Segmentation and classification of non-stationary signals : Application on heart sounds analysis and auto-diagnosis domain

Cette thèse dans le domaine du traitement des signaux non-stationnaires, appliqué aux bruits du cœur mesurés avec un stéthoscope numérique, vise à concevoir un outil automatisé et « intelligent », permettant aux médecins de disposer d’une source d’information supplémentaire à celle du stéthoscope traditionnel. Une première étape dans l’analyse des signaux du cœur, consiste à localiser le premier et le deuxième son cardiaque (S1 et S2) afin de le segmenter en quatre parties : S1, systole, S2 et diastole. Plusieurs méthodes de localisation des sons cardiaques existent déjà dans la littérature. Une étude comparative entre les méthodes les plus pertinentes est réalisée et deux nouvelles méthodes basées sur la transformation temps-fréquence de Stockwell sont proposées. La première méthode, nommée SRBF, utilise des descripteurs issus du domaine temps-fréquence comme vecteur d’entré au réseau de neurones RBF qui génère l’enveloppe d’amplitude du signal cardiaque, la deuxième méthode, nommée SSE, calcule l’énergie de Shannon du spectre local obtenu par la transformée en S. Ensuite, une phase de détection des extrémités (onset, ending) est nécessaire. Une méthode d’extraction des signaux S1 et S2, basée sur la transformée en S optimisée, est discutée et comparée avec les différentes approches qui existent dans la littérature. Concernant la classification des signaux cardiaques, les méthodes décrites dans la littérature pour classifier S1 et S2, se basent sur des critères temporels (durée de systole et diastole) qui ne seront plus valables dans plusieurs cas pathologiques comme par exemple la tachycardie sévère. Un nouveau descripteur issu du domaine temps-fréquence est évalué et validé pour discriminer S1 de S2. Ensuite, une nouvelle méthode de génération des attributs, basée sur la décomposition modale empirique (EMD) est proposée.Des descripteurs non-linéaires sont également testés, dans le but de classifier des sons cardiaques normaux et sons pathologiques en présence des souffles systoliques. Des outils de traitement et de reconnaissance des signaux non-stationnaires basés sur des caractéristiques morphologique, temps-fréquences et non linéaire du signal, ont été explorés au cours de ce projet de thèse afin de proposer un module d’aide au diagnostic, qui ne nécessite pas d’information à priori sur le sujet traité, robuste vis à vis du bruit et applicable dans des conditions cliniques.This thesis in the field of biomedical signal processing, applied to the heart sounds, aims to develop an automated and intelligent module, allowing medical doctors to have an additional source of information than the traditional stethoscope. A first step in the analysis of heart sounds is the segmentation process. The heart sounds segmentation process segments the PCG (PhonoCardioGram) signal into four parts: S1 (first heart sound), systole, S2 (second heart sound) and diastole. It can be considered one of the most important phases in the auto-analysis of PCG signals. The proposed segmentation module in this thesis can be divided into three main blocks: localization of heart sounds, boundaries detection of the localized heart sounds and classification block to distinguish between S1and S2. Several methods of heart sound localization exist in the literature. A comparative study between the most relevant methods is performed and two new localization methods of heart sounds are proposed in this study. Both of them are based on the S-transform, the first method uses Radial Basis Functions (RBF) neural network to extract the envelope of the heart sound signal after a feature extraction process that operates on the S-matrix. The second method named SSE calculates the Shannon Energy of the local spectrum calculated by the S-transform for each sample of the heart sound signal. The second block contains a novel approach for the boundaries detection of S1 and S2 (onset & ending). The energy concentrations of the S-transform of localized sounds are optimized by using a window width optimization algorithm. Then the SSE envelope is recalculated and a local adaptive threshold is applied to refine the estimated boundaries. For the classification block, most of the existing methods in the literature use the systole and diastole duration (systole regularity) as a criterion to discriminate between S1 and S2. These methods do not perform well for all types of heart sounds, especially in the presence of high heart rate or in the presence of arrhythmic pathologies. To deal with this problem, two feature extraction methods based on Singular Value Decomposition (SVD) technique are examined. The first method uses the S-Transform and the second method uses the Intrinsic Mode Functions (IMF) calculated by the Empirical Mode Decomposition (EMD) technique. The features are applied to a KNN classifier to estimate the performance of each feature extraction method. Nonlinear features are also tested in order to classify the normal and pathological heart sounds in the presence of systolic murmurs. Processing and recognition signal processing tools based on morphological, time-frequency and nonlinear signal features, were explored in this thesis in order to propose an auto-diagnosis module, robust against noise and applicable in clinical conditions

Segmentation et classification des signaux non-stationnaires : application au traitement des sons cardiaque et à l'aide au diagnostic

This thesis in the field of biomedical signal processing, applied to the heart sounds, aims to develop an automated and intelligent module, allowing medical doctors to have an additional source of information than the traditional stethoscope. A first step in the analysis of heart sounds is the segmentation process. The heart sounds segmentation process segments the PCG (PhonoCardioGram) signal into four parts: S1 (first heart sound), systole, S2 (second heart sound) and diastole. It can be considered one of the most important phases in the auto-analysis of PCG signals. The proposed segmentation module in this thesis can be divided into three main blocks: localization of heart sounds, boundaries detection of the localized heart sounds and classification block to distinguish between S1and S2. Several methods of heart sound localization exist in the literature. A comparative study between the most relevant methods is performed and two new localization methods of heart sounds are proposed in this study. Both of them are based on the S-transform, the first method uses Radial Basis Functions (RBF) neural network to extract the envelope of the heart sound signal after a feature extraction process that operates on the S-matrix. The second method named SSE calculates the Shannon Energy of the local spectrum calculated by the S-transform for each sample of the heart sound signal. The second block contains a novel approach for the boundaries detection of S1 and S2 (onset & ending). The energy concentrations of the S-transform of localized sounds are optimized by using a window width optimization algorithm. Then the SSE envelope is recalculated and a local adaptive threshold is applied to refine the estimated boundaries. For the classification block, most of the existing methods in the literature use the systole and diastole duration (systole regularity) as a criterion to discriminate between S1 and S2. These methods do not perform well for all types of heart sounds, especially in the presence of high heart rate or in the presence of arrhythmic pathologies. To deal with this problem, two feature extraction methods based on Singular Value Decomposition (SVD) technique are examined. The first method uses the S-Transform and the second method uses the Intrinsic Mode Functions (IMF) calculated by the Empirical Mode Decomposition (EMD) technique. The features are applied to a KNN classifier to estimate the performance of each feature extraction method. Nonlinear features are also tested in order to classify the normal and pathological heart sounds in the presence of systolic murmurs. Processing and recognition signal processing tools based on morphological, time-frequency and nonlinear signal features, were explored in this thesis in order to propose an auto-diagnosis module, robust against noise and applicable in clinical conditions.Cette thèse dans le domaine du traitement des signaux non-stationnaires, appliqué aux bruits du cœur mesurés avec un stéthoscope numérique, vise à concevoir un outil automatisé et « intelligent », permettant aux médecins de disposer d’une source d’information supplémentaire à celle du stéthoscope traditionnel. Une première étape dans l’analyse des signaux du cœur, consiste à localiser le premier et le deuxième son cardiaque (S1 et S2) afin de le segmenter en quatre parties : S1, systole, S2 et diastole. Plusieurs méthodes de localisation des sons cardiaques existent déjà dans la littérature. Une étude comparative entre les méthodes les plus pertinentes est réalisée et deux nouvelles méthodes basées sur la transformation temps-fréquence de Stockwell sont proposées. La première méthode, nommée SRBF, utilise des descripteurs issus du domaine temps-fréquence comme vecteur d’entré au réseau de neurones RBF qui génère l’enveloppe d’amplitude du signal cardiaque, la deuxième méthode, nommée SSE, calcule l’énergie de Shannon du spectre local obtenu par la transformée en S. Ensuite, une phase de détection des extrémités (onset, ending) est nécessaire. Une méthode d’extraction des signaux S1 et S2, basée sur la transformée en S optimisée, est discutée et comparée avec les différentes approches qui existent dans la littérature. Concernant la classification des signaux cardiaques, les méthodes décrites dans la littérature pour classifier S1 et S2, se basent sur des critères temporels (durée de systole et diastole) qui ne seront plus valables dans plusieurs cas pathologiques comme par exemple la tachycardie sévère. Un nouveau descripteur issu du domaine temps-fréquence est évalué et validé pour discriminer S1 de S2. Ensuite, une nouvelle méthode de génération des attributs, basée sur la décomposition modale empirique (EMD) est proposée.Des descripteurs non-linéaires sont également testés, dans le but de classifier des sons cardiaques normaux et sons pathologiques en présence des souffles systoliques. Des outils de traitement et de reconnaissance des signaux non-stationnaires basés sur des caractéristiques morphologique, temps-fréquences et non linéaire du signal, ont été explorés au cours de ce projet de thèse afin de proposer un module d’aide au diagnostic, qui ne nécessite pas d’information à priori sur le sujet traité, robuste vis à vis du bruit et applicable dans des conditions cliniques

Segmentation et classification des signaux non-stationnaires (application au traitement des sons cardiaque et à l'aide au diagnostic)

Cette thèse dans le domaine du traitement des signaux non-stationnaires, appliqué aux bruits du cœur mesurés avec un stéthoscope numérique, vise à concevoir un outil automatisé et intelligent , permettant aux médecins de disposer d une source d information supplémentaire à celle du stéthoscope traditionnel. Une première étape dans l analyse des signaux du cœur, consiste à localiser le premier et le deuxième son cardiaque (S1 et S2) afin de le segmenter en quatre parties : S1, systole, S2 et diastole. Plusieurs méthodes de localisation des sons cardiaques existent déjà dans la littérature. Une étude comparative entre les méthodes les plus pertinentes est réalisée et deux nouvelles méthodes basées sur la transformation temps-fréquence de Stockwell sont proposées. La première méthode, nommée SRBF, utilise des descripteurs issus du domaine temps-fréquence comme vecteur d entré au réseau de neurones RBF qui génère l enveloppe d amplitude du signal cardiaque, la deuxième méthode, nommée SSE, calcule l énergie de Shannon du spectre local obtenu par la transformée en S. Ensuite, une phase de détection des extrémités (onset, ending) est nécessaire. Une méthode d extraction des signaux S1 et S2, basée sur la transformée en S optimisée, est discutée et comparée avec les différentes approches qui existent dans la littérature. Concernant la classification des signaux cardiaques, les méthodes décrites dans la littérature pour classifier S1 et S2, se basent sur des critères temporels (durée de systole et diastole) qui ne seront plus valables dans plusieurs cas pathologiques comme par exemple la tachycardie sévère. Un nouveau descripteur issu du domaine temps-fréquence est évalué et validé pour discriminer S1 de S2. Ensuite, une nouvelle méthode de génération des attributs, basée sur la décomposition modale empirique (EMD) est proposée.Des descripteurs non-linéaires sont également testés, dans le but de classifier des sons cardiaques normaux et sons pathologiques en présence des souffles systoliques. Des outils de traitement et de reconnaissance des signaux non-stationnaires basés sur des caractéristiques morphologique, temps-fréquences et non linéaire du signal, ont été explorés au cours de ce projet de thèse afin de proposer un module d aide au diagnostic, qui ne nécessite pas d information à priori sur le sujet traité, robuste vis à vis du bruit et applicable dans des conditions cliniques.This thesis in the field of biomedical signal processing, applied to the heart sounds, aims to develop an automated and intelligent module, allowing medical doctors to have an additional source of information than the traditional stethoscope. A first step in the analysis of heart sounds is the segmentation process. The heart sounds segmentation process segments the PCG (PhonoCardioGram) signal into four parts: S1 (first heart sound), systole, S2 (second heart sound) and diastole. It can be considered one of the most important phases in the auto-analysis of PCG signals. The proposed segmentation module in this thesis can be divided into three main blocks: localization of heart sounds, boundaries detection of the localized heart sounds and classification block to distinguish between S1and S2. Several methods of heart sound localization exist in the literature. A comparative study between the most relevant methods is performed and two new localization methods of heart sounds are proposed in this study. Both of them are based on the S-transform, the first method uses Radial Basis Functions (RBF) neural network to extract the envelope of the heart sound signal after a feature extraction process that operates on the S-matrix. The second method named SSE calculates the Shannon Energy of the local spectrum calculated by the S-transform for each sample of the heart sound signal. The second block contains a novel approach for the boundaries detection of S1 and S2 (onset & ending). The energy concentrations of the S-transform of localized sounds are optimized by using a window width optimization algorithm. Then the SSE envelope is recalculated and a local adaptive threshold is applied to refine the estimated boundaries. For the classification block, most of the existing methods in the literature use the systole and diastole duration (systole regularity) as a criterion to discriminate between S1 and S2. These methods do not perform well for all types of heart sounds, especially in the presence of high heart rate or in the presence of arrhythmic pathologies. To deal with this problem, two feature extraction methods based on Singular Value Decomposition (SVD) technique are examined. The first method uses the S-Transform and the second method uses the Intrinsic Mode Functions (IMF) calculated by the Empirical Mode Decomposition (EMD) technique. The features are applied to a KNN classifier to estimate the performance of each feature extraction method. Nonlinear features are also tested in order to classify the normal and pathological heart sounds in the presence of systolic murmurs. Processing and recognition signal processing tools based on morphological, time-frequency and nonlinear signal features, were explored in this thesis in order to propose an auto-diagnosis module, robust against noise and applicable in clinical conditions.MULHOUSE-SCD Sciences (682242102) / SudocSudocFranceF

High Order Statistics and Time-Frequency Domain to Classify Heart Sounds for Subjects under Cardiac Stress Test

This paper considers the problem of classification of the first and the second heart sounds (S1 and S2) under cardiac stress test. The main objective is to classify these sounds without electrocardiogram (ECG) reference and without taking into consideration the systolic and the diastolic time intervals criterion which can become problematic and useless in several real life settings as severe tachycardia and tachyarrhythmia or in the case of subjects being under cardiac stress activity. First, the heart sounds are segmented by using a modified time-frequency based envelope. Then, to distinguish between the first and the second heart sounds, new features, named αopt, β, and γ, based on high order statistics and energy concentration measures of the Stockwell transform (S-transform) are proposed in this study. A study of the variation of the high frequency content of S1 and S2 over the HR (heart rate) is also discussed. The proposed features are validated on a database that contains 2636 S1 and S2 sounds corresponding to 62 heart signals and 8 subjects under cardiac stress test collected from healthy subjects. Results and comparisons with existing methods in the literature show a large superiority for our proposed features

An open access database for the evaluation of heart sound algorithms

International audienceIn the past few decades, analysis of heart sound signals (i.e., the phonocardiogram or PCG),especially for automated heart sound segmentation and classification, has been widely studied and hasbeen reported to have the potential value to detect pathology accurately in clinical applications. However,comparative analyses of algorithms in the literature have been hindered by the lack of high-quality,rigorously validated, and standardized open databases of heart sound recordings. This paper describes apublic heart sound database, assembled for an international competition, the PhysioNet/Computing inCardiology (CinC) Challenge 2016. The archive comprises nine different heart sound databases sourcedfrom multiple research groups around the world. It includes 2,435 heart sound recordings in totalcollected from 1,297 healthy subjects and patients with a variety of conditions, including heart valvedisease and coronary artery disease. The recordings were collected from a variety of clinical ornonclinical (such as in-home visits) environments and equipment. The length of recording varied fromseveral seconds to several minutes. This article reports detailed information about the subjects/patientsincluding demographics (number, age, gender), recordings (number, location, state and time length),associated synchronously recorded signals, sampling frequency and sensor type used. We also provide abrief summary of the commonly used heart sound segmentation and classification methods, includingopen source code provided concurrently for the Challenge. A description of the PhysioNet/CinCChallenge 2016, including the main aims, the training and test sets, the hand corrected annotations fordifferent heart sound states, the scoring mechanism, and associated open source code are provided. Inaddition, several potential benefits from the public heart sound database are discussed

A new optimized Stockwell transform applied on synthetic and real non-stationary signals

International audienceThe aim of this paper is to improve the energy concentration of the Stockwell transform (S-transform) in the time–frequency domain. Amodified S-transform is proposed with several parameters to control the width of ahybrid Gaussian window. Aconstrained optimization problem is proposed based on an energy concentration measure as objective function and inequalities constraints to define the bounds of the Gaussian window. An active-set algorithm is applied to resolve the optimization problem. The optimization of the energy concentration in the time–frequency plane can lead to more reliable applications for non-stationary signals. The simulation results show a significant improvement of the proposed methodology most notably in the presence of noise comparing with the standard S-transform and existing modified S-transform in the literature. Moreover, comparisonwith other knowntime–frequency transforms such as Short-time Fourier transform (STFT) and smoothed-pseudo Wigner–Ville distribution (SPWVD) is also performed and discussed. The proposed S-transform is tested also on real non-stationary signals through an example of split detection in heart sound

Generalizable Features for Anonymizing Motion Signals Based on the Zeros of the Short-Time Fourier Transform

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Anonymizing motion sensor data through time-frequency domain

International audienceThe recent development of Internet of Things (IoT) has democratized activity monitoring. Even if the data collected can be useful for healthcare, sharing this sensitive information exposes users to privacy threats and re-identification. This paper presents two approaches to anonymize the motion sensor data. The first is an extension of an earlier work based on filtering in the time-frequency plane and convolutional neural network; and the second is based on handcrafted features extracted from the zeros distribution of the time-frequency representation. The two approaches are evaluated on a public dataset to assess the accuracy of activity recognition and user re-identification. With the first approach we obtained an accuracy rate in activity recognition of 73% while limiting the identity recognition to an accuracy rate of 30% which corresponds to an activity identity ratio of 2.4. With the second approach we succeeded in improving the activity and identity ratio to 2.67 by attaining an accuracy rate in activity recognition of 80% while maintaining the re-identification rate at 30%