Patrick E. McSharry

Bio: Patrick E. McSharry is an academic researcher from Carnegie Mellon University. The author has contributed to research in topics: Probabilistic forecasting & Bipolar disorder. The author has an hindex of 35, co-authored 117 publications receiving 8273 citations. Previous affiliations of Patrick E. McSharry include National University of Rwanda & London School of Economics and Political Science.

A dynamical model for generating synthetic electrocardiogram signals

Abstract: A dynamical model based on three coupled ordinary differential equations is introduced which is capable of generating realistic synthetic electrocardiogram (ECG) signals. The operator can specify the mean and standard deviation of the heart rate, the morphology of the PQRST cycle, and the power spectrum of the RR tachogram. In particular, both respiratory sinus arrhythmia at the high frequencies (HFs) and Mayer waves at the low frequencies (LFs) together with the LF/HF ratio are incorporated in the model. Much of the beat-to-beat variation in morphology and timing of the human ECG, including QT dispersion and R-peak amplitude modulation are shown to result. This model may be employed to assess biomedical signal processing techniques which are used to compute clinical statistics from the ECG.

Suitability of Dysphonia Measurements for Telemonitoring of Parkinson's Disease

Abstract: In this paper, we present an assessment of the practical value of existing traditional and nonstandard measures for discriminating healthy people from people with Parkinson's disease (PD) by detecting dysphonia. We introduce a new measure of dysphonia, pitch period entropy (PPE), which is robust to many uncontrollable confounding effects including noisy acoustic environments and normal, healthy variations in voice frequency. We collected sustained phonations from 31 people, 23 with PD. We then selected ten highly uncorrelated measures, and an exhaustive search of all possible combinations of these measures finds four that in combination lead to overall correct classification performance of 91.4%, using a kernel support vector machine. In conclusion, we find that nonstandard methods in combination with traditional harmonics-to-noise ratios are best able to separate healthy from PD subjects. The selected nonstandard methods are robust to many uncontrollable variations in acoustic environment and individual subjects, and are thus well suited to telemonitoring applications.

Advanced Methods And Tools for ECG Data Analysis

Abstract: This cutting-edge resource provides you with a practical and theoretical understanding of state-of-the-art techniques for electrocardiogram (ECG) data analysis. Placing an emphasis on the fundamentals of signal etiology, acquisition, data selection, and testing, this comprehensive volume presents guidelines to help you design, implement, and evaluate algorithms used for the analysis of ECG and related data. Additionally, explanations of open source software and related databases for signal processing are given. The book focuses on the modeling, classification, and interpretation of features derived from advanced signal processing and artificial intelligence techniques. Key topics covered include physiological origin, hardware acquisition and filtering, time-frequency quantification of the ECG and derived signals (including heart rate variability and respiration), analysis of noise and artifact, models for ECG and RR interval processes, linear and nonlinear filtering techniques, and adaptive algorithms such as neural networks. Much of the book is devoted to deriving robust, clinically meaningful parameters such as the QRS axis, QT-interval, the ST-level, and T-wave alternan metrics. Methods for applying these metrics to clinical classification are also discussed, together with supervised and unsupervised classification techniques. Including over 190 illustrations, the book offers you a solid grounding in the relevant basics of physiology, data acquisition and database design, and addresses the practical issues of improving existing data analysis methods and developing new applications.

Exploiting Nonlinear Recurrence and Fractal Scaling Properties for Voice Disorder Detection

Abstract: Voice disorders affect patients profoundly, and acoustic tools can potentially measure voice function objectively. Disordered sustained vowels exhibit wide-ranging phenomena, from nearly periodic to highly complex, aperiodic vibrations, and increased "breathiness". Modelling and surrogate data studies have shown significant nonlinear and non-Gaussian random properties in these sounds. Nonetheless, existing tools are limited to analysing voices displaying near periodicity, and do not account for this inherent biophysical nonlinearity and non-Gaussian randomness, often using linear signal processing methods insensitive to these properties. They do not directly measure the two main biophysical symptoms of disorder: complex nonlinear aperiodicity, and turbulent, aeroacoustic, non-Gaussian randomness. Often these tools cannot be applied to more severe disordered voices, limiting their clinical usefulness. This paper introduces two new tools to speech analysis: recurrence and fractal scaling, which overcome the range limitations of existing tools by addressing directly these two symptoms of disorder, together reproducing a "hoarseness" diagram. A simple bootstrapped classifier then uses these two features to distinguish normal from disordered voices. On a large database of subjects with a wide variety of voice disorders, these new techniques can distinguish normal from disordered cases, using quadratic discriminant analysis, to overall correct classification performance of 91.8 ± 2.0%. The true positive classification performance is 95.4 ± 3.2%, and the true negative performance is 91.5 ± 2.3% (95% confidence). This is shown to outperform all combinations of the most popular classical tools. Given the very large number of arbitrary parameters and computational complexity of existing techniques, these new techniques are far simpler and yet achieve clinically useful classification performance using only a basic classification technique. They do so by exploiting the inherent nonlinearity and turbulent randomness in disordered voice signals. They are widely applicable to the whole range of disordered voice phenomena by design. These new measures could therefore be used for a variety of practical clinical purposes.

Novel Speech Signal Processing Algorithms for High-Accuracy Classification of Parkinson's Disease

Abstract: There has been considerable recent research into the connection between Parkinson's disease (PD) and speech impairment. Recently, a wide range of speech signal processing algorithms (dysphonia measures) aiming to predict PD symptom severity using speech signals have been introduced. In this paper, we test how accurately these novel algorithms can be used to discriminate PD subjects from healthy controls. In total, we compute 132 dysphonia measures from sustained vowels. Then, we select four parsimonious subsets of these dysphonia measures using four feature selection algorithms, and map these feature subsets to a binary classification response using two statistical classifiers: random forests and support vector machines. We use an existing database consisting of 263 samples from 43 subjects, and demonstrate that these new dysphonia measures can outperform state-of-the-art results, reaching almost 99% overall classification accuracy using only ten dysphonia features. We find that some of the recently proposed dysphonia measures complement existing algorithms in maximizing the ability of the classifiers to discriminate healthy controls from PD subjects. We see these results as an important step toward noninvasive diagnostic decision support in PD.

Pattern Recognition and Machine Learning

Abstract: Probability Distributions.- Linear Models for Regression.- Linear Models for Classification.- Neural Networks.- Kernel Methods.- Sparse Kernel Machines.- Graphical Models.- Mixture Models and EM.- Approximate Inference.- Sampling Methods.- Continuous Latent Variables.- Sequential Data.- Combining Models.

Modern Applied Statistics With S

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“Bioinformatics” 특집을 내면서

Abstract: BIOE 402. Medical Technology Assessment. 2 or 3 hours. Bioentrepreneur course. Assessment of medical technology in the context of commercialization. Objectives, competition, market share, funding, pricing, manufacturing, growth, and intellectual property; many issues unique to biomedical products. Course Information: 2 undergraduate hours. 3 graduate hours. Prerequisite(s): Junior standing or above and consent of the instructor.

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study

Abstract: Summary Background Since December, 2019, Wuhan, China, has experienced an outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Epidemiological and clinical characteristics of patients with COVID-19 have been reported but risk factors for mortality and a detailed clinical course of illness, including viral shedding, have not been well described. Methods In this retrospective, multicentre cohort study, we included all adult inpatients (≥18 years old) with laboratory-confirmed COVID-19 from Jinyintan Hospital and Wuhan Pulmonary Hospital (Wuhan, China) who had been discharged or had died by Jan 31, 2020. Demographic, clinical, treatment, and laboratory data, including serial samples for viral RNA detection, were extracted from electronic medical records and compared between survivors and non-survivors. We used univariable and multivariable logistic regression methods to explore the risk factors associated with in-hospital death. Findings 191 patients (135 from Jinyintan Hospital and 56 from Wuhan Pulmonary Hospital) were included in this study, of whom 137 were discharged and 54 died in hospital. 91 (48%) patients had a comorbidity, with hypertension being the most common (58 [30%] patients), followed by diabetes (36 [19%] patients) and coronary heart disease (15 [8%] patients). Multivariable regression showed increasing odds of in-hospital death associated with older age (odds ratio 1·10, 95% CI 1·03–1·17, per year increase; p=0·0043), higher Sequential Organ Failure Assessment (SOFA) score (5·65, 2·61–12·23; p Interpretation The potential risk factors of older age, high SOFA score, and d-dimer greater than 1 μg/mL could help clinicians to identify patients with poor prognosis at an early stage. Prolonged viral shedding provides the rationale for a strategy of isolation of infected patients and optimal antiviral interventions in the future. Funding Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences; National Science Grant for Distinguished Young Scholars; National Key Research and Development Program of China; The Beijing Science and Technology Project; and Major Projects of National Science and Technology on New Drug Creation and Development.