Dis-AE: Multi-domain & Multi-task Generalisation on Real-World Clinical Data

Clinical data is often affected by clinically irrelevant factors such as discrepancies between measurement devices or differing processing methods between sites. In the field of machine learning (ML), these factors are known as domains and the distribution differences they cause in the data are known as domain shifts. ML models trained using data from one domain often perform poorly when applied to data from another domain, potentially leading to wrong predictions. As such, developing machine learning models that can generalise well across multiple domains is a challenging yet essential task in the successful application of ML in clinical practice. In this paper, we propose a novel disentangled autoencoder (Dis-AE) neural network architecture that can learn domain-invariant data representations for multi-label classification of medical measurements even when the data is influenced by multiple interacting domain shifts at once. The model utilises adversarial training to produce data representations from which the domain can no longer be determined. We evaluate the model's domain generalisation capabilities on synthetic datasets and full blood count (FBC) data from blood donors as well as primary and secondary care patients, showing that Dis-AE improves model generalisation on multiple domains simultaneously while preserving clinically relevant information.

Variational Diffusion Auto-encoder: Deep Latent Variable Model with Unconditional Diffusion Prior

Variational auto-encoders (VAEs) are one of the most popular approaches to deep generative modeling. Despite their success, images generated by VAEs are known to suffer from blurriness, due to a highly unrealistic modeling assumption that the conditional data distribution $ p(\textbf{x} | \textbf{z})$ can be approximated as an isotropic Gaussian. In this work we introduce a principled approach to modeling the conditional data distribution $p(\textbf{x} | \textbf{z})$ by incorporating a diffusion model. We show that it is possible to create a VAE-like deep latent variable model without making the Gaussian assumption on $ p(\textbf{x} | \textbf{z}) $ or even training a decoder network. A trained encoder and an unconditional diffusion model can be combined via Bayes' rule for score functions to obtain an expressive model for $ p(\textbf{x} | \textbf{z}) $. Our approach avoids making strong assumptions on the parametric form of $ p(\textbf{x} | \textbf{z}) $, and thus allows to significantly improve the performance of VAEs.

Class-Guided Image-to-Image Diffusion: Cell Painting from Brightfield Images with Class Labels

Image-to-image reconstruction problems with free or inexpensive metadata in the form of class labels appear often in biological and medical image domains. Existing text-guided or style-transfer image-to-image approaches do not translate to datasets where additional information is provided as discrete classes. We introduce and implement a model which combines image-to-image and class-guided denoising diffusion probabilistic models. We train our model on a real-world dataset of microscopy images used for drug discovery, with and without incorporating metadata labels. By exploring the properties of image-to-image diffusion with relevant labels, we show that class-guided image-to-image diffusion can improve the meaningful content of the reconstructed images and outperform the unguided model in useful downstream tasks.

DiffMIC: Dual-Guidance Diffusion Network for Medical Image Classification

Diffusion Probabilistic Models have recently shown remarkable performance in generative image modeling, attracting significant attention in the computer vision community. However, while a substantial amount of diffusion-based research has focused on generative tasks, few studies have applied diffusion models to general medical image classification. In this paper, we propose the first diffusion-based model (named DiffMIC) to address general medical image classification by eliminating unexpected noise and perturbations in medical images and robustly capturing semantic representation. To achieve this goal, we devise a dual conditional guidance strategy that conditions each diffusion step with multiple granularities to improve step-wise regional attention. Furthermore, we propose learning the mutual information in each granularity by enforcing Maximum-Mean Discrepancy regularization during the diffusion forward process. We evaluate the effectiveness of our DiffMIC on three medical classification tasks with different image modalities, including placental maturity grading on ultrasound images, skin lesion classification using dermatoscopic images, and diabetic retinopathy grading using fundus images. Our experimental results demonstrate that DiffMIC outperforms state-of-the-art methods by a significant margin, indicating the universality and effectiveness of the proposed model. Our code will be publicly available at https://github.com/scott-yjyang/DiffMIC.

HGIB: Prognosis for Alzheimer's Disease via Hypergraph Information Bottleneck

Alzheimer's disease prognosis is critical for early Mild Cognitive Impairment patients for timely treatment to improve the patient's quality of life. Whilst existing prognosis techniques demonstrate potential results, they are highly limited in terms of using a single modality. Most importantly, they fail in considering a key element for prognosis: not all features extracted at the current moment may contribute to the prognosis prediction several years later. To address the current drawbacks of the literature, we propose a novel hypergraph framework based on an information bottleneck strategy (HGIB). Firstly, our framework seeks to discriminate irrelevant information, and therefore, solely focus on harmonising relevant information for future MCI conversion prediction e.g., two years later). Secondly, our model simultaneously accounts for multi-modal data based on imaging and non-imaging modalities. HGIB uses a hypergraph structure to represent the multi-modality data and accounts for various data modality types. Thirdly, the key of our model is based on a new optimisation scheme. It is based on modelling the principle of information bottleneck into loss functions that can be integrated into our hypergraph neural network. We demonstrate, through extensive experiments on ADNI, that our proposed HGIB framework outperforms existing state-of-the-art hypergraph neural networks for Alzheimer's disease prognosis. We showcase our model even under fewer labels. Finally, we further support the robustness and generalisation capabilities of our framework under both topological and feature perturbations.

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.