on voxel coordinates and benchmarked our approach using synthetic measurements and a real 4D flow MRI scan. Our optimized SIREN architecture outperformed state-of-the-art techniques, producing denoised and super-resolved velocity fields from clinical data. Our approach is quick to execute and straightforward to implement for novel cases, achieving 4D super-resolution.

Can Physics-Informed Neural Networks beat the Finite Element Method?

Partial differential equations play a fundamental role in the mathematical modelling of many processes and systems in physical, biological and other sciences. To simulate such processes and systems, the solutions of PDEs often need to be approximated numerically. The finite element method, for instance, is a usual standard methodology to do so. The recent success of deep neural networks at various approximation tasks has motivated their use in the numerical solution of PDEs. These so-called physics-informed neural networks and their variants have shown to be able to successfully approximate a large range of partial differential equations. So far, physics-informed neural networks and the finite element method have mainly been studied in isolation of each other. In this work, we compare the methodologies in a systematic computational study. Indeed, we employ both methods to numerically solve various linear and nonlinear partial differential equations: Poisson in 1D, 2D, and 3D, Allen-Cahn in 1D, semilinear Schr\"odinger in 1D and 2D. We then compare computational costs and approximation accuracies. In terms of solution time and accuracy, physics-informed neural networks have not been able to outperform the finite element method in our study. In some experiments, they were faster at evaluating the solved PDE.

Continuous U-Net: Faster, Greater and Noiseless

Image segmentation is a fundamental task in image analysis and clinical practice. The current state-of-the-art techniques are based on U-shape type encoder-decoder networks with skip connections, called U-Net. Despite the powerful performance reported by existing U-Net type networks, they suffer from several major limitations. Issues include the hard coding of the receptive field size, compromising the performance and computational cost, as well as the fact that they do not account for inherent noise in the data. They have problems associated with discrete layers, and do not offer any theoretical underpinning. In this work we introduce continuous U-Net, a novel family of networks for image segmentation. Firstly, continuous U-Net is a continuous deep neural network that introduces new dynamic blocks modelled by second order ordinary differential equations. Secondly, we provide theoretical guarantees for our network demonstrating faster convergence, higher robustness and less sensitivity to noise. Thirdly, we derive qualitative measures to tailor-made segmentation tasks. We demonstrate, through extensive numerical and visual results, that our model outperforms existing U-Net blocks for several medical image segmentation benchmarking datasets.

Your diffusion model secretly knows the dimension of the data manifold

In this work, we propose a novel framework for estimating the dimension of the data manifold using a trained diffusion model. A trained diffusion model approximates the gradient of the log density of a noise-corrupted version of the target distribution for varying levels of corruption. If the data concentrates around a manifold embedded in the high-dimensional ambient space, then as the level of corruption decreases, the score function points towards the manifold, as this direction becomes the direction of maximum likelihood increase. Therefore, for small levels of corruption, the diffusion model provides us with access to an approximation of the normal bundle of the data manifold. This allows us to estimate the dimension of the tangent space, thus, the intrinsic dimension of the data manifold. Our method outperforms linear methods for dimensionality detection such as PPCA in controlled experiments.

SCOTCH and SODA: A Transformer Video Shadow Detection Framework

Shadows in videos are difficult to detect because of the large shadow deformation between frames. In this work, we argue that accounting for the shadow deformation is essential when designing a video shadow detection method. To this end, we introduce the shadow deformation attention trajectory (SODA), a new type of video self-attention module, specially designed to handle the large shadow deformations in videos. Moreover, we present a shadow contrastive learning mechanism (SCOTCH) which aims at guiding the network to learn a high-level representation of shadows, unified across different videos. We demonstrate empirically the effectiveness of our two contributions in an ablation study. Furthermore, we show that SCOTCH and SODA significantly outperforms existing techniques for video shadow detection. Code will be available upon the acceptance of this work.

Dynamical systems' based neural networks

Neural networks have gained much interest because of their effectiveness in many applications. However, their mathematical properties are generally not well understood. If there is some underlying geometric structure inherent to the data or to the function to approximate, it is often desirable to take this into account in the design of the neural network. In this work, we start with a non-autonomous ODE and build neural networks using a suitable, structure-preserving, numerical time-discretisation. The structure of the neural network is then inferred from the properties of the ODE vector field. Besides injecting more structure into the network architectures, this modelling procedure allows a better theoretical understanding of their behaviour. We present two universal approximation results and demonstrate how to impose some particular properties on the neural networks. A particular focus is on 1-Lipschitz architectures including layers that are not 1-Lipschitz. These networks are expressive and robust against adversarial attacks, as shown for the CIFAR-10 dataset.