578 research outputs found
Explainable Anatomical Shape Analysis through Deep Hierarchical Generative Models
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
Explainable anatomical shape analysis through deep hierarchical generative models.
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 highthroughput analysis of normal anatomy and pathology in largescale studies of volumetric imaging
Machine learning approaches to model cardiac shape in large-scale imaging studies
Recent improvements in non-invasive imaging, together with the introduction of fully-automated segmentation algorithms and big data analytics, has paved the way for large-scale population-based imaging studies. These studies promise to increase our understanding of a large number of medical conditions, including cardiovascular diseases. However, analysis of cardiac shape in such studies is often limited to simple morphometric indices, ignoring large part of the information available in medical images. Discovery of new biomarkers by machine learning has recently gained traction, but often lacks interpretability. The research presented in this thesis aimed at developing novel explainable machine learning and computational methods capable of better summarizing shape variability, to better inform association and predictive clinical models in large-scale imaging studies.
A powerful and flexible framework to model the relationship between three-dimensional (3D) cardiac atlases, encoding multiple phenotypic traits, and genetic variables is first presented. The proposed approach enables the detection of regional phenotype-genotype associations that would be otherwise neglected by conventional association analysis. Three learning-based systems based on deep generative models are then proposed. In the first model, I propose a classifier of cardiac shapes which exploits task-specific generative shape features, and it is designed to enable the visualisation of the anatomical effect these features encode in 3D, making the classification task transparent. The second approach models a database of anatomical shapes via a hierarchy of conditional latent variables and it is capable of detecting, quantifying and visualising onto a template shape the most discriminative anatomical features that characterize distinct clinical conditions. Finally, a preliminary analysis of a deep learning system capable of reconstructing 3D high-resolution cardiac segmentations from a sparse set of 2D views segmentations is reported. This thesis demonstrates that machine learning approaches can facilitate high-throughput analysis of normal and pathological anatomy and of its determinants without losing clinical interpretability.Open Acces
Explainable artificial intelligence (XAI) in deep learning-based medical image analysis
With an increase in deep learning-based methods, the call for explainability
of such methods grows, especially in high-stakes decision making areas such as
medical image analysis. This survey presents an overview of eXplainable
Artificial Intelligence (XAI) used in deep learning-based medical image
analysis. A framework of XAI criteria is introduced to classify deep
learning-based medical image analysis methods. Papers on XAI techniques in
medical image analysis are then surveyed and categorized according to the
framework and according to anatomical location. The paper concludes with an
outlook of future opportunities for XAI in medical image analysis.Comment: Submitted for publication. Comments welcome by email to first autho
Explainable deep learning models in medical image analysis
Deep learning methods have been very effective for a variety of medical
diagnostic tasks and has even beaten human experts on some of those. However,
the black-box nature of the algorithms has restricted clinical use. Recent
explainability studies aim to show the features that influence the decision of
a model the most. The majority of literature reviews of this area have focused
on taxonomy, ethics, and the need for explanations. A review of the current
applications of explainable deep learning for different medical imaging tasks
is presented here. The various approaches, challenges for clinical deployment,
and the areas requiring further research are discussed here from a practical
standpoint of a deep learning researcher designing a system for the clinical
end-users.Comment: Preprint submitted to J.Imaging, MDP
MedSyn: Text-guided Anatomy-aware Synthesis of High-Fidelity 3D CT Images
This paper introduces an innovative methodology for producing high-quality 3D
lung CT images guided by textual information. While diffusion-based generative
models are increasingly used in medical imaging, current state-of-the-art
approaches are limited to low-resolution outputs and underutilize radiology
reports' abundant information. The radiology reports can enhance the generation
process by providing additional guidance and offering fine-grained control over
the synthesis of images. Nevertheless, expanding text-guided generation to
high-resolution 3D images poses significant memory and anatomical
detail-preserving challenges. Addressing the memory issue, we introduce a
hierarchical scheme that uses a modified UNet architecture. We start by
synthesizing low-resolution images conditioned on the text, serving as a
foundation for subsequent generators for complete volumetric data. To ensure
the anatomical plausibility of the generated samples, we provide further
guidance by generating vascular, airway, and lobular segmentation masks in
conjunction with the CT images. The model demonstrates the capability to use
textual input and segmentation tasks to generate synthesized images. The
results of comparative assessments indicate that our approach exhibits superior
performance compared to the most advanced models based on GAN and diffusion
techniques, especially in accurately retaining crucial anatomical features such
as fissure lines, airways, and vascular structures. This innovation introduces
novel possibilities. This study focuses on two main objectives: (1) the
development of a method for creating images based on textual prompts and
anatomical components, and (2) the capability to generate new images
conditioning on anatomical elements. The advancements in image generation can
be applied to enhance numerous downstream tasks
Invariant Scattering Transform for Medical Imaging
Over the years, the Invariant Scattering Transform (IST) technique has become
popular for medical image analysis, including using wavelet transform
computation using Convolutional Neural Networks (CNN) to capture patterns'
scale and orientation in the input signal. IST aims to be invariant to
transformations that are common in medical images, such as translation,
rotation, scaling, and deformation, used to improve the performance in medical
imaging applications such as segmentation, classification, and registration,
which can be integrated into machine learning algorithms for disease detection,
diagnosis, and treatment planning. Additionally, combining IST with deep
learning approaches has the potential to leverage their strengths and enhance
medical image analysis outcomes. This study provides an overview of IST in
medical imaging by considering the types of IST, their application,
limitations, and potential scopes for future researchers and practitioners
Hippocampal representations for deep learning on Alzheimer’s disease
Deep learning offers a powerful approach for analyzing hippocampal changes in Alzheimer’s disease (AD) without relying on handcrafted features. Nevertheless, an input format needs to be selected to pass the image information to the neural network, which has wide ramifications for the analysis, but has not been evaluated yet. We compare five hippocampal representations (and their respective tailored network architectures) that span from raw images to geometric representations like meshes and point clouds. We performed a thorough evaluation for the prediction of AD diagnosis and time-to-dementia prediction with experiments on an independent test dataset. In addition, we evaluated the ease of interpretability for each representation–network pair. Our results show that choosing an appropriate representation of the hippocampus for predicting Alzheimer’s disease with deep learning is crucial, since it impacts performance and ease of interpretation
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