A Review of the Assessment Methods of Voice Disorders in the Context of Parkinson's Disease

In recent years, a significant progress in the field of research dedicated to the treatment of disabilities has been witnessed. This is particularly true for neurological diseases, which generally influence the system that controls the execution of learned motor patterns. In addition to its importance for communication with the outside world and interaction with others, the voice is a reflection of our personality, moods and emotions. It is a way to provide information on health status, shape, intentions, age and even the social environment. It is also a working tool for many, but an important element of life for all. Patients with Parkinson’s disease (PD) are numerous and they suffer from hypokinetic dysarthria, which is manifested in all aspects of speech production: respiration, phonation, articulation, nasalization and prosody. This paper provides a review of the methods of the assessment of speech disorders in the context of PD and also discusses the limitations

An algorithm for Parkinson's disease speech classification based on isolated words analysis

Introduction Automatic assessment of speech impairment is a cutting edge topic in Parkinson's disease (PD). Language disorders are known to occur several years earlier than typical motor symptoms, thus speech analysis may contribute to the early diagnosis of the disease. Moreover, the remote monitoring of dysphonia could allow achieving an effective follow-up of PD clinical condition, possibly performed in the home environment. Methods In this work, we performed a multi-level analysis, progressively combining features extracted from the entire signal, the voiced segments, and the on-set/off-set regions, leading to a total number of 126 features. Furthermore, we compared the performance of early and late feature fusion schemes, aiming to identify the best model configuration and taking advantage of having 25 isolated words pronounced by each subject. We employed data from the PC-GITA database (50 healthy controls and 50 PD patients) for validation and testing. Results We implemented an optimized k-Nearest Neighbours model for the binary classification of PD patients versus healthy controls. We achieved an accuracy of 99.4% in 10-fold cross-validation and 94.3% in testing on the PC-GITA database (average value of male and female subjects). Conclusion The promising performance yielded by our model confirms the feasibility of automatic assessment of PD using voice recordings. Moreover, a post-hoc analysis of the most relevant features discloses the option of voice processing using a simple smartphone application

Smart Phone Based Data Mining for Human Activity Recognition

AbstractAutomatic activity recognition systems aim to capture the state of the user and its environment by exploiting heterogeneous sensors, and permit continuous monitoring of numerous physiological signals, where these sensors are attached to the subject's body. This can be immensely useful in healthcare applications, for automatic and intelligent daily activity monitoring for elderly people. In this paper, we present novel data analytic scheme for intelligent Human Activity Recognition (AR) using smartphone inertial sensors based on information theory based feature ranking algorithm and classifiers based on random forests, ensemble learning and lazy learning. Extensive experiments with a publicly available database1 of human activity with smart phone inertial sensors show that the proposed approach can indeed lead to development of intelligent and automatic real time human activity monitoring for eHealth application scenarios for elderly, disabled and people with special needs

Ensemble methods for meningitis aetiology diagnosis

In this work, we explore data-driven techniques for the fast and early diagnosis concerning the etiological origin of meningitis, more specifically with regard to differentiating between viral and bacterial meningitis. We study how machine learning can be used to predict meningitis aetiology once a patient has been diagnosed with this disease. We have a dataset of 26,228 patients described by 19 attributes, mainly about the patient's observable symptoms and the early results of the cerebrospinal fluid analysis. Using this dataset, we have explored several techniques of dataset sampling, feature selection and classification models based both on ensemble methods and on simple techniques (mainly, decision trees). Experiments with 27 classification models (19 of them involving ensemble methods) have been conducted for this paper. Our main finding is that the combination of ensemble methods with decision trees leads to the best meningitis aetiology classifiers. The best performance indicator values (precision, recall and f-measure of 89% and an AUC value of 95%) have been achieved by the synergy between bagging and NBTrees. Nonetheless, our results also suggest that the combination of ensemble methods with certain decision tree clearly improves the performance of diagnosis in comparison with those obtained with only the corresponding decision tree.This research did not receive any specific grant from funding agencies in the public, commercial, or not-for-profit sectors. We would like to thank the Health Department of the Brazilian Government for providing the dataset and for authorizing its use in this study. We would also like to express our gratitude to the reviewers for their thoughtful comments and efforts towards improving our manuscript. Funding for open access charge: Universidad de Málaga / CBUA

Cross-lingual dysphonic speech detection using pretrained speaker embeddings

In this study, cross-lingual binary classification and severity estimation of dysphonic speech have been carried out. Hand-crafted acoustic feature extraction is replaced by the speaker embedding techniques used in the speaker verification. Two state of art deep learning methods for speaker verification have been used: the X-vector and ECAPA-TDNN. Embeddings are extracted from speech samples in Hungarian and Dutch languages and used to train Support Vector Machine (SVM) and Support Vector Regressor (SVR) for binary classification and severity estimation, in a cross-language manner. Our results were competitive with manual feature engineering, when the models were trained on Hungarian samples and evaluated on Dutch samples in the binary classification of dysphonic speech and outperformed in estimating the severity level of dysphonic speech. Moreover, our model achieved 0.769 and 0.771 in Spearman and Pearson correlations. Also, our results in both classification and regression were superior compared to manual feature extraction technique when models were trained on Dutch samples and evaluated on Hungarian samples with only a limited number of samples are available for training. An accuracy of 86.8% was reached with features extracted from embedding methods, while the maximum accuracy using hand-crafted acoustic features was 66.8%. Overall results show that Emphasized Channel Attention, Propagation and Aggregation in Time Delay Neural Network (ECAPA-TDNN) performs better than the former X-vector in both tasks

Detecting purely epistatic multi-locus interactions by an omnibus permutation test on ensembles of two-locus analyses

<p>Abstract</p> <p>Background</p> <p>Purely epistatic multi-locus interactions cannot generally be detected via single-locus analysis in case-control studies of complex diseases. Recently, many two-locus and multi-locus analysis techniques have been shown to be promising for the epistasis detection. However, exhaustive multi-locus analysis requires prohibitively large computational efforts when problems involve large-scale or genome-wide data. Furthermore, there is no explicit proof that a combination of multiple two-locus analyses can lead to the correct identification of multi-locus interactions.</p> <p>Results</p> <p>The proposed 2LOmb algorithm performs an omnibus permutation test on ensembles of two-locus analyses. The algorithm consists of four main steps: two-locus analysis, a permutation test, global <it>p</it>-value determination and a progressive search for the best ensemble. 2LOmb is benchmarked against an exhaustive two-locus analysis technique, a set association approach, a correlation-based feature selection (CFS) technique and a tuned ReliefF (TuRF) technique. The simulation results indicate that 2LOmb produces a low false-positive error. Moreover, 2LOmb has the best performance in terms of an ability to identify all causative single nucleotide polymorphisms (SNPs) and a low number of output SNPs in purely epistatic two-, three- and four-locus interaction problems. The interaction models constructed from the 2LOmb outputs via a multifactor dimensionality reduction (MDR) method are also included for the confirmation of epistasis detection. 2LOmb is subsequently applied to a type 2 diabetes mellitus (T2D) data set, which is obtained as a part of the UK genome-wide genetic epidemiology study by the Wellcome Trust Case Control Consortium (WTCCC). After primarily screening for SNPs that locate within or near 372 candidate genes and exhibit no marginal single-locus effects, the T2D data set is reduced to 7,065 SNPs from 370 genes. The 2LOmb search in the reduced T2D data reveals that four intronic SNPs in <it>PGM1 </it>(phosphoglucomutase 1), two intronic SNPs in <it>LMX1A </it>(LIM homeobox transcription factor 1, alpha), two intronic SNPs in <it>PARK2 </it>(Parkinson disease (autosomal recessive, juvenile) 2, parkin) and three intronic SNPs in <it>GYS2 </it>(glycogen synthase 2 (liver)) are associated with the disease. The 2LOmb result suggests that there is no interaction between each pair of the identified genes that can be described by purely epistatic two-locus interaction models. Moreover, there are no interactions between these four genes that can be described by purely epistatic multi-locus interaction models with marginal two-locus effects. The findings provide an alternative explanation for the aetiology of T2D in a UK population.</p> <p>Conclusion</p> <p>An omnibus permutation test on ensembles of two-locus analyses can detect purely epistatic multi-locus interactions with marginal two-locus effects. The study also reveals that SNPs from large-scale or genome-wide case-control data which are discarded after single-locus analysis detects no association can still be useful for genetic epidemiology studies.</p

Sistema para análise automatizada de movimento durante a marcha usando uma câmara RGB-D

Nowadays it is still common in clinical practice to assess the gait (or way of walking) of a given subject through the visual observation and use of a rating scale, which is a subjective approach. However, sensors including RGB-D cameras, such as the Microsoft Kinect, can be used to obtain quantitative information that allows performing gait analysis in a more objective way. The quantitative gait analysis results can be very useful for example to support the clinical assessment of patients with diseases that can affect their gait, such as Parkinson’s disease. The main motivation of this thesis was thus to provide support to gait assessment, by allowing to carry out quantitative gait analysis in an automated way. This objective was achieved by using 3-D data, provided by a single RGB-D camera, to automatically select the data corresponding to walking and then detect the gait cycles performed by the subject while walking. For each detected gait cycle, we obtain several gait parameters, which are used together with anthropometric measures to automatically identify the subject being assessed. The automated gait data selection relies on machine learning techniques to recognize three different activities (walking, standing, and marching), as well as two different positions of the subject in relation to the camera (facing the camera and facing away from it). For gait cycle detection, we developed an algorithm that estimates the instants corresponding to given gait events. The subject identification based on gait is enabled by a solution that was also developed by relying on machine learning. The developed solutions were integrated into a system for automated gait analysis, which we found to be a viable alternative to gold standard systems for obtaining several spatiotemporal and some kinematic gait parameters. Furthermore, the system is suitable for use in clinical environments, as well as ambulatory scenarios, since it relies on a single markerless RGB-D camera that is less expensive, more portable, less intrusive and easier to set up, when compared with the gold standard systems (multiple cameras and several markers attached to the subject’s body).Atualmente ainda é comum na prática clínica avaliar a marcha (ou o modo de andar) de uma certa pessoa através da observação visual e utilização de uma escala de classificação, o que é uma abordagem subjetiva. No entanto, existem sensores incluindo câmaras RGB-D, como a Microsoft Kinect, que podem ser usados para obter informação quantitativa que permite realizar a análise da marcha de um modo mais objetivo. Os resultados quantitativos da análise da marcha podem ser muito úteis, por exemplo, para apoiar a avaliação clínica de pessoas com doenças que podem afetar a sua marcha, como a doença de Parkinson. Assim, a principal motivação desta tese foi fornecer apoio à avaliação da marcha, permitindo realizar a análise quantitativa da marcha de forma automatizada. Este objetivo foi atingido usando dados em 3-D, fornecidos por uma única câmara RGB-D, para automaticamente selecionar os dados correspondentes a andar e, em seguida, detetar os ciclos de marcha executados pelo sujeito durante a marcha. Para cada ciclo de marcha identificado, obtemos vários parâmetros de marcha, que são usados em conjunto com medidas antropométricas para identificar automaticamente o sujeito que está a ser avaliado. A seleção automatizada de dados de marcha usa técnicas de aprendizagem máquina para reconhecer três atividades diferentes (andar, estar parado em pé e marchar), bem como duas posições diferentes do sujeito em relação à câmara (de frente para a câmara e de costas para ela). Para a deteção dos ciclos da marcha, desenvolvemos um algoritmo que estima os instantes correspondentes a determinados eventos da marcha. A identificação do sujeito com base na sua marcha é realizada usando uma solução que também foi desenvolvida com base em aprendizagem máquina. As soluções desenvolvidas foram integradas num sistema de análise automatizada de marcha, que demonstrámos ser uma alternativa viável a sistemas padrão de referência para obter vários parâmetros de marcha espácio-temporais e alguns parâmetros angulares. Além disso, o sistema é adequado para uso em ambientes clínicos, bem como em cenários ambulatórios, pois depende de apenas de uma câmara RGB-D que não usa marcadores e é menos dispendiosa, mais portátil, menos intrusiva e mais fácil de configurar, quando comparada com os sistemas padrão de referência (múltiplas câmaras e vários marcadores colocados no corpo do sujeito).Programa Doutoral em Informátic

Immersive analytics for oncology patient cohorts

This thesis proposes a novel interactive immersive analytics tool and methods to interrogate the cancer patient cohort in an immersive virtual environment, namely Virtual Reality to Observe Oncology data Models (VROOM). The overall objective is to develop an immersive analytics platform, which includes a data analytics pipeline from raw gene expression data to immersive visualisation on virtual and augmented reality platforms utilising a game engine. Unity3D has been used to implement the visualisation. Work in this thesis could provide oncologists and clinicians with an interactive visualisation and visual analytics platform that helps them to drive their analysis in treatment efficacy and achieve the goal of evidence-based personalised medicine. The thesis integrates the latest discovery and development in cancer patients’ prognoses, immersive technologies, machine learning, decision support system and interactive visualisation to form an immersive analytics platform of complex genomic data. For this thesis, the experimental paradigm that will be followed is in understanding transcriptomics in cancer samples. This thesis specifically investigates gene expression data to determine the biological similarity revealed by the patient's tumour samples' transcriptomic profiles revealing the active genes in different patients. In summary, the thesis contributes to i) a novel immersive analytics platform for patient cohort data interrogation in similarity space where the similarity space is based on the patient's biological and genomic similarity; ii) an effective immersive environment optimisation design based on the usability study of exocentric and egocentric visualisation, audio and sound design optimisation; iii) an integration of trusted and familiar 2D biomedical visual analytics methods into the immersive environment; iv) novel use of the game theory as the decision-making system engine to help the analytics process, and application of the optimal transport theory in missing data imputation to ensure the preservation of data distribution; and v) case studies to showcase the real-world application of the visualisation and its effectiveness

Accurate telemonitoring of Parkinson's disease symptom severity using nonlinear speech signal processing and statistical machine learning

This study focuses on the development of an objective, automated method to extract clinically useful information from sustained vowel phonations in the context of Parkinson’s disease (PD). The aim is twofold: (a) differentiate PD subjects from healthy controls, and (b) replicate the Unified Parkinson’s Disease Rating Scale (UPDRS) metric which provides a clinical impression of PD symptom severity. This metric spans the range 0 to 176, where 0 denotes a healthy person and 176 total disability. Currently, UPDRS assessment requires the physical presence of the subject in the clinic, is subjective relying on the clinical rater’s expertise, and logistically costly for national health systems. Hence, the practical frequency of symptom tracking is typically confined to once every several months, hindering recruitment for large-scale clinical trials and under-representing the true time scale of PD fluctuations. We develop a comprehensive framework to analyze speech signals by: (1) extracting novel, distinctive signal features, (2) using robust feature selection techniques to obtain a parsimonious subset of those features, and (3a) differentiating PD subjects from healthy controls, or (3b) determining UPDRS using powerful statistical machine learning tools. Towards this aim, we also investigate 10 existing fundamental frequency (F_0) estimation algorithms to determine the most useful algorithm for this application, and propose a novel ensemble F_0 estimation algorithm which leads to a 10% improvement in accuracy over the best individual approach. Moreover, we propose novel feature selection schemes which are shown to be very competitive against widely-used schemes which are more complex. We demonstrate that we can successfully differentiate PD subjects from healthy controls with 98.5% overall accuracy, and also provide rapid, objective, and remote replication of UPDRS assessment with clinically useful accuracy (approximately 2 UPDRS points from the clinicians’ estimates), using only simple, self-administered, and non-invasive speech tests. The findings of this study strongly support the use of speech signal analysis as an objective basis for practical clinical decision support tools in the context of PD assessment.EThOS - Electronic Theses Online ServiceGBUnited Kingdo