Standard Principal Component Analysis Research Articles

Economic Growth Channels from Human Capital: A Dynamic Panel Analysis for Brazil

The purpose of this paper is to test the effect of human capital on Brazilian economic growth through the factor accumulation channel and the total factor productivity channel. We used new human capital measures, covering the period from 1996 to 2015. We used the two-step SYS-GMM method, with standard finite sample error correction and principal components analysis for the control of the proliferation of instruments. The results show that basic and advanced human capital have a positive impact on economic growth through both channels, being the effect of greater magnitude through the factor accumulation channel.

DRIFT ANALYSIS OF A Pd LOADED SnO2 BASED LINALOOL SENSOR

An approach is made in this work to analyze sensitivity drift in a Pd doped SnO 2 sensor developed for detection of linalool, a significant aroma compound in tea. Prior to the drift analysis, an attempt is made to choose the optimum loading percentage of Pd in SnO 2 for linalool sensing. An inexpensive and simplistic hydrothermal method is used to develop five different Pd doped SnO 2 sensors (0.5 wt%, 2 wt%, 5 wt%, 6 wt% and 8 wt%) and compare their sensitivities when exposed to linalool vapour. The analysis shows that 6 wt% exhibits better sensitivity (62.7%) towards Linalool at a relatively lower temperature (100 0 C) as compared to all the other synthesized sensors. Henceforth, extensive experiments were performed on the 6 wt% Pd doped SnO 2 sensor for a period of one month to analyze its stability. Relative standard deviation and principal component analysis based drift analysis are performed to understand its changing attributes under repeated measurements.

Spectral compression method for LCD display based on color difference weighted function

Spectrum is the essence of color, which can retain the main information of color. Spectral color information is generally used in the liquid crystal displays (LCDs) color field. Color spectrum of LCDs is usually a very large file, but an appropriate compression method can significantly reduce the required storage space while minimizing the loss of information. In this paper, a color difference weighted principal component analysis (CDWPCA) method for LCDs spectral compression is proposed. First, we investigated the importance of wavelength to color information. Then, a weighted function considering wavelength change and human visual system is introduced into spectral compression. The performance of CDWPCA are tested by comparing the results of standard principal component analysis and other weighted function principal component analysis by compressing and reconstructing the test samples from the eigenvectors of different training samples. The results show that the proposed CDWPCA method can significantly improve the retention rate of color information in the compression process of principal component analysis.

Predicting Influenza A Tropism with End-to-End Learning of Deep Networks.

The type of host that a virus can infect, referred to as host specificity or tropism, influences infectivity and thus is important for disease diagnosis, epidemic response, and prevention. Advances in DNA sequencing technology have enabled rapid metagenomic analyses of viruses, but the prediction of virus phenotype from genome sequences is an active area of research. As such, automatic prediction of host tropism from analysis of genomic information is of considerable utility. Previous research has applied machine learning methods to accomplish this task, although deep learning (particularly deep convolutional neural network, CNN) techniques have not yet been applied. These techniques have the ability to learn how to recognize critical hierarchical structures within the genome in a data-driven manner. We designed deep CNN models to identify host tropism for human and avian influenza A viruses based on protein sequences and performed a detailed analysis of the results. Our findings show that deep CNN techniques work as well as existing approaches (with 99% mean accuracy on the binary prediction task) while performing end-to-end learning of the prediction model (without the need to specify handcrafted features). The findings also show that these models, combined with standard principal component analysis, can be used to quantify and visualize viral strain similarity.

Application of machine learning methodology to assess the performance of DIABETIMSS program for patients with type 2 diabetes in family medicine clinics in Mexico

BackgroundThe study aimed to assess the performance of a multidisciplinary-team diabetes care program called DIABETIMSS on glycemic control of type 2 diabetes (T2D) patients, by using available observational patient data and machine-learning-based targeted learning methods.MethodsWe analyzed electronic health records and laboratory databases from the year 2012 to 2016 of T2D patients from six family medicine clinics (FMCs) delivering the DIABETIMSS program, and five FMCs providing routine care. All FMCs belong to the Mexican Institute of Social Security and are in Mexico City and the State of Mexico. The primary outcome was glycemic control. The study covariates included: patient sex, age, anthropometric data, history of glycemic control, diabetic complications and comorbidity. We measured the effects of DIABETIMSS program through 1) simple unadjusted mean differences; 2) adjusted via standard logistic regression and 3) adjusted via targeted machine learning. We treated the data as a serial cross-sectional study, conducted a standard principal components analysis to explore the distribution of covariates among clinics, and performed regression tree on data transformed to use the prediction model to identify patient sub-groups in whom the program was most successful. To explore the robustness of the machine learning approaches, we conducted a set of simulations and the sensitivity analysis with process-of-care indicators as possible confounders.ResultsThe study included 78,894 T2D patients, from which 37,767patients received care through DIABETIMSS. The impact of DIABETIMSS ranged, among clinics, from 2 to 8% improvement in glycemic control, with an overall (pooled) estimate of 5% improvement. T2D patients with fewer complications have more significant benefit from DIABETIMSS than those with more complications. At the FMC’s delivering the conventional model the predicted impacts were like what was observed empirically in the DIABETIMSS clinics. The sensitivity analysis did not change the overall estimate average across clinics.ConclusionsDIABETIMSS program had a small, but significant increase in glycemic control. The use of machine learning methods yields both population-level effects and pinpoints the sub-groups of patients the program benefits the most. These methods exploit the potential of routine observational patient data within complex healthcare systems to inform decision-makers.

Nonstationary Discrete Convolution Kernel for Multimodal Process Monitoring.

Data-driven process monitoring has benefited from the development and application of kernel transformations, especially when various types of nonlinearity exist in the data. However, when dealing with the multimodality behavior that is frequently observed in the process operations, the most widely used radial basis function (RBF) kernel has limitations in describing process data collected from multiple normal operating modes. In this article, we highlight this limitation via a synthesized example. In order to account for the multimodality behavior and improve the fault detection performance accordingly, we propose a novel nonstationary discrete convolution kernel, which derives from the convolution kernel structure, as an alternative to the RBF kernel. By assuming the training samples to be the support of the discrete convolution, this new kernel can properly address these training samples from different operating modes with diverse properties and, therefore, can improve the data description and fault detection performance. Its performance is compared with RBF kernels under a standard kernel principal component analysis framework and with other methods proposed for multimode process monitoring via numerical examples. Moreover, a benchmark data set collected from a pilot-scale multiphase flow facility is used to demonstrate the advantages of the new kernel when applied to an experimental data set.

Generalized Principal Component Analysis: Projection of Saturated Model Parameters

Principal component analysis (PCA) is very useful for a wide variety of data analysis tasks, but its implicit connection to the Gaussian distribution can be undesirable for discrete data such as binary and multi-category responses or counts. We generalize PCA to handle various types of data using the generalized linear model framework. In contrast to the existing approach of matrix factorizations for exponential family data, our generalized PCA provides low-rank estimates of the natural parameters by projecting the saturated model parameters. This difference in formulation leads to the favorable properties that the number of parameters does not grow with the sample size and simple matrix multiplication suffices for computation of the principal component scores on new data. A practical algorithm which can incorporate missing data and case weights is developed for finding the projection matrix. Examples on simulated and real count data show the improvement of generalized PCA over standard PCA for matrix completion, visualization, and collaborative filtering. Supplementary material for this article is available online.

Visualization of Chemical Space using Kernel Based Principal Component Research

Principal Component analysis (PCA) is one of the important and popular multivariate statistical methods applied over various data modeling applications. Traditional PCA handles linear variance in molecular descriptors or features. Handling complicated data by standard PCA will not be very helpful. This drawback can be handled by introducing kernel matrix over PCA. Kernel Principal Component Analysis (KPCA) is an extension of conventional PCA which handles non-linear hidden patterns exists in variables. It results in computational efficiency for data analysis and data visualization. In this paper, KPCA has been applied over dug-likeness dataset for visualization of non-linear relations exists in variables.

Evaluation of methods for adjusting population stratification in genome-wide association studies: Standard versus categorical principal component analysis.

Unaccounted population stratification can lead to false-positive findings and can mask the true association signals in identification of disease-related genetic variants. The computational simplicity of principal component analysis (PCA) makes it a widely used method for population stratification adjustment. However, given that genotype data are generally represented by numerical values 0, 1, and 2, corresponding to the number of minor alleles, it is more reasonable to consider genotype data as categorical data. Because PCA is inherently only suitable for continuous variables, it is not appropriate to directly apply PCA on genotype data. Second, although common variants have been extensively studied, little is known about the stratification of rare variants and its impact on association tests. Over the last decade, there has been a shift in the genome-wide association studies toward studying low-frequency (minor allele frequency [MAF] between 0.01 and 0.05) and rare (MAF less than 0.01) variants, which are now widely reputed as complex trait determinants. The fact that rare variants are not stratified in the same way as common variants necessitates the development of statistical methods that can capture stratification patterns for low-frequency and rare variants. To address these limitations, we investigate performances of generalized PCA and similarity-matrix-based PCA methods to detect underlying structures for rare and common variants. We demonstrate, through simulated and real datasets, that a special case of generalized PCA (i.e., logistic PCA) is able to adjust for population stratification in rare variants much more effectively than standard PCA while their performances are comparable for common variants.

Neural Networks Principal Component Analysis for estimating the generative multifactor model of returns under a statistical approach to the Arbitrage Pricing Theory. Evidence from the Mexican Stock Exchange

A nonlinear principal component analysis (NLPCA) represents an extension of the standard principal component analysis (PCA) that overcomes the limitation of the PCA’s assumption about the linearity of the model. The NLPCA belongs to the family of nonlinear versions of dimension reduction or the extraction techniques of underlying features, including nonlinear factor analysis and nonlinear independent component analysis, where the principal components are generalized from straight lines to curves. The NLPCA can be achieved via an artificial neural network specification where the PCA classic model is generalized to a nonlinear mode, namely, Neural Networks Principal Component Analysis (NNPCA). In order to extract a set of nonlinear underlying systematic risk factors, we estimate the generative multifactor model of returns in a statistical version of the Arbitrage Pricing Theory (APT), in the context of the Mexican Stock Exchange. We used an auto-associative multilayer perceptron neural network or autoencoder, where the ‘bottleneck’ layer represented the nonlinear principal components, or in our context, the scores of the underlying factors of systematic risk. This neural network represents a powerful technique capable of performing a nonlinear transformation of the observed variables into the nonlinear principal components, and to execute a nonlinear mapping that reproduces the original variables. We propose a network architecture capable of generating a loading matrix that enables us to make a first approach to the interpretation of the extracted latent risk factors. In addition, we used a two stage methodology for the econometric contrast of the APT involving first, a simultaneous estimation of the system of equations via Seemingly Unrelated Regression (SUR), and secondly, a cross-section estimation via Ordinary Least Squared corrected by heteroskedasticity and autocorrelation by means of the Newey-West heteroskedasticity and autocorrelation consistent covariances estimates (HEC). The evidence found shows that the reproductions of the observed returns using the estimated components via NNPCA are suitable in almost all cases; nevertheless, the results in an econometric contrast lead us to a partial acceptance of the APT in the samples and periods studied.

Building anatomically realistic jaw kinematics model from data

This paper considers a different aspect of anatomical face modeling: kinematic modeling of the jaw, i.e., the Temporo-Mandibular Joint (TMJ). Previous work often relies on simple models of jaw kinematics, even though the actual physiological behavior of the TMJ is quite complex, allowing not only for mouth opening, but also for some amount of sideways (lateral) and front-to-back (protrusion) motions. Fortuitously, the TMJ is the only joint whose kinematics can be accurately measured with optical methods, because the bones of the lower and upper jaw are rigidly connected to the lower and upper teeth. We construct a person-specific jaw kinematic model by asking an actor to exercise the entire range of motion of the jaw while keeping the lips open so that the teeth are at least partially visible. This performance is recorded with three calibrated cameras. We obtain highly accurate 3D models of the teeth with a standard dental scanner and use these models to reconstruct the rigid body trajectories of the teeth from the videos (markerless tracking). The relative rigid transformations samples between the lower and upper teeth are mapped to the Lie algebra of rigid body motions in order to linearize the rotational motion. Our main contribution is to fit these samples with a three-dimensional nonlinear model parameterizing the entire range of motion of the TMJ. We show that standard Principal Component Analysis (PCA) fails to capture the nonlinear trajectories of the moving mandible. However, we found these nonlinearities can be captured with a special modification of autoencoder neural networks known as Nonlinear PCA. By mapping back to the Lie group of rigid transformations, we obtain parameterization of the jaw kinematics which provides an intuitive interface allowing the animators to explore realistic jaw motions in a user-friendly way.

Image-based translucency transfer through correlation analysis over multi-scale spatial color distribution

This paper introduces an image-based material transfer framework which only requires single input and reference images as an ordinary color transfer method. In contrast to previous material transfer methods, we focus on transferring the appearances of translucent objects. There are two challenging problems in such material transfer for translucent objects. First, the appearances of translucent materials are characterized by not only colors but also their spatial distribution. Unfortunately, the traditional color transfer methods can hardly handle the translucency because they only consider the colors of the objects. Second, temporal coherency in the transferred results cannot be handled by the traditional methods and furthermore by recent neural style transfer methods, as we demonstrated in this paper. To address these problems, we propose a novel image-based material transfer method based on the analysis of spatial color distribution. We focus on “subbands,” which represent multi-scale image structures, and find that the correlation between color distribution and subbands is a key feature for reproducing the appearances of translucent materials. Our method relies on a standard principal component analysis, which harmonizes the correlation of input and reference images to reproduce the translucent appearance. Considering the spatial color distribution in the input and reference images, our method can be naturally applied to video sequences in a frame-by-frame manner without any additional pre-/post-process. Through experimental analyses, we demonstrate that the proposed method can be applied to a broad variety of translucent materials, and their resulting appearances are perceptually similar to those of the reference images.

A Novel, Dose-Adjusted Tacrolimus Trough-Concentration Model for Predicting and Estimating Variance After Kidney Transplantation.

Background and ObjectiveGiven that a high intrapatient variability (IPV) of tacrolimus whole blood concentration increases the risk for a poor kidney transplant outcome, some experts advocate routine IPV monitoring for detection of high-risk patients. However, attempts to estimate the variance of tacrolimus trough concentrations (TTC) are limited by the need for patients to receive a fixed dose over time and/or the use of linear statistical models. A goal of this study is to overcome the current limitations through the novel application of statistical methodology generalizing the relationship between TTC and dose through the use of nonparametric functional regression modeling. MethodsWith TTC as a response and dose as a covariate, the model employs an unknown bivariate function, allowing for the potentially complex, nonlinear relationship between the two parameters. A dose-adjusted variance of TTC is then derived based on standard functional principal component analysis (FPCA). To assess the model, it was compared against an FPCA-based model and linear mixed-effects models using prediction error, bias, and coverage probabilities for simulated data as well as phase III data from the Astellas new drug application studies for extended-release tacrolimus.ResultsOur numerical investigation indicates that the new model better predicts dose-adjusted TTCs compared with the prediction of linear mixed effects models. Estimated coverage probabilities also indicate that the new model accurately accounts for the variance of TTC during the periods of large fluctuation in dose, whereas the linear mixed effects model consistently underestimates the coverage probabilities because of the inaccurate characterization of TTC fluctuation.ConclusionThis is the first known application of a functional regression model to assess complex relationships between TTC and dose in a real clinical setting. This new method has applicability in future clinical trials including real-world data sets due to flexibility of the nonparametric modeling approach.Electronic supplementary materialThe online version of this article (10.1007/s40268-019-0271-2) contains supplementary material, which is available to authorized users.

Rapid detection of grape syrup adulteration with an array of metal oxide sensors and chemometrics

Among the different cases of emerging food fraud during the post-harvest processing, the adulteration in grape syrup is one. Typically, the grape syrup is adulterated with some illegitimate foreign materials such as grape paste (sauce), date syrup and even adding sugar-water solution to the pure grape syrup. The present study deals with assessing an electronic nose (e-nose) consisting of eight different metal oxide semiconductor (MOS) sensors for prompt detection of adulteration in the grape syrup. Three different adulterants i.e. grape paste, date syrup and sugar-water solution, each at three levels of 50, 60 and 75%, were tested. The collected data from MOS were normalised and visualised with the help of standard normal variate (SNV) and principal component analysis (PCA), respectively. Moreover, the scores obtained from PCA were used to perform hierarchal cluster analysis (HCA) to identify the similarities between different adulterated mixtures and pure grape syrup. Three different classification cases were considered to (i) address the presence of adulteration, (ii) detect the different adulterants and (iii) classify the amount of each adulteration. Linear discriminant analysis (LDA) and multi-class support vector machine (SVM) were used for classification analyses. Results showed that PCA identified provided separate clusters for the MOS data corresponding to different adulterants and their levels. The HCA showed a hierarchal of similarities between pure grape syrup and different levels of adulterations. LDA and SVM resulted in a successful classification modelling. However, the performance of SVM was considerably better than LDA with classification accuracies of 98.6 ± 0.10%, 98.9 ± 1.16% and 95.1 ± 1.39% for detecting adulteration, different adulterants and different concentrations of adulterants, respectively. MOS sensors coupled with chemometrics could provide a useful instrument and fast procedure for detection of adulteration in grape syrup.

A bilateral symmetry based pose normalization framework applied to livestock body measurement in point clouds

The shape of a livestock is a vital indicator of its health and value, whether for breeding or growth. Cutting-edge remote sensing technology provides an efficient and affordable way for acquiring point clouds of livestock, so that automated procedures of obtaining body measurements need to be established. A novel pose normalization method for 3D point clouds of livestock with similar forms of cows or pigs based on its bilateral symmetry properties is proposed in order to increase the degree of measuring automation. The proposed algorithm is combined in a hybrid scheme, which serves as the pose normalization procedure in an automatic body measurement system for livestock. Our extensive experiments on both synthetic and real world point clouds data show that the proposed approach has potential for generalizing well across livestock species and handles noise successfully in test data. In addition, the proposed pose normalization scheme outperforms current standard approach Principal Component Analysis (PCA) and state-of-the-art pose normalization method for pigs.

Compression of Head-Related Transfer Function Based on Tucker and Tensor Train Decomposition

Head-related transfer function (HRTF) plays an important role in three-dimensional spatial sound system. However, the direct application of a large amount of original HRTF data would involve a great deal of computational burden, especially for high-spatial-resolution individual HRTF. To address this problem, we propose a novel compression method (called TT-Tucker) combining Tucker model with tensor train decomposition based on a 5-order HRTF tensor model developed in subspaces of an ear, subject, azimuth, elevation, and frequency. Lots of HRTF data can be decomposed into several low-parametric factors representing the key spectrum information of HRTF by capturing the hidden interactions among different subspaces. To evaluate the reconstruction performance, the numerical experiments were conducted on the CIPIC HRTF database. Under the same compression ratio of nearly 98%, the results suggest that the proposed method has a better performance in spectral distortion and signal-to-distortion ratio than that of the usual tensor method and the standard method principal component analysis (PCA). Moreover, the subjective listening test shows that the TT-Tucker method performs better in that, the compressed and reconstructed HRTF is closer to the original HRTF in the sound localization similarity.

Functional principal components analysis on the example of the achievements of students in the years 2009-2017

The functional principal components analysis combines the advantages of the standard principal components analysis and enables analysing data of a dynamic nature. The main difference in both methods is the type of data: the PCA is based on multivariate data, whereas the FPCA on the functional data including curves and trajectories, i.e. a series of individual observations, not a single observation, as usual. The purpose of the article is to apply functional principal components analysis to the problem of student’s achievements. The article was compared the level of knowledge presented by students during various stages of education in 2009-2017. The analysis covers the average exam results after the second, third and fourth stage of education. The functional principal components analysis, based on functional data, will be used in the analysis. This method allows the analysis of dynamic data

Raman spectroscopic detection of high-grade cervical cytology: Using morphologically normal appearing cells

This study aims to detect high grade squamous intraepithelial cells (HSIL) by investigating HSIL associated biochemical changes in morphologically normal appearing intermediate and superficial cells using Raman spectroscopy. Raman spectra (n = 755) were measured from intermediate and superficial cells from negative cytology ThinPrep specimens (n = 18) and from morphologically normal appearing intermediate and superficial cells from HSIL cytology ThinPrep specimens (n = 17). The Raman data was subjected to multivariate algorithms including the standard principal component analysis (PCA)-linear discriminant analysis (LDA) and partial least squares discriminant analysis (PLS-DA) together with random subsets cross-validation for discriminating negative cytology from HSIL. The PCA-LDA method yielded sensitivities of 74.9%, 72.8%, and 75.6% and specificities of 89.9%, 81.9%, and 84.5%, for HSIL diagnosis based on the dataset obtained from intermediate, superficial and mixed intermediate/superficial cells, respectively. The PLS-DA method provided improved sensitivities of 95.5%, 95.2% and 96.1% and specificities of 92.7%, 94.7% and 93.5% compared to the PCA-LDA method. The results demonstrate that the biochemical signatures of morphologically normal appearing cells can be used to discriminate between negative and HSIL cytology. In addition, it was found that mixed intermediate and superficial cells could be used for HSIL diagnosis as the biochemical differences between negative and HSIL cytology were greater than the biochemical differences between intermediate and superficial cell types.

Sparse common component analysis for multiple high-dimensional datasets via noncentered principal component analysis

There is currently much discussion about the analysis of multiple datasets from different groups, among which especially identifying a common basic structure of multiple groups has drawn a large amount of attention. In order to identify a common basic structure, common component analysis (CCA) was proposed by generalizing techniques for principal component analysis (PCA); i.e., CCA becomes standard PCA when applied to only one dataset. Although CCA can identify the common structure of multiple datasets, which cannot be extracted by standard PCA, CCA suffers from the following drawbacks. The common components are estimated as linear combinations of all variables, and thus it is difficult to interpret the identified common components. The fully dense loadings lead to erroneous results in CCA, because noisy features are inevitably included in datasets. To address these issues, we incorporate sparsity into CCA, and propose a novel strategy for sparse common component analysis based on $$L_{1}$$ -type regularized regression modeling. We focus CCA which is formulated as the eigenvalue decomposition (EVD) of a Gram matrix (i.e., common loadings of multiple datasets can be estimated by EVD of a Gram matrix), and it can be performed by Singular value decomposition of a square root of the Gram matrix. We then propose sparse common component analysis based on sparse PCA to estimate sparse common loadings of multiple datasets. We also propose an algorithm to estimate sparse common loadings of multiple datasets. The proposed method can not only identify a common subspace but also select crucial common-features for multiple groups. Monte Carlo simulations and real-data analysis are conducted to examine the efficiency of the proposed sparse CCA. We observe from the numerical studies that our strategies can incorporate sparsity into the common loading estimation and efficiently recover a sparse common structure efficiently in multiple dataset analysis.

Statistical Shape Model to Generate a Planning Library for Cervical Adaptive Radiotherapy.

External beam radiotherapy is extensively used to treat cervical carcinomas. A single planning CT scan enables the calculation of the dose distribution. The treatment is delivered over five weeks. Large per-treatment anatomical variations may hamper the dose delivery, with the potential of an organ-at-risk (OAR) overdose and a tumor underdose. To anticipate these deformations, a recent approach proposed three planning CTs with variable bladder volumes, which had the limitation of not covering all per-treatment anatomical variations. An original patient-specific population-based library has been proposed. It consisted of generating two representative anatomies, in addition to the standard planning CT anatomy. First, the cervix and bladder meshes of a population of 20 patients (314 images) were registered to an anatomical template, using a deformable mesh registration. An iterative point-matching algorithm was developed based on local shape context (histogram of polar or cylindrical coordinates and geodesic distance to the base) and on a topology constraint filter. Second, a standard principal component analysis (PCA) model of the cervix and bladder was generated to extract the dominant deformation modes. Finally, specific deformations were obtained using posterior PCA models, with a constraint representing the top of the uterus deformation. For a new patient, the cervix-uterus and bladder were registered to the template, and the patient's modeled planning library was built according to the model deformations. This method was applied following a leave-one-patient-out cross-validation. The performances of the modeled library were compared to those of the three-CT-based library, showing an improvement in both target coverage and OAR sparing.