Univariate and multivariate pattern analysis of preterm subjects: a multimodal neuroimaging study

Background: Widespread lasting functional connectivity (FC) and brain volume changes in cortices and subcortices after premature birth have been researched in recent studies. However, the relationship remains unclear between spontaneously slow blood oxygen dependent level (BOLD) fluctuations and gray matter volume (GMV) changes in specific brain areas, such as temporal insular cortices, and whether classification methods based on MRI could be successfully applied to the identification of preterm individuals. In this thesis I hypothesized that in prematurely born adults 1. Ongoing neural excitability and brain activity, as estimated by regional functional connectivity of resting state functional MRI (rs-fMRI) is accompanied with altered low-frequency fluctuations and neonatal complications; 2. Altered regional functional connectivity is connected with superimposed cerebral structural reductions; and 3. multivariate neuroanatomical and functional brain patterns could be treated as features to identify preterm subjects from term subjects individually. Methods: To investigate these hypotheses, the principal results of structural alterations were measured with voxel-based morphometry (VBM), while rs-fMRI outcomes were estimated with amplitude of low-frequency fluctuations (ALFF) in analysis with ninety-four very preterm/very low birth weight (VP/VLBW) and ninety-two full-term (FT) born young adults. Results: The results of the thesis support the hypotheses by showing that, in univariate results, first in VP/VLBW grownups, ALFF was decreased in the left lateral temporal cortices no matter with global signal regression, and this reduction was closely associated with neonatal complications and cognitive variables. Second overlapped brain regions were found between reduced ALFF and reduced brain volumes in the left temporal cortices, and positively associated with each other, demonstrating a potential relationship between VBM and ALFF in this brain area. In multimodal multivariate pattern recognition analysis (MVPA), the gray matter volume (GMV) classifier displayed a higher accuracy (80.7%) contrast with the ALFF classifier (77.4%). The late fusion of GMV and ALFF did not outperform single GMV modality classification by reaching 80.4% accuracy. Moderator analysis from both rs-fMRI and structural MRI (sMRI) uncovered that the neuro-prematurity performance was predominantly determined by neonatal complications. Conclusions: In conclusion, these outcomes exhibit the long term effects of premature labour on lateral temporal cortices, which changed in both ongoing BOLD fluctuations and decreased cerebral structural volumes. This thesis further provided evidence that multivariate pattern analysis such as support vector machine (SVM) may identify imaging-based biomarkers and reliably detect signatures of preterm birth

Univariate and multivariate pattern analysis of preterm subjects: a multimodal neuroimaging study

Background: Widespread lasting functional connectivity (FC) and brain volume changes in cortices and subcortices after premature birth have been researched in recent studies. However, the relationship remains unclear between spontaneously slow blood oxygen dependent level (BOLD) fluctuations and gray matter volume (GMV) changes in specific brain areas, such as temporal insular cortices, and whether classification methods based on MRI could be successfully applied to the identification of preterm individuals. In this thesis I hypothesized that in prematurely born adults 1. Ongoing neural excitability and brain activity, as estimated by regional functional connectivity of resting state functional MRI (rs-fMRI) is accompanied with altered low-frequency fluctuations and neonatal complications; 2. Altered regional functional connectivity is connected with superimposed cerebral structural reductions; and 3. multivariate neuroanatomical and functional brain patterns could be treated as features to identify preterm subjects from term subjects individually. Methods: To investigate these hypotheses, the principal results of structural alterations were measured with voxel-based morphometry (VBM), while rs-fMRI outcomes were estimated with amplitude of low-frequency fluctuations (ALFF) in analysis with ninety-four very preterm/very low birth weight (VP/VLBW) and ninety-two full-term (FT) born young adults. Results: The results of the thesis support the hypotheses by showing that, in univariate results, first in VP/VLBW grownups, ALFF was decreased in the left lateral temporal cortices no matter with global signal regression, and this reduction was closely associated with neonatal complications and cognitive variables. Second overlapped brain regions were found between reduced ALFF and reduced brain volumes in the left temporal cortices, and positively associated with each other, demonstrating a potential relationship between VBM and ALFF in this brain area. In multimodal multivariate pattern recognition analysis (MVPA), the gray matter volume (GMV) classifier displayed a higher accuracy (80.7%) contrast with the ALFF classifier (77.4%). The late fusion of GMV and ALFF did not outperform single GMV modality classification by reaching 80.4% accuracy. Moderator analysis from both rs-fMRI and structural MRI (sMRI) uncovered that the neuro-prematurity performance was predominantly determined by neonatal complications. Conclusions: In conclusion, these outcomes exhibit the long term effects of premature labour on lateral temporal cortices, which changed in both ongoing BOLD fluctuations and decreased cerebral structural volumes. This thesis further provided evidence that multivariate pattern analysis such as support vector machine (SVM) may identify imaging-based biomarkers and reliably detect signatures of preterm birth

Automatic Autism Spectrum Disorder Detection Using Artificial Intelligence Methods with MRI Neuroimaging: A Review

Autism spectrum disorder (ASD) is a brain condition characterized by diverse signs and symptoms that appear in early childhood. ASD is also associated with communication deficits and repetitive behavior in affected individuals. Various ASD detection methods have been developed, including neuroimaging modalities and psychological tests. Among these methods, magnetic resonance imaging (MRI) imaging modalities are of paramount importance to physicians. Clinicians rely on MRI modalities to diagnose ASD accurately. The MRI modalities are non-invasive methods that include functional (fMRI) and structural (sMRI) neuroimaging methods. However, the process of diagnosing ASD with fMRI and sMRI for specialists is often laborious and time-consuming; therefore, several computer-aided design systems (CADS) based on artificial intelligence (AI) have been developed to assist the specialist physicians. Conventional machine learning (ML) and deep learning (DL) are the most popular schemes of AI used for diagnosing ASD. This study aims to review the automated detection of ASD using AI. We review several CADS that have been developed using ML techniques for the automated diagnosis of ASD using MRI modalities. There has been very limited work on the use of DL techniques to develop automated diagnostic models for ASD. A summary of the studies developed using DL is provided in the appendix. Then, the challenges encountered during the automated diagnosis of ASD using MRI and AI techniques are described in detail. Additionally, a graphical comparison of studies using ML and DL to diagnose ASD automatically is discussed. We conclude by suggesting future approaches to detecting ASDs using AI techniques and MRI neuroimaging

Dealing with heterogeneity in the prediction of clinical diagnosis

Le diagnostic assisté par ordinateur est un domaine de recherche en émergence et se situe à l’intersection de l’imagerie médicale et de l’apprentissage machine. Les données médi- cales sont de nature très hétérogène et nécessitent une attention particulière lorsque l’on veut entraîner des modèles de prédiction. Dans cette thèse, j’ai exploré deux sources d’hétérogénéité, soit l’agrégation multisites et l’hétérogénéité des étiquettes cliniques dans le contexte de l’imagerie par résonance magnétique (IRM) pour le diagnostic de la maladie d’Alzheimer (MA). La première partie de ce travail consiste en une introduction générale sur la MA, l’IRM et les défis de l’apprentissage machine en imagerie médicale. Dans la deuxième partie de ce travail, je présente les trois articles composant la thèse. Enfin, la troisième partie porte sur une discussion des contributions et perspectives fu- tures de ce travail de recherche. Le premier article de cette thèse montre que l’agrégation des données sur plusieurs sites d’acquisition entraîne une certaine perte, comparative- ment à l’analyse sur un seul site, qui tend à diminuer plus la taille de l’échantillon aug- mente. Le deuxième article de cette thèse examine la généralisabilité des modèles de prédiction à l’aide de divers schémas de validation croisée. Les résultats montrent que la formation et les essais sur le même ensemble de sites surestiment la précision du modèle, comparativement aux essais sur des nouveaux sites. J’ai également montré que l’entraînement sur un grand nombre de sites améliore la précision sur des nouveaux sites. Le troisième et dernier article porte sur l’hétérogénéité des étiquettes cliniques et pro- pose un nouveau cadre dans lequel il est possible d’identifier un sous-groupe d’individus qui partagent une signature homogène hautement prédictive de la démence liée à la MA. Cette signature se retrouve également chez les patients présentant des symptômes mod- érés. Les résultats montrent que 90% des sujets portant la signature ont progressé vers la démence en trois ans. Les travaux de cette thèse apportent ainsi de nouvelles con- tributions à la manière dont nous approchons l’hétérogénéité en diagnostic médical et proposent des pistes de solution pour tirer profit de cette hétérogénéité.Computer assisted diagnosis has emerged as a popular area of research at the intersection of medical imaging and machine learning. Medical data are very heterogeneous in nature and therefore require careful attention when one wants to train prediction models. In this thesis, I explored two sources of heterogeneity, multisite aggregation and clinical label heterogeneity, in an application of magnetic resonance imaging to the diagnosis of Alzheimer’s disease. In the process, I learned about the feasibility of multisite data aggregation and how to leverage that heterogeneity in order to improve generalizability of prediction models. Part one of the document is a general context introduction to Alzheimer’s disease, magnetic resonance imaging, and machine learning challenges in medical imaging. In part two, I present my research through three articles (two published and one in preparation). Finally, part three provides a discussion of my contributions and hints to possible future developments. The first article shows that data aggregation across multiple acquisition sites incurs some loss, compared to single site analysis, that tends to diminish as the sample size increase. These results were obtained through semisynthetic Monte-Carlo simulations based on real data. The second article investigates the generalizability of prediction models with various cross-validation schemes. I showed that training and testing on the same batch of sites over-estimates the accuracy of the model, compared to testing on unseen sites. However, I also showed that training on a large number of sites improves the accuracy on unseen sites. The third article, on clinical label heterogeneity, proposes a new framework where we can identify a subgroup of individuals that share a homogeneous signature highly predictive of AD dementia. That signature could also be found in patients with mild symptoms, 90% of whom progressed to dementia within three years. The thesis thus makes new contributions to dealing with heterogeneity in medical diagnostic applications and proposes ways to leverage that heterogeneity to our benefit

Intracranial Volume Estimation and Graph Theoretical Analysis of Brain Functional Connectivity Networks

Understanding pathways of neurological disorders requires extensive research on both functional and structural characteristics of the brain. This dissertation introduced two interrelated research endeavors, describing (1) a novel integrated approach for constructing functional connectivity networks (FCNs) of brain using non-invasive scalp EEG recordings; and (2) a decision aid for estimating intracranial volume (ICV). The approach in (1) was developed to study the alterations of networks in patients with pediatric epilepsy. Results demonstrated the existence of statistically significant (

Deep Learning in EEG: Advance of the Last Ten-Year Critical Period

Deep learning has achieved excellent performance in a wide range of domains, especially in speech recognition and computer vision. Relatively less work has been done for EEG, but there is still significant progress attained in the last decade. Due to the lack of a comprehensive and topic widely covered survey for deep learning in EEG, we attempt to summarize recent progress to provide an overview, as well as perspectives for future developments. We first briefly mention the artifacts removal for EEG signal and then introduce deep learning models that have been utilized in EEG processing and classification. Subsequently, the applications of deep learning in EEG are reviewed by categorizing them into groups such as brain-computer interface, disease detection, and emotion recognition. They are followed by the discussion, in which the pros and cons of deep learning are presented and future directions and challenges for deep learning in EEG are proposed. We hope that this paper could serve as a summary of past work for deep learning in EEG and the beginning of further developments and achievements of EEG studies based on deep learning

Influence of deep structures on the EEG and their invasive and non-invasive assessment

Tesis inédita de la Universidad Complutense de Madrid, Facultad de Medicina, Departamento de Fisiología, leída el 22-11-2019El EEG es la prueba diagnóstica de mayor utilidad en el diagnóstico de la epilepsia. Consiste esencialmente en la representación gráfica de los potenciales postsinápticos generados en las neuronas piramidales de la corteza. Los campos eléctricos registrados en la superficie tienen principalmente dos mecanismos de origen: conducción de volumen desde regiones adyacentes y propagación interneuronal sináptica. Las neuronal piramidales se agrupan formando microcircuitos locales siendo estos circuitos los responsables de la generación delos ritmos registrados en el EEG. Uno de los principales retos de la electroencefalografía consiste en descifrar la relación entre la actividad registrada y la actividad subyacente en las redes neuronales. Para encontrar la fuente de dichas actividades, es necesario tener en cuenta complejos mecanismos tanto no lineales como lineales, así como el efecto de la conducción de volumen y la influencia de la morfología y las propiedades eléctricas del cerebro y el cráneo. Además, las regiones cerebrales se encuentran profusamente interconectadas a menudo produciendo una modulación recíproca que añade un mayor grado complejidad...The EEG is the most valuable diagnostic test in epilepsy. In essence, it mainly consists in agraphical representation of the summated postsynaptic potentials generated in the pyramidal neurons from the cortex. The electrical fields can be generated on the scalp by two mechanisms: volume conduction from nearby regions and synaptic inter‐neuronal propagation. Pyramidal cells align conforming local microcircuit configurations which activation lead to the generation of EEG rhythms. One of the main challenges of EEG is to decipher the relation between the recorded EEG activity and the activity in the neuronal networks. To find the source of EEG activity, complex non‐linear and linear mechanisms as well as volume conduction effect and influence of the shape and electrical properties of the brain and skull need to be taken in consideration. In addition, brain regions are profusely interconnected and functionally connected regions often produce mutual modulation that adds additional complexity...Depto. de FisiologíaFac. de MedicinaTRUEunpu

Machine Learning Methods for Structural Brain MRIs: Applications for Alzheimer’s Disease and Autism Spectrum Disorder

This thesis deals with the development of novel machine learning applications to automatically detect brain disorders based on magnetic resonance imaging (MRI) data, with a particular focus on Alzheimer’s disease and the autism spectrum disorder. Machine learning approaches are used extensively in neuroimaging studies of brain disorders to investigate abnormalities in various brain regions. However, there are many technical challenges in the analysis of neuroimaging data, for example, high dimensionality, the limited amount of data, and high variance in that data due to many confounding factors. These limitations make the development of appropriate computational approaches more challenging. To deal with these existing challenges, we target multiple machine learning approaches, including supervised and semi-supervised learning, domain adaptation, and dimensionality reduction methods.In the current study, we aim to construct effective biomarkers with sufficient sensitivity and specificity that can help physicians better understand the diseases and make improved diagnoses or treatment choices. The main contributions are 1) development of a novel biomarker for predicting Alzheimer’s disease in mild cognitive impairment patients by integrating structural MRI data and neuropsychological test results and 2) the development of a new computational approach for predicting disease severity in autistic patients in agglomerative data by automatically combining structural information obtained from different brain regions.In addition, we investigate various data-driven feature selection and classification methods for whole brain, voxel-based classification analysis of structural MRI and the use of semi-supervised learning approaches to predict Alzheimer’s disease. We also analyze the relationship between disease-related structural changes and cognitive states of patients with Alzheimer’s disease.The positive results of this effort provide insights into how to construct better biomarkers based on multisource data analysis of patient and healthy cohorts that may enable early diagnosis of brain disorders, detection of brain abnormalities and understanding effective processing in patient and healthy groups. Further, the methodologies and basic principles presented in this thesis are not only suited to the studied cases, but also are applicable to other similar problems