scholarly journals Robust functional clustering of ERP data with application to a study of implicit learning in autism

Biostatistics ◽  
2016 ◽  
Vol 17 (3) ◽  
pp. 484-498 ◽  
Author(s):  
Kyle Hasenstab ◽  
Catherine Sugar ◽  
Donatello Telesca ◽  
Shafali Jeste ◽  
Damla Şentürk
Keyword(s):  
Implicit Learning ◽  
Clustering Algorithm ◽  
Signal To Noise Ratio ◽  
Principal Component ◽  
Autism Spectrum ◽  
Event Related Potential ◽  
Functional Principal Component Analysis ◽  
Sliding Windows ◽  
Cluster Membership ◽  
Functional Clustering

Abstract Motivated by a study on visual implicit learning in young children with Autism Spectrum Disorder (ASD), we propose a robust functional clustering (RFC) algorithm to identify subgroups within electroencephalography (EEG) data. The proposed RFC is an iterative algorithm based on functional principal component analysis, where cluster membership is updated via predictions of the functional trajectories obtained through a non-parametric random effects model. We consider functional data resulting from event-related potential (ERP) waveforms representing EEG time-locked to stimuli over the course of an implicit learning experiment, after applying a previously proposed meta-preprocessing step. This meta-preprocessing is designed to increase the low signal-to-noise ratio in the raw data and to mitigate the longitudinal changes in the ERP waveforms which characterize the nature and speed of learning. The resulting functional ERP components (peak amplitudes and latencies) inherently exhibit covariance heterogeneity due to low data quality over some stimuli inducing the averaging of different numbers of waveforms in sliding windows of the meta-preprocessing step. The proposed RFC algorithm incorporates this known covariance heterogeneity into the clustering algorithm, improving cluster quality, as illustrated in the data application and extensive simulation studies. ASD is a heterogeneous syndrome and identifying subgroups within ASD children is of interest for understanding the diverse nature of this complex disorder. Applications to the implicit learning paradigm identify subgroups within ASD and typically developing children with diverse learning patterns over the course of the experiment, which may inform clinical stratification of ASD.

A generalization of functional clustering for discrete multivariate longitudinal data

2020 ◽  
Vol 29 (11) ◽  
pp. 3205-3217
Author(s):  
Yaeji Lim ◽  
Ying Kuen Cheung ◽  
Hee-Seok Oh
Keyword(s):  
Longitudinal Data ◽  
Gaussian Process ◽  
Clustering Algorithm ◽  
Principal Component ◽  
Real Data ◽  
Functional Principal Component Analysis ◽  
Functional Clustering ◽  
Multivariate Gaussian ◽  
Discrete Longitudinal Data ◽  
Multivariate Gaussian Process

This paper presents a new model-based generalized functional clustering method for discrete longitudinal data, such as multivariate binomial and Poisson distributed data. For this purpose, we propose a multivariate functional principal component analysis (MFPCA)-based clustering procedure for a latent multivariate Gaussian process instead of the original functional data directly. The main contribution of this study is two-fold: modeling of discrete longitudinal data with the latent multivariate Gaussian process and developing of a clustering algorithm based on MFPCA coupled with the latent multivariate Gaussian process. Numerical experiments, including real data analysis and a simulation study, demonstrate the promising empirical properties of the proposed approach.

scholarly journals Functional Data Analysis in Sport Science: Example of Swimmers’ Progression Curves Clustering

2018 ◽  
Vol 8 (10) ◽  
pp. 1766 ◽  
Author(s):  
Arthur Leroy ◽  
Andy MARC ◽  
Olivier DUPAS ◽  
Jean Lionel REY ◽  
Servane Gey
Keyword(s):  
Data Analysis ◽  
Functional Data Analysis ◽  
Functional Data ◽  
Clustering Algorithms ◽  
Principal Component ◽  
Continuous Functions ◽  
Functional Principal Component Analysis ◽  
Data Set ◽  
Functional Clustering ◽  
Sport Science

Many data collected in sport science come from time dependent phenomenon. This article focuses on Functional Data Analysis (FDA), which study longitudinal data by modelling them as continuous functions. After a brief review of several FDA methods, some useful practical tools such as Functional Principal Component Analysis (FPCA) or functional clustering algorithms are presented and compared on simulated data. Finally, the problem of the detection of promising young swimmers is addressed through a curve clustering procedure on a real data set of performance progression curves. This study reveals that the fastest improvement of young swimmers generally appears before 16 years old. Moreover, several patterns of improvement are identified and the functional clustering procedure provides a useful detection tool.

scholarly journals What Can We Learn from the Functional Clustering of Mortality Data? An Application to the Human Mortality Database

2021 ◽  
Author(s):  
Ainhoa-Elena Léger ◽  
Stefano Mazzuco
Keyword(s):  
Principal Component ◽  
Premature Mortality ◽  
Developed Countries ◽  
Functional Principal Component Analysis ◽  
Mortality Data ◽  
Human Mortality ◽  
Functional Clustering ◽  
Scalar Data ◽  
Functional Principal Component ◽  
Eastern European Countries

AbstractThis study analyzed whether there are different patterns of mortality decline among low-mortality countries by identifying the role played by all the mortality components. We implemented a cluster analysis using a functional data analysis (FDA) approach, which allowed us to consider age-specific mortality rather than summary measures, as it analyses curves rather than scalar data. Combined with a functional principal component analysis, it can identify what part of the curves is responsible for assigning one country to a specific cluster. FDA clustering was applied to the data from 32 countries in the Human Mortality Database from 1960 to 2018 to provide a comprehensive understanding of their patterns of mortality. The results show that the evolution of developed countries followed the same pattern of stages (with different timings): (1) a reduction of infant mortality, (2) an increase of premature mortality and (3) a shift and compression of deaths. Some countries were following this scheme and recovering the gap with precursors; others did not show signs of recovery. Eastern European countries were still at Stage (2), and it was not clear if and when they will enter Stage 3. All the country differences related to the different timings with which countries underwent the stages, as identified by the clusters.

Application of Machine Learning in Animal Disease Analysis and Prediction

2020 ◽  
Vol 15 ◽  
Author(s):  
Shuwen Zhang ◽  
Qiang Su ◽  
Qin Chen
Keyword(s):  
Machine Learning ◽  
Unsupervised Learning ◽  
Supervised Learning ◽  
Clustering Algorithm ◽  
Principal Component ◽  
Support Vector ◽  
Animal Disease ◽  
Human Beings ◽  
Animal Diseases ◽  
Disease Analysis

Abstract: Major animal diseases pose a great threat to animal husbandry and human beings. With the deepening of globalization and the abundance of data resources, the prediction and analysis of animal diseases by using big data are becoming more and more important. The focus of machine learning is to make computers learn how to learn from data and use the learned experience to analyze and predict. Firstly, this paper introduces the animal epidemic situation and machine learning. Then it briefly introduces the application of machine learning in animal disease analysis and prediction. Machine learning is mainly divided into supervised learning and unsupervised learning. Supervised learning includes support vector machines, naive bayes, decision trees, random forests, logistic regression, artificial neural networks, deep learning, and AdaBoost. Unsupervised learning has maximum expectation algorithm, principal component analysis hierarchical clustering algorithm and maxent. Through the discussion of this paper, people have a clearer concept of machine learning and understand its application prospect in animal diseases.

scholarly journals Autism Spectrum Disorder (ASD) with and without Mental Regression is Associated with Changes in the Fecal Microbiota

Nutrients ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 337 ◽  
Author(s):  
Julio Plaza-Díaz ◽  
Antonio Gómez-Fernández ◽  
Natalia Chueca ◽  
María Torre-Aguilar ◽  
Ángel Gil ◽  
...  
Keyword(s):  
Intestinal Microbiota ◽  
Present Report ◽  
Principal Component ◽  
Autism Spectrum ◽  
Control Group ◽  
Healthy Group ◽  
Sequencing Platform ◽  
Preliminary Results ◽  
Children With Asd ◽  
Mental Regression

New microbiome sequencing technologies provide novel information about the potential interactions among intestinal microorganisms and the host in some neuropathologies as autism spectrum disorders (ASD). The microbiota–gut–brain axis is an emerging aspect in the generation of autistic behaviors; evidence from animal models suggests that intestinal microbial shifts may produce changes fitting the clinical picture of autism. The aim of the present study was to evaluate the fecal metagenomic profiles in children with ASD and compare them with healthy participants. This comparison allows us to ascertain how mental regression (an important variable in ASD) could influence the intestinal microbiota profile. For this reason, a subclassification in children with ASD by mental regression (AMR) and no mental regression (ANMR) phenotype was performed. The present report was a descriptive observational study. Forty-eight children aged 2–6 years with ASD were included: 30 with ANMR and 18 with AMR. In addition, a control group of 57 normally developing children was selected and matched to the ASD group by sex and age. Fecal samples were analyzed with a metagenomic approach using a next-generation sequencing platform. Several differences between children with ASD, compared with the healthy group, were detected. Namely, Actinobacteria and Proteobacteria at phylum level, as well as, Actinobacteria, Bacilli, Erysipelotrichi, and Gammaproteobacteria at class level were found at higher proportions in children with ASD. Additionally, Proteobacteria levels showed to be augmented exclusively in AMR children. Preliminary results, using a principal component analysis, showed differential patterns in children with ASD, ANMR and AMR, compared to healthy group, both for intestinal microbiota and food patterns. In this study, we report, higher levels of Actinobacteria, Proteobacteria and Bacilli, aside from Erysipelotrichi, and Gammaproteobacteria in children with ASD compared to healthy group. Furthermore, AMR children exhibited higher levels of Proteobacteria. Further analysis using these preliminary results and mixing metagenomic and other “omic” technologies are needed in larger cohorts of children with ASD to confirm these intestinal microbiota changes.

scholarly journals Separation of Chromatographic Co-Eluted Compounds by Clustering and by Functional Data Analysis

Metabolites ◽  
2021 ◽  
Vol 11 (4) ◽  
pp. 214
Author(s):  
Aneta Sawikowska ◽  
Anna Piasecka ◽  
Piotr Kachlicki ◽  
Paweł Krajewski
Keyword(s):  
Simulated Data ◽  
Principal Component ◽  
Real Data ◽  
Functional Principal Component Analysis ◽  
Additional Advantage ◽  
Time Alignment ◽  
Peak Separation ◽  
Biological Mixtures ◽  
Overlapping Peaks ◽  
Retention Time Alignment

Peak overlapping is a common problem in chromatography, mainly in the case of complex biological mixtures, i.e., metabolites. Due to the existence of the phenomenon of co-elution of different compounds with similar chromatographic properties, peak separation becomes challenging. In this paper, two computational methods of separating peaks, applied, for the first time, to large chromatographic datasets, are described, compared, and experimentally validated. The methods lead from raw observations to data that can form inputs for statistical analysis. First, in both methods, data are normalized by the mass of sample, the baseline is removed, retention time alignment is conducted, and detection of peaks is performed. Then, in the first method, clustering is used to separate overlapping peaks, whereas in the second method, functional principal component analysis (FPCA) is applied for the same purpose. Simulated data and experimental results are used as examples to present both methods and to compare them. Real data were obtained in a study of metabolomic changes in barley (Hordeum vulgare) leaves under drought stress. The results suggest that both methods are suitable for separation of overlapping peaks, but the additional advantage of the FPCA is the possibility to assess the variability of individual compounds present within the same peaks of different chromatograms.

scholarly journals Associations between Google Search Trends for Symptoms and COVID-19 Confirmed and Death Cases in the United States

2021 ◽  
Vol 18 (9) ◽  
pp. 4560
Author(s):  
Mostafa Abbas ◽  
Thomas B. Morland ◽  
Eric S. Hall ◽  
Yasser EL-Manzalawy
Keyword(s):  
Functional Data ◽  
Time Series Data ◽  
Principal Component ◽  
State Level ◽  
The United States ◽  
Functional Principal Component Analysis ◽  
Series Data ◽  
Dynamic Correlation ◽  
The Us ◽  
Google Search

We utilize functional data analysis techniques to investigate patterns of COVID-19 positivity and mortality in the US and their associations with Google search trends for COVID-19-related symptoms. Specifically, we represent state-level time series data for COVID-19 and Google search trends for symptoms as smoothed functional curves. Given these functional data, we explore the modes of variation in the data using functional principal component analysis (FPCA). We also apply functional clustering analysis to identify patterns of COVID-19 confirmed case and death trajectories across the US. Moreover, we quantify the associations between Google COVID-19 search trends for symptoms and COVID-19 confirmed case and death trajectories using dynamic correlation. Finally, we examine the dynamics of correlations for the top nine Google search trends of symptoms commonly associated with COVID-19 confirmed case and death trajectories. Our results reveal and characterize distinct patterns for COVID-19 spread and mortality across the US. The dynamics of these correlations suggest the feasibility of using Google queries to forecast COVID-19 cases and mortality for up to three weeks in advance. Our results and analysis framework set the stage for the development of predictive models for forecasting COVID-19 confirmed cases and deaths using historical data and Google search trends for nine symptoms associated with both outcomes.

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