Models and Analysis of Vocal Emissions for Biomedical Applications

The MAVEBA Workshop proceedings, held on a biannual basis, collect the scientific papers presented both as oral and poster contributions, during the conference. The main subjects are: development of theoretical and mechanical models as an aid to the study of main phonatory dysfunctions, as well as the biomedical engineering methods for the analysis of voice signals and images, as a support to clinical diagnosis and classification of vocal pathologies

Use of Large, Immunosignature Databases to Pose New Questions About Infection and Health Status

abstract: Immunosignature is a technology that retrieves information from the immune system. The technology is based on microarrays with peptides chosen from random sequence space. My thesis focuses on improving the Immunosignature platform and using Immunosignatures to improve diagnosis for diseases. I first contributed to the optimization of the immunosignature platform by introducing scoring metrics to select optimal parameters, considering performance as well as practicality. Next, I primarily worked on identifying a signature shared across various pathogens that can distinguish them from the healthy population. I further retrieved consensus epitopes from the disease common signature and proposed that most pathogens could share the signature by studying the enrichment of the common signature in the pathogen proteomes. Following this, I worked on studying cancer samples from different stages and correlated the immune response with whether the epitope presented by tumor is similar to the pathogen proteome. An effective immune response is defined as an antibody titer increasing followed by decrease, suggesting elimination of the epitope. I found that an effective immune response usually correlates with epitopes that are more similar to pathogens. This suggests that the immune system might occupy a limited space and can be effective against only certain epitopes that have similarity with pathogens. I then participated in the attempt to solve the antibiotic resistance problem by developing a classification algorithm that can distinguish bacterial versus viral infection. This algorithm outperforms other currently available classification methods. Finally, I worked on the concept of deriving a single number to represent all the data on the immunosignature platform. This is in resemblance to the concept of temperature, which is an approximate measurement of whether an individual is healthy. The measure of Immune Entropy was found to work best as a single measurement to describe the immune system information derived from the immunosignature. Entropy is relatively invariant in healthy population, but shows significant differences when comparing healthy donors with patients either infected with a pathogen or have cancer.Dissertation/ThesisDoctoral Dissertation Molecular and Cellular Biology 201

Autoencoder for clinical data analysis and classification : data imputation, dimensional reduction, and pattern recognition

Over the last decade, research has focused on machine learning and data mining to develop frameworks that can improve data analysis and output performance; to build accurate decision support systems that benefit from real-life datasets. This leads to the field of clinical data analysis, which has attracted a significant amount of interest in the computing, information systems, and medical fields. To create and develop models by machine learning algorithms, there is a need for a particular type of data for the existing algorithms to build an efficient model. Clinical datasets pose several issues that can affect the classification of the dataset: missing values, high dimensionality, and class imbalance. In order to build a framework for mining the data, it is necessary first to preprocess data, by eliminating patients’ records that have too many missing values, imputing missing values, addressing high dimensionality, and classifying the data for decision support.This thesis investigates a real clinical dataset to solve their challenges. Autoencoder is employed as a tool that can compress data mining methodology, by extracting features and classifying data in one model. The first step in data mining methodology is to impute missing values, so several imputation methods are analysed and employed. Then high dimensionality is demonstrated and used to discard irrelevant and redundant features, in order to improve prediction accuracy and reduce computational complexity. Class imbalance is manipulated to investigate the effect on feature selection algorithms and classification algorithms.The first stage of analysis is to investigate the role of the missing values. Results found that techniques based on class separation will outperform other techniques in predictive ability. The next stage is to investigate the high dimensionality and a class imbalance. However it was found a small set of features that can improve the classification performance, the balancing class does not affect the performance as much as imbalance class

Non-invasive wearable sensing systems for continuous health monitoring and long-term behavior modeling

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, February 2006.Includes bibliographical references (p. 212-228).Deploying new healthcare technologies for proactive health and elder care will become a major priority over the next decade, as medical care systems worldwide become strained by the aging populations. This thesis presents LiveNet, a distributed mobile system based on low-cost commodity hardware that can be deployed for a variety of healthcare applications. LiveNet embodies a flexible infrastructure platform intended for long-term ambulatory health monitoring with real-time data streaming and context classification capabilities. Using LiveNet, we are able to continuously monitor a wide range of physiological signals together with the user's activity and context, to develop a personalized, data-rich health profile of a user over time. Most clinical sensing technologies that exist have focused on accuracy and reliability, at the expense of cost-effectiveness, burden on the patient, and portability. Future proactive health technologies, on the other hand, must be affordable, unobtrusive, and non-invasive if the general population is going to adopt them.(cont.) In this thesis, we focus on the potential of using features derived from minimally invasive physiological and contextual sensors such as motion, speech, heart rate, skin conductance, and temperature/heat flux that can be used in combination with mobile technology to create powerful context-aware systems that are transparent to the user. In many cases, these non-invasive sensing technologies can completely replace more invasive diagnostic sensing for applications in long-term monitoring, behavior and physiology trending, and real-time proactive feedback and alert systems. Non-invasive sensing technologies are particularly important in ambulatory and continuous monitoring applications, where more cumbersome sensing equipment that is typically found in medical and clinical research settings is not usable. The research in this thesis demonstrates that it is possible to use simple non-invasive physiological and contextual sensing using the LiveNet system to accurately classify a variety of physiological conditions. We demonstrate that non-invasive sensing can be correlated to a variety of important physiological and behavioral phenomenon, and thus can serve as substitutes to more invasive and unwieldy forms of medical monitoring devices while still providing a high level of diagnostic power.(cont.) From this foundation, the LiveNet system is deployed in a number of studies to quantify physiological and contextual state. First, a number of classifiers for important health and general contextual cues such as activity state and stress level are developed from basic non-invasive physiological sensing. We then demonstrate that the LiveNet system can be used to develop systems that can classify clinically significant physiological and pathological conditions and that are robust in the presence of noise, motion artifacts, and other adverse conditions found in real-world situations. This is highlighted in a cold exposure and core body temperature study in collaboration with the U.S. Army Research Institute of Environmental Medicine. In this study, we show that it is possible to develop real-time implementations of these classifiers for proactive health monitors that can provide instantaneous feedback relevant in soldier monitoring applications. This thesis also demonstrates that the LiveNet platform can be used for long-term continuous monitoring applications to study physiological trends that vary slowly with time.(cont.) In a clinical study with the Psychiatry Department at the Massachusetts General Hospital, the LiveNet platform is used to continuously monitor clinically depressed patients during their stays on an in-patient ward for treatment. We show that we can accurately correlate physiology and behavior to depression state, as well as to track changes in depression state over time through the course of treatment. This study demonstrates how long-term physiology and behavioral changes can be captured to objectively measure medical treatment and medication efficacy. In another long-term monitoring study, the LiveNet platform is used to collect data on people's everyday behavior as they go through daily life. By collecting long-term behavioral data, we demonstrate the possibility of modeling and predicting high-level behavior using simple physiologic and contextual information derived solely from ambulatory mobile sensing technology.by Michael Sung.Ph.D

Deep learning of brain asymmetry digital biomarkers to support early diagnosis of cognitive decline and dementia

Early identification of degenerative processes in the human brain is essential for proper care and treatment. This may involve different instrumental diagnostic methods, including the most popular computer tomography (CT), magnetic resonance imaging (MRI) and positron emission tomography (PET) scans. These technologies provide detailed information about the shape, size, and function of the human brain. Structural and functional cerebral changes can be detected by computational algorithms and used to diagnose dementia and its stages (amnestic early mild cognitive impairment - EMCI, Alzheimer’s Disease - AD). They can help monitor the progress of the disease. Transformation shifts in the degree of asymmetry between the left and right hemispheres illustrate the initialization or development of a pathological process in the brain. In this vein, this study proposes a new digital biomarker for the diagnosis of early dementia based on the detection of image asymmetries and crosssectional comparison of NC (normal cognitively), EMCI and AD subjects. Features of brain asymmetries extracted from MRI of the ADNI and OASIS databases are used to analyze structural brain changes and machine learning classification of the pathology. The experimental part of the study includes results of supervised machine learning algorithms and transfer learning architectures of convolutional neural networks for distinguishing between cognitively normal subjects and patients with early or progressive dementia. The proposed pipeline offers a low-cost imaging biomarker for the classification of dementia. It can be potentially helpful to other brain degenerative disorders accompanied by changes in brain asymmetries

Design, implementation and realization of an integrated platform dedicated to e-public health, for analysing health data and supporting the management control in healthcare companies.

In healthcare, the information is a fundamental aspect and the human body is the major source of every kind of data: the challenge is to benefit from this huge amount of unstructured data by applying technologic solutions, called Big Data Analysis, that allows the management of data and the extraction of information through informatic systems. This thesis aims to introduce a technologic solution made up of two open source platforms: Power BI and Knime Analytics Platform. First, the importance, the role and the processes of business intelligence and machine learning in healthcare will be discussed; secondly, the platforms will be described, particularly enhancing their feasibility and capacities. Then, the clinical specialties, where they have been applied, will be shown by highlighting the international literature that have been produced: neurology, cardiology, oncology, fetal-monitoring and others. An application in the current pandemic situation due to SARS-CoV-2 will be described by using more than 50000 records: a cascade of 3 platforms helping health facilities to deal with the current worldwide pandemic. Finally, the advantages, the disadvantages, the limitations and the future developments in this framework will be discussed while the architectural technologic solution containing a data warehouse, a platform to collect data, two platforms to analyse health and management data and the possible applications will be shown

Linguistic- and Acoustic-based Automatic Dementia Detection using Deep Learning Methods

Dementia can affect a person's speech and language abilities, even in the early stages. Dementia is incurable, but early detection can enable treatment that can slow down and maintain mental function. Therefore, early diagnosis of dementia is of great importance. However, current dementia detection procedures in clinical practice are expensive, invasive, and sometimes inaccurate. In comparison, computational tools based on the automatic analysis of spoken language have the potential to be applied as a cheap, easy-to-use, and objective clinical assistance tool for dementia detection. In recent years, several studies have shown promise in this area. However, most studies focus heavily on the machine learning aspects and, as a consequence, often lack sufficient incorporation of clinical knowledge. Many studies also concentrate on clinically less relevant tasks such as the distinction between HC and people with AD which is relatively easy and therefore less interesting both in terms of the machine learning and the clinical application. The studies in this thesis concentrate on automatically identifying signs of neurodegenerative dementia in the early stages and distinguishing them from other clinical, diagnostic categories related to memory problems: (FMD, MCI, and HC). A key focus, when designing the proposed systems has been to better consider (and incorporate) currently used clinical knowledge and also to bear in mind how these machine-learning based systems could be translated for use in real clinical settings. Firstly, a state-of-the-art end-to-end system is constructed for extracting linguistic information from automatically transcribed spontaneous speech. The system's architecture is based on hierarchical principles thereby mimicking those used in clinical practice where information at both word-, sentence- and paragraph-level is used when extracting information to be used for diagnosis. Secondly, hand-crafted features are designed that are based on clinical knowledge of the importance of pausing and rhythm. These are successfully joined with features extracted from the end-to-end system. Thirdly, different classification tasks are explored, each set up so as to represent the types of diagnostic decision-making that is relevant in clinical practice. Finally, experiments are conducted to explore how to better deal with the known problem of confounding and overlapping symptoms on speech and language from age and cognitive decline. A multi-task system is constructed that takes age into account while predicting cognitive decline. The studies use the publicly available DementiaBank dataset as well as the IVA dataset, which has been collected by our collaborators at the Royal Hallamshire Hospital, UK. In conclusion, this thesis proposes multiple methods of using speech and language information for dementia detection with state-of-the-art deep learning technologies, confirming the automatic system's potential for dementia detection

Models and Analysis of Vocal Emissions for Biomedical Applications

The International Workshop on Models and Analysis of Vocal Emissions for Biomedical Applications (MAVEBA) came into being in 1999 from the particularly felt need of sharing know-how, objectives and results between areas that until then seemed quite distinct such as bioengineering, medicine and singing. MAVEBA deals with all aspects concerning the study of the human voice with applications ranging from the newborn to the adult and elderly. Over the years the initial issues have grown and spread also in other fields of research such as occupational voice disorders, neurology, rehabilitation, image and video analysis. MAVEBA takes place every two years in Firenze, Italy. This edition celebrates twenty-two years of uninterrupted and successful research in the field of voice analysis