Non-Uniform Diffusion Models

Diffusion models have emerged as one of the most promising frameworks for deep generative modeling. In this work, we explore the potential of non-uniform diffusion models. We show that non-uniform diffusion leads to multi-scale diffusion models which have similar structure to this of multi-scale normalizing flows. We experimentally find that in the same or less training time, the multi-scale diffusion model achieves better FID score than the standard uniform diffusion model. More importantly, it generates samples $4.4$ times faster in $128\times 128$ resolution. The speed-up is expected to be higher in higher resolutions where more scales are used. Moreover, we show that non-uniform diffusion leads to a novel estimator for the conditional score function which achieves on par performance with the state-of-the-art conditional denoising estimator. Our theoretical and experimental findings are accompanied by an open source library MSDiff which can facilitate further research of non-uniform diffusion models.

Classification of datasets with imputed missing values: does imputation quality matter?

Classifying samples in incomplete datasets is a common aim for machine learning practitioners, but is non-trivial. Missing data is found in most real-world datasets and these missing values are typically imputed using established methods, followed by classification of the now complete, imputed, samples. The focus of the machine learning researcher is then to optimise the downstream classification performance. In this study, we highlight that it is imperative to consider the quality of the imputation. We demonstrate how the commonly used measures for assessing quality are flawed and propose a new class of discrepancy scores which focus on how well the method recreates the overall distribution of the data. To conclude, we highlight the compromised interpretability of classifier models trained using poorly imputed data.

Learned reconstruction with convergence guarantees

In recent years, deep learning has achieved remarkable empirical success for image reconstruction. This has catalyzed an ongoing quest for precise characterization of correctness and reliability of data-driven methods in critical use-cases, for instance in medical imaging. Notwithstanding the excellent performance and efficacy of deep learning-based methods, concerns have been raised regarding their stability, or lack thereof, with serious practical implications. Significant advances have been made in recent years to unravel the inner workings of data-driven image recovery methods, challenging their widely perceived black-box nature. In this article, we will specify relevant notions of convergence for data-driven image reconstruction, which will form the basis of a survey of learned methods with mathematically rigorous reconstruction guarantees. An example that is highlighted is the role of ICNN, offering the possibility to combine the power of deep learning with classical convex regularization theory for devising methods that are provably convergent. This survey article is aimed at both methodological researchers seeking to advance the frontiers of our understanding of data-driven image reconstruction methods as well as practitioners, by providing an accessible description of convergence concepts and by placing some of the existing empirical practices on a solid mathematical foundation.

Unsupervised Learning of the Total Variation Flow

The total variation (TV) flow generates a scale-space representation of an image based on the TV functional. This gradient flow observes desirable features for images such as sharp edges and enables spectral, scale, and texture analysis. The standard numerical approach for TV flow requires solving multiple non-smooth optimisation problems. Even with state-of-the-art convex optimisation techniques, this is often prohibitively expensive and strongly motivates the use of alternative, faster approaches. Inspired by and extending the framework of physics-informed neural networks (PINNs), we propose the TVflowNET, a neural network approach to compute the solution of the TV flow given an initial image and a time instance. We significantly speed up the computation time by more than one order of magnitude and show that the TVflowNET approximates the TV flow solution with high fidelity. This is a preliminary report, more details are to follow.

Multi-Modal Hypergraph Diffusion Network with Dual Prior for Alzheimer Classification

The automatic early diagnosis of prodromal stages of Alzheimer's disease is of great relevance for patient treatment to improve quality of life. We address this problem as a multi-modal classification task. Multi-modal data provides richer and complementary information. However, existing techniques only consider either lower order relations between the data and single/multi-modal imaging data. In this work, we introduce a novel semi-supervised hypergraph learning framework for Alzheimer's disease diagnosis. Our framework allows for higher-order relations among multi-modal imaging and non-imaging data whilst requiring a tiny labelled set. Firstly, we introduce a dual embedding strategy for constructing a robust hypergraph that preserves the data semantics. We achieve this by enforcing perturbation invariance at the image and graph levels using a contrastive based mechanism. Secondly, we present a dynamically adjusted hypergraph diffusion model, via a semi-explicit flow, to improve the predictive uncertainty. We demonstrate, through our experiments, that our framework is able to outperform current techniques for Alzheimer's disease diagnosis.

Multi-modal learning for predicting the genotype of glioma

The isocitrate dehydrogenase (IDH) gene mutation is an essential biomarker for the diagnosis and prognosis of glioma. It is promising to better predict glioma genotype by integrating focal tumor image and geometric features with brain network features derived from MRI. Convolutions neural networks show reasonable performance in predicting IDH mutation, which, however, cannot learn from non-Euclidean data, e.g., geometric and network data. In this study, we propose a multi-modal learning framework using three separate encoders to extract features of focal tumor image, tumor geometrics and global brain networks. To mitigate the limited availability of diffusion MRI, we develop a self-supervised approach to generate brain networks from anatomical multi-sequence MRI. Moreover, to extract tumor-related features from the brain network, we design a hierarchical attention module for the brain network encoder. Further, we design a bi-level multi-modal contrastive loss to align the multi-modal features and tackle the domain gap at the focal tumor and global brain. Finally, we propose a weighted population graph to integrate the multi-modal features for genotype prediction. Experimental results on the testing set show that the proposed model outperforms the baseline deep learning models. The ablation experiments validate the performance of different components of the framework. The visualized interpretation corresponds to clinical knowledge with further validation. In conclusion, the proposed learning framework provides a novel approach for predicting the genotype of glioma.

Unsupervised Clustering of Roman Potsherds via Variational Autoencoders

In this paper we propose an artificial intelligence imaging solution to support archaeologists in the classification task of Roman commonware potsherds. Usually, each potsherd is represented by its sectional profile as a two dimensional black-white image and printed in archaeological books related to specific archaeological excavations. The partiality and handcrafted variance of the fragments make their matching a challenging problem: we propose to pair similar profiles via the unsupervised hierarchical clustering of non-linear features learned in the latent space of a deep convolutional Variational Autoencoder (VAE) network. Our contribution also include the creation of a ROman COmmonware POTtery (ROCOPOT) database, with more than 4000 potsherds profiles extracted from 25 Roman pottery corpora, and a MATLAB GUI software for the easy inspection of shape similarities. Results are commented both from a mathematical and archaeological perspective so as to unlock new research directions in both communities.

PC-SwinMorph: Patch Representation for Unsupervised Medical Image Registration and Segmentation

Medical image registration and segmentation are critical tasks for several clinical procedures. Manual realisation of those tasks is time-consuming and the quality is highly dependent on the level of expertise of the physician. To mitigate that laborious task, automatic tools have been developed where the majority of solutions are supervised techniques. However, in medical domain, the strong assumption of having a well-representative ground truth is far from being realistic. To overcome this challenge, unsupervised techniques have been investigated. However, they are still limited in performance and they fail to produce plausible results. In this work, we propose a novel unified unsupervised framework for image registration and segmentation that we called PC-SwinMorph. The core of our framework is two patch-based strategies, where we demonstrate that patch representation is key for performance gain. We first introduce a patch-based contrastive strategy that enforces locality conditions and richer feature representation. Secondly, we utilise a 3D window/shifted-window multi-head self-attention module as a patch stitching strategy to eliminate artifacts from the patch splitting. We demonstrate, through a set of numerical and visual results, that our technique outperforms current state-of-the-art unsupervised techniques.

Predicting conversion of mild cognitive impairment to Alzheimer's disease

Alzheimer's disease (AD) is the most common age-related dementia. Mild cognitive impairment (MCI) is the early stage of cognitive decline before AD. It is crucial to predict the MCI-to-AD conversion for precise management, which remains challenging due to the diversity of patients. Previous evidence shows that the brain network generated from diffusion MRI promises to classify dementia using deep learning. However, the limited availability of diffusion MRI challenges the model training. In this study, we develop a self-supervised contrastive learning approach to generate structural brain networks from routine anatomical MRI under the guidance of diffusion MRI. The generated brain networks are applied to train a learning framework for predicting the MCI-to-AD conversion. Instead of directly modelling the AD brain networks, we train a graph encoder and a variational autoencoder to model the healthy ageing trajectories from brain networks of healthy controls. To predict the MCI-to-AD conversion, we further design a recurrent neural networks based approach to model the longitudinal deviation of patients' brain networks from the healthy ageing trajectory. Numerical results show that the proposed methods outperform the benchmarks in the prediction task. We also visualize the model interpretation to explain the prediction and identify abnormal changes of white matter tracts.

Mutual Contrastive Learning to Disentangle Whole Slide Image Representations for Glioma Grading

Whole slide images (WSI) provide valuable phenotypic information for histological assessment and malignancy grading of tumors. The WSI-based computational pathology promises to provide rapid diagnostic support and facilitate digital health. The most commonly used WSI are derived from formalin-fixed paraffin-embedded (FFPE) and frozen sections. Currently, the majority of automatic tumor grading models are developed based on FFPE sections, which could be affected by the artifacts introduced by tissue processing. Here we propose a mutual contrastive learning scheme to integrate FFPE and frozen sections and disentangle cross-modality representations for glioma grading. We first design a mutual learning scheme to jointly optimize the model training based on FFPE and frozen sections. Further, we develop a multi-modality domain alignment mechanism to ensure semantic consistency in the backbone model training. We finally design a sphere normalized temperature-scaled cross-entropy loss (NT-Xent), which could promote cross-modality representation disentangling of FFPE and frozen sections. Our experiments show that the proposed scheme achieves better performance than the model trained based on each single modality or mixed modalities. The sphere NT-Xent loss outperforms other typical metrics loss functions.