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

Regional Deep Atrophy: a Self-Supervised Learning Method to Automatically Identify Regions Associated With Alzheimer's Disease Progression From Longitudinal MRI

Longitudinal assessment of brain atrophy, particularly in the hippocampus, is a well-studied biomarker for neurodegenerative diseases, such as Alzheimer's disease (AD). In clinical trials, estimation of brain progressive rates can be applied to track therapeutic efficacy of disease modifying treatments. However, most state-of-the-art measurements calculate changes directly by segmentation and/or deformable registration of MRI images, and may misreport head motion or MRI artifacts as neurodegeneration, impacting their accuracy. In our previous study, we developed a deep learning method DeepAtrophy that uses a convolutional neural network to quantify differences between longitudinal MRI scan pairs that are associated with time. DeepAtrophy has high accuracy in inferring temporal information from longitudinal MRI scans, such as temporal order or relative inter-scan interval. DeepAtrophy also provides an overall atrophy score that was shown to perform well as a potential biomarker of disease progression and treatment efficacy. However, DeepAtrophy is not interpretable, and it is unclear what changes in the MRI contribute to progression measurements. In this paper, we propose Regional Deep Atrophy (RDA), which combines the temporal inference approach from DeepAtrophy with a deformable registration neural network and attention mechanism that highlights regions in the MRI image where longitudinal changes are contributing to temporal inference. RDA has similar prediction accuracy as DeepAtrophy, but its additional interpretability makes it more acceptable for use in clinical settings, and may lead to more sensitive biomarkers for disease monitoring in clinical trials of early AD.Comment: Submitted to NeuroImage for revie

Pacific Symposium on Biocomputing 2023

The Pacific Symposium on Biocomputing (PSB) 2023 is an international, multidisciplinary conference for the presentation and discussion of current research in the theory and application of computational methods in problems of biological significance. Presentations are rigorously peer reviewed and are published in an archival proceedings volume. PSB 2023 will be held on January 3-7, 2023 in Kohala Coast, Hawaii. Tutorials and workshops will be offered prior to the start of the conference.PSB 2023 will bring together top researchers from the US, the Asian Pacific nations, and around the world to exchange research results and address open issues in all aspects of computational biology. It is a forum for the presentation of work in databases, algorithms, interfaces, visualization, modeling, and other computational methods, as applied to biological problems, with emphasis on applications in data-rich areas of molecular biology.The PSB has been designed to be responsive to the need for critical mass in sub-disciplines within biocomputing. For that reason, it is the only meeting whose sessions are defined dynamically each year in response to specific proposals. PSB sessions are organized by leaders of research in biocomputing's 'hot topics.' In this way, the meeting provides an early forum for serious examination of emerging methods and approaches in this rapidly changing field

Texture Analysis Platform for Imaging Biomarker Research

abstract: The rate of progress in improving survival of patients with solid tumors is slow due to late stage diagnosis and poor tumor characterization processes that fail to effectively reflect the nature of tumor before treatment or the subsequent change in its dynamics because of treatment. Further advancement of targeted therapies relies on advancements in biomarker research. In the context of solid tumors, bio-specimen samples such as biopsies serve as the main source of biomarkers used in the treatment and monitoring of cancer, even though biopsy samples are susceptible to sampling error and more importantly, are local and offer a narrow temporal scope. Because of its established role in cancer care and its non-invasive nature imaging offers the potential to complement the findings of cancer biology. Over the past decade, a compelling body of literature has emerged suggesting a more pivotal role for imaging in the diagnosis, prognosis, and monitoring of diseases. These advances have facilitated the rise of an emerging practice known as Radiomics: the extraction and analysis of large numbers of quantitative features from medical images to improve disease characterization and prediction of outcome. It has been suggested that radiomics can contribute to biomarker discovery by detecting imaging traits that are complementary or interchangeable with other markers. This thesis seeks further advancement of imaging biomarker discovery. This research unfolds over two aims: I) developing a comprehensive methodological pipeline for converting diagnostic imaging data into mineable sources of information, and II) investigating the utility of imaging data in clinical diagnostic applications. Four validation studies were conducted using the radiomics pipeline developed in aim I. These studies had the following goals: (1 distinguishing between benign and malignant head and neck lesions (2) differentiating benign and malignant breast cancers, (3) predicting the status of Human Papillomavirus in head and neck cancers, and (4) predicting neuropsychological performances as they relate to Alzheimer’s disease progression. The long-term objective of this thesis is to improve patient outcome and survival by facilitating incorporation of routine care imaging data into decision making processes.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201

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

Data efficient deep learning for medical image analysis: A survey

The rapid evolution of deep learning has significantly advanced the field of medical image analysis. However, despite these achievements, the further enhancement of deep learning models for medical image analysis faces a significant challenge due to the scarcity of large, well-annotated datasets. To address this issue, recent years have witnessed a growing emphasis on the development of data-efficient deep learning methods. This paper conducts a thorough review of data-efficient deep learning methods for medical image analysis. To this end, we categorize these methods based on the level of supervision they rely on, encompassing categories such as no supervision, inexact supervision, incomplete supervision, inaccurate supervision, and only limited supervision. We further divide these categories into finer subcategories. For example, we categorize inexact supervision into multiple instance learning and learning with weak annotations. Similarly, we categorize incomplete supervision into semi-supervised learning, active learning, and domain-adaptive learning and so on. Furthermore, we systematically summarize commonly used datasets for data efficient deep learning in medical image analysis and investigate future research directions to conclude this survey.Comment: Under Revie

P5 eHealth: An Agenda for the Health Technologies of the Future

This open access volume focuses on the development of a P5 eHealth, or better, a methodological resource for developing the health technologies of the future, based on patients’ personal characteristics and needs as the fundamental guidelines for design. It provides practical guidelines and evidence based examples on how to design, implement, use and elevate new technologies for healthcare to support the management of incurable, chronic conditions. The volume further discusses the criticalities of eHealth, why it is difficult to employ eHealth from an organizational point of view or why patients do not always accept the technology, and how eHealth interventions can be improved in the future. By dealing with the state-of-the-art in eHealth technologies, this volume is of great interest to researchers in the field of physical and mental healthcare, psychologists, stakeholders and policymakers as well as technology developers working in the healthcare sector