932 research outputs found
-Equivariant Networks for Spherical Deconvolution in Diffusion MRI
We present Roto-Translation Equivariant Spherical Deconvolution (RT-ESD), an
equivariant framework for sparse deconvolution of volumes
where each voxel contains a spherical signal. Such 6D data naturally arises in
diffusion MRI (dMRI), a medical imaging modality widely used to measure
microstructure and structural connectivity. As each dMRI voxel is typically a
mixture of various overlapping structures, there is a need for blind
deconvolution to recover crossing anatomical structures such as white matter
tracts. Existing dMRI work takes either an iterative or deep learning approach
to sparse spherical deconvolution, yet it typically does not account for
relationships between neighboring measurements. This work constructs
equivariant deep learning layers which respect to symmetries of spatial
rotations, reflections, and translations, alongside the symmetries of voxelwise
spherical rotations. As a result, RT-ESD improves on previous work across
several tasks including fiber recovery on the DiSCo dataset,
deconvolution-derived partial volume estimation on real-world \textit{in vivo}
human brain dMRI, and improved downstream reconstruction of fiber tractograms
on the Tractometer dataset. Our implementation is available at
https://github.com/AxelElaldi/e3so3_convComment: Accepted to Medical Imaging with Deep Learning (MIDL) 2023. Code
available at https://github.com/AxelElaldi/e3so3_conv . 19 pages with 6
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Validation of deep learning techniques for quality augmentation in diffusion MRI for clinical studies
The objective of this study is to evaluate the efficacy of deep learning (DL) techniques in improving the quality of diffusion MRI (dMRI) data in clinical applications. The study aims to determine whether the use of artificial intelligence (AI) methods in medical images may result in the loss of critical clinical information and/or the appearance of false information. To assess this, the focus was on the angular resolution of dMRI and a clinical trial was conducted on migraine, specifically between episodic and chronic migraine patients. The number of gradient directions had an impact on white matter analysis results, with statistically significant differences between groups being drastically reduced when using 21 gradient directions instead of the original 61. Fourteen teams from different institutions were tasked to use DL to enhance three diffusion metrics (FA, AD and MD) calculated from data acquired with 21 gradient directions and a b-value of 1000 s/mm2. The goal was to produce results that were comparable to those calculated from 61 gradient directions. The results were evaluated using both standard image quality metrics and Tract-Based Spatial Statistics (TBSS) to compare episodic and chronic migraine patients. The study results suggest that while most DL techniques improved the ability to detect statistical differences between groups, they also led to an increase in false positive. The results showed that there was a constant growth rate of false positives linearly proportional to the new true positives, which highlights the risk of generalization of AI-based tasks when assessing diverse clinical cohorts and training using data from a single group. The methods also showed divergent performance when replicating the original distribution of the data and some exhibited significant bias. In conclusion, extreme caution should be exercised when using AI methods for harmonization or synthesis in clinical studies when processing heterogeneous data in clinical studies, as important information may be altered, even when global metrics such as structural similarity or peak signal-to-noise ratio appear to suggest otherwise
Physics-Informed Computer Vision: A Review and Perspectives
Incorporation of physical information in machine learning frameworks are
opening and transforming many application domains. Here the learning process is
augmented through the induction of fundamental knowledge and governing physical
laws. In this work we explore their utility for computer vision tasks in
interpreting and understanding visual data. We present a systematic literature
review of formulation and approaches to computer vision tasks guided by
physical laws. We begin by decomposing the popular computer vision pipeline
into a taxonomy of stages and investigate approaches to incorporate governing
physical equations in each stage. Existing approaches in each task are analyzed
with regard to what governing physical processes are modeled, formulated and
how they are incorporated, i.e. modify data (observation bias), modify networks
(inductive bias), and modify losses (learning bias). The taxonomy offers a
unified view of the application of the physics-informed capability,
highlighting where physics-informed learning has been conducted and where the
gaps and opportunities are. Finally, we highlight open problems and challenges
to inform future research. While still in its early days, the study of
physics-informed computer vision has the promise to develop better computer
vision models that can improve physical plausibility, accuracy, data efficiency
and generalization in increasingly realistic applications
EXplainable Artificial Intelligence: enabling AI in neurosciences and beyond
The adoption of AI models in medicine and neurosciences has the potential to play a significant role not only in bringing scientific advancements but also in clinical decision-making. However, concerns mounts due to the eventual biases AI could have which could result in far-reaching consequences particularly in a critical field like biomedicine. It is challenging to achieve usable intelligence because not only it is fundamental to learn from prior data, extract knowledge and guarantee generalization capabilities, but also to disentangle the underlying explanatory factors in order to deeply understand the variables leading to the final decisions. There hence has been a call for approaches to open the AI `black box' to increase trust and reliability on the decision-making capabilities of AI algorithms. Such approaches are commonly referred to as XAI and are starting to be applied in medical fields even if not yet fully exploited. With this thesis we aim at contributing to enabling the use of AI in medicine and neurosciences by taking two fundamental steps: (i) practically pervade AI models with XAI (ii) Strongly validate XAI models. The first step was achieved on one hand by focusing on XAI taxonomy and proposing some guidelines specific for the AI and XAI applications in the neuroscience domain. On the other hand, we faced concrete issues proposing XAI solutions to decode the brain modulations in neurodegeneration relying on the morphological, microstructural and functional changes occurring at different disease stages as well as their connections with the genotype substrate. The second step was as well achieved by firstly defining four attributes related to XAI validation, namely stability, consistency, understandability and plausibility. Each attribute refers to a different aspect of XAI ranging from the assessment of explanations stability across different XAI methods, or highly collinear inputs, to the alignment of the obtained explanations with the state-of-the-art literature. We then proposed different validation techniques aiming at practically fulfilling such requirements. With this thesis, we contributed to the advancement of the research into XAI aiming at increasing awareness and critical use of AI methods opening the way to real-life applications enabling the development of personalized medicine and treatment by taking a data-driven and objective approach to healthcare
Deep Learning in Medical Image Analysis
The computer-assisted analysis for better interpreting images have been longstanding issues in the medical imaging field. On the image-understanding front, recent advances in machine learning, especially, in the way of deep learning, have made a big leap to help identify, classify, and quantify patterns in medical images. Specifically, exploiting hierarchical feature representations learned solely from data, instead of handcrafted features mostly designed based on domain-specific knowledge, lies at the core of the advances. In that way, deep learning is rapidly proving to be the state-of-the-art foundation, achieving enhanced performances in various medical applications. In this article, we introduce the fundamentals of deep learning methods; review their successes to image registration, anatomical/cell structures detection, tissue segmentation, computer-aided disease diagnosis or prognosis, and so on. We conclude by raising research issues and suggesting future directions for further improvements
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