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A Generalized Linear Model for Principal Component Analysis of Binary Data
A Generalized Linear Model for Principal Component Analysis of Binary Data Andrew I. Schein Lawrence K. Saul Lyle H. Ungar Department of Computer and Information Science University of Pennsylvania Moore School Building 200 South 33rd Street Philadelphia, PA 19104-6389 {ais,lsaul,ungar}@cis.upenn.edu Abstract they are not generally appropriate for other data types. Recently, Collins et al.[5] derived generalized criteria We investigate a generalized linear model for for dimensionality reduction by appealing to proper- dimensionality reduction of binary data. The ties of distributions in the exponential family. In their model is related to principal component anal- framework, the conventional PCA of real-valued data ysis (PCA) in the same way that logistic re- emerges naturally from assuming a Gaussian distribu- gression is related to linear regression. Thus tion over a set of observations, while generalized ver- we refer to the model as logistic PCA. In this sions of PCA for binary and nonnegative data emerge paper, we derive an alternating least squares respectively by substituting the Bernoulli and Pois- method to estimate the basis vectors and gen- son distributions for the Gaussian. For binary data, eralized linear coefficients of the logistic PCA the generalized model's relationship to PCA is anal- model. The resulting updates have a simple ogous to the relationship between logistic and linear closed form and are guaranteed at each iter- regression[12]. In particular, the model exploits the ation to improve the model's likelihood. We log-odds as the natural parameter of the Bernoulli dis- evaluate the performance of logistic PCA|as tribution and the logistic function as its canonical link. -
Exploratory and Confirmatory Factor Analysis Course Outline Part 1
Course Outline Exploratory and Confirmatory Factor Analysis 1 Principal components analysis Part 1: Overview, PCA and Biplots FA vs. PCA Least squares fit to a data matrix Biplots Michael Friendly 2 Basic Ideas of Factor Analysis Parsimony– common variance small number of factors. Linear regression on common factors→ Partial linear independence Psychology 6140 Common vs. unique variance 3 The Common Factor Model Factoring methods: Principal factors, Unweighted Least Squares, Maximum λ1 X1 z1 likelihood ξ λ2 Factor rotation X2 z2 4 Confirmatory Factor Analysis Development of CFA models Applications of CFA PCA and Factor Analysis: Overview & Goals Why do Factor Analysis? Part 1: Outline Why do “Factor Analysis”? 1 PCA and Factor Analysis: Overview & Goals Why do Factor Analysis? Data Reduction: Replace a large number of variables with a smaller Two modes of Factor Analysis number which reflect most of the original data [PCA rather than FA] Brief history of Factor Analysis Example: In a study of the reactions of cancer patients to radiotherapy, measurements were made on 10 different reaction variables. Because it 2 Principal components analysis was difficult to interpret all 10 variables together, PCA was used to find Artificial PCA example simpler measure(s) of patient response to treatment that contained most of the information in data. 3 PCA: details Test and Scale Construction: Develop tests and scales which are “pure” 4 PCA: Example measures of some construct. Example: In developing a test of English as a Second Language, 5 Biplots investigators calculate correlations among the item scores, and use FA to Low-D views based on PCA construct subscales. -
A Resampling Test for Principal Component Analysis of Genotype-By-Environment Interaction
A RESAMPLING TEST FOR PRINCIPAL COMPONENT ANALYSIS OF GENOTYPE-BY-ENVIRONMENT INTERACTION JOHANNES FORKMAN Abstract. In crop science, genotype-by-environment interaction is of- ten explored using the \genotype main effects and genotype-by-environ- ment interaction effects” (GGE) model. Using this model, a singular value decomposition is performed on the matrix of residuals from a fit of a linear model with main effects of environments. Provided that errors are independent, normally distributed and homoscedastic, the signifi- cance of the multiplicative terms of the GGE model can be tested using resampling methods. The GGE method is closely related to principal component analysis (PCA). The present paper describes i) the GGE model, ii) the simple parametric bootstrap method for testing multi- plicative genotype-by-environment interaction terms, and iii) how this resampling method can also be used for testing principal components in PCA. 1. Introduction Forkman and Piepho (2014) proposed a resampling method for testing in- teraction terms in models for analysis of genotype-by-environment data. The \genotype main effects and genotype-by-environment interaction ef- fects"(GGE) analysis (Yan et al. 2000; Yan and Kang, 2002) is closely related to principal component analysis (PCA). For this reason, the method proposed by Forkman and Piepho (2014), which is called the \simple para- metric bootstrap method", can be used for testing principal components in PCA as well. The proposed resampling method is parametric in the sense that it assumes homoscedastic and normally distributed observations. The method is \simple", because it only involves repeated sampling of standard normal distributed values. Specifically, no parameters need to be estimated. -
GGL Biplot Analysis of Durum Wheat (Triticum Turgidum Spp
756 Bulgarian Journal of Agricultural Science, 19 (No 4) 2013, 756-765 Agricultural Academy GGL BIPLOT ANALYSIS OF DURUM WHEAT (TRITICUM TURGIDUM SPP. DURUM) YIELD IN MULTI-ENVIRONMENT TRIALS N. SABAGHNIA2*, R. KARIMIZADEH1 and M. MOHAMMADI1 1 Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Maragheh, Maragheh, Iran 2 Dryland Agricultural Research Institute (DARI), Gachsaran, Iran Abstract SABAGHNIA, N., R. KARIMIZADEH and M. MOHAMMADI, 2013. GGL biplot analysis of durum wheat (Triticum turgidum spp. durum) yield in multi-environment trials. Bulg. J. Agric. Sci., 19: 756-765 Durum wheat (Triticum turgidum spp. durum) breeders have to determine the new genotypes responsive to the environ- mental changes for grain yield. Matching durum wheat genotype selection with its production environment is challenged by the occurrence of significant genotype by environment (GE) interaction in multi-environment trials (MET). This investigation was conducted to evaluate 20 durum wheat genotypes for their stability grown in five different locations across three years using randomized completely block design with 4 replications. According to combined analysis of variance, the main effects of genotypes, locations and years, were significant as well as the interactions effects. The first two principal components of the site regression model accounted for 60.3 % of the total variation. Polygon view of genotype plus genotype by location (GGL) biplot indicated that there were three winning genotypes in three mega-environments for durum wheat in rain-fed conditions. Genotype G14 was the most favorable genotype for location Gachsaran and the most favorable genotype of mega-environment Kouhdasht and Ilam was G12 while G10 was the most favorable genotypes for mega-environment Gonbad and Moghan. -
A Biplot-Based PCA Approach to Study the Relations Between Indoor and Outdoor Air Pollutants Using Case Study Buildings
buildings Article A Biplot-Based PCA Approach to Study the Relations between Indoor and Outdoor Air Pollutants Using Case Study Buildings He Zhang * and Ravi Srinivasan UrbSys (Urban Building Energy, Sensing, Controls, Big Data Analysis, and Visualization) Laboratory, M.E. Rinker, Sr. School of Construction Management, University of Florida, Gainesville, FL 32603, USA; sravi@ufl.edu * Correspondence: rupta00@ufl.edu Abstract: The 24 h and 14-day relationship between indoor and outdoor PM2.5, PM10, NO2, relative humidity, and temperature were assessed for an elementary school (site 1), a laboratory (site 2), and a residential unit (site 3) in Gainesville city, Florida. The primary aim of this study was to introduce a biplot-based PCA approach to visualize and validate the correlation among indoor and outdoor air quality data. The Spearman coefficients showed a stronger correlation among these target environmental measurements on site 1 and site 2, while it showed a weaker correlation on site 3. The biplot-based PCA regression performed higher dependency for site 1 and site 2 (p < 0.001) when compared to the correlation values and showed a lower dependency for site 3. The results displayed a mismatch between the biplot-based PCA and correlation analysis for site 3. The method utilized in this paper can be implemented in studies and analyzes high volumes of multiple building environmental measurements along with optimized visualization. Keywords: air pollution; indoor air quality; principal component analysis; biplot Citation: Zhang, H.; Srinivasan, R. A Biplot-Based PCA Approach to Study the Relations between Indoor and 1. Introduction Outdoor Air Pollutants Using Case The 2020 Global Health Observatory (GHO) statistics show that indoor and outdoor Buildings 2021 11 Study Buildings. -
Logistic Biplot by Conjugate Gradient Algorithms and Iterated SVD
mathematics Article Logistic Biplot by Conjugate Gradient Algorithms and Iterated SVD Jose Giovany Babativa-Márquez 1,2,* and José Luis Vicente-Villardón 1 1 Department of Statistics, University of Salamanca, 37008 Salamanca, Spain; [email protected] 2 Facultad de Ciencias de la Salud y del Deporte, Fundación Universitaria del Área Andina, Bogotá 1321, Colombia * Correspondence: [email protected] Abstract: Multivariate binary data are increasingly frequent in practice. Although some adaptations of principal component analysis are used to reduce dimensionality for this kind of data, none of them provide a simultaneous representation of rows and columns (biplot). Recently, a technique named logistic biplot (LB) has been developed to represent the rows and columns of a binary data matrix simultaneously, even though the algorithm used to fit the parameters is too computationally demanding to be useful in the presence of sparsity or when the matrix is large. We propose the fitting of an LB model using nonlinear conjugate gradient (CG) or majorization–minimization (MM) algo- rithms, and a cross-validation procedure is introduced to select the hyperparameter that represents the number of dimensions in the model. A Monte Carlo study that considers scenarios with several sparsity levels and different dimensions of the binary data set shows that the procedure based on cross-validation is successful in the selection of the model for all algorithms studied. The comparison of the running times shows that the CG algorithm is more efficient in the presence of sparsity and when the matrix is not very large, while the performance of the MM algorithm is better when the binary matrix is balanced or large. -
2. Graphing Distributions
2. Graphing Distributions A. Qualitative Variables B. Quantitative Variables 1. Stem and Leaf Displays 2. Histograms 3. Frequency Polygons 4. Box Plots 5. Bar Charts 6. Line Graphs 7. Dot Plots C. Exercises Graphing data is the first and often most important step in data analysis. In this day of computers, researchers all too often see only the results of complex computer analyses without ever taking a close look at the data themselves. This is all the more unfortunate because computers can create many types of graphs quickly and easily. This chapter covers some classic types of graphs such bar charts that were invented by William Playfair in the 18th century as well as graphs such as box plots invented by John Tukey in the 20th century. 65 by David M. Lane Prerequisites • Chapter 1: Variables Learning Objectives 1. Create a frequency table 2. Determine when pie charts are valuable and when they are not 3. Create and interpret bar charts 4. Identify common graphical mistakes When Apple Computer introduced the iMac computer in August 1998, the company wanted to learn whether the iMac was expanding Apple’s market share. Was the iMac just attracting previous Macintosh owners? Or was it purchased by newcomers to the computer market and by previous Windows users who were switching over? To find out, 500 iMac customers were interviewed. Each customer was categorized as a previous Macintosh owner, a previous Windows owner, or a new computer purchaser. This section examines graphical methods for displaying the results of the interviews. We’ll learn some general lessons about how to graph data that fall into a small number of categories. -
Pcatools: Everything Principal Components Analysis
Package ‘PCAtools’ October 1, 2021 Type Package Title PCAtools: Everything Principal Components Analysis Version 2.5.15 Description Principal Component Analysis (PCA) is a very powerful technique that has wide applica- bility in data science, bioinformatics, and further afield. It was initially developed to anal- yse large volumes of data in order to tease out the differences/relationships between the logi- cal entities being analysed. It extracts the fundamental structure of the data with- out the need to build any model to represent it. This 'summary' of the data is ar- rived at through a process of reduction that can transform the large number of vari- ables into a lesser number that are uncorrelated (i.e. the 'principal compo- nents'), while at the same time being capable of easy interpretation on the original data. PCA- tools provides functions for data exploration via PCA, and allows the user to generate publica- tion-ready figures. PCA is performed via BiocSingular - users can also identify optimal num- ber of principal components via different metrics, such as elbow method and Horn's paral- lel analysis, which has relevance for data reduction in single-cell RNA-seq (scRNA- seq) and high dimensional mass cytometry data. License GPL-3 Depends ggplot2, ggrepel Imports lattice, grDevices, cowplot, methods, reshape2, stats, Matrix, DelayedMatrixStats, DelayedArray, BiocSingular, BiocParallel, Rcpp, dqrng Suggests testthat, scran, BiocGenerics, knitr, Biobase, GEOquery, hgu133a.db, ggplotify, beachmat, RMTstat, ggalt, DESeq2, airway, -
Chapter 16.Tst
Chapter 16 Statistical Quality Control- Prof. Dr. Samir Safi TRUE/FALSE. Write 'T' if the statement is true and 'F' if the statement is false. 1) Statistical process control uses regression and other forecasting tools to help control processes. 1) 2) It is impossible to develop a process that has zero variability. 2) 3) If all of the control points on a control chart lie between the UCL and the LCL, the process is always 3) in control. 4) An x-bar chart would be appropriate to monitor the number of defects in a production lot. 4) 5) The central limit theorem provides the statistical foundation for control charts. 5) 6) If we are tracking quality of performance for a class of students, we should plot the individual 6) grades on an x-bar chart, and the pass/fail result on a p-chart. 7) A p-chart could be used to monitor the average weight of cereal boxes. 7) 8) If we are attempting to control the diameter of bowling bowls, we will find a p-chart to be quite 8) helpful. 9) A c-chart would be appropriate to monitor the number of weld defects on the steel plates of a 9) ship's hull. MULTIPLE CHOICE. Choose the one alternative that best completes the statement or answers the question. 1) Which of the following is not a popular definition of quality? 1) A) Quality is fitness for use. B) Quality is the totality of features and characteristics of a product or service that bears on its ability to satisfy stated or implied needs. -
Section 2.2: Bar Charts and Pie Charts
Section 2.2: Bar Charts and Pie Charts 1 Raw Data is Ugly Graphical representations of data always look pretty in newspapers, magazines and books. What you haven’tseen is the blood, sweat and tears that it some- times takes to get those results. http://seatgeek.com/blog/mlb/5-useful-charts-for-baseball-fans-mlb-ticket-prices- by-day-time 1 Google listing for Ru San’sKennesaw location 2 The previous examples are informative graphical displays of data. They all started life as bland data sets. 2 Bar Charts Bar charts are a visual way to organize data. The height or length of a bar rep- resents the number of points of data (frequency distribution) in a particular category. One can also let the bar represent the percentage of data (relative frequency distribution) in a category. Example 1 From (http://vgsales.wikia.com/wiki/Halo) consider the sales …g- ures for Microsoft’s videogame franchise, Halo. Here is the raw data. Year Game Units Sold (in millions) 2001 Halo: Combat Evolved 5.5 2004 Halo 2 8 2007 Halo 3 12.06 2009 Halo Wars 2.54 2009 Halo 3: ODST 6.32 2010 Halo: Reach 9.76 2011 Halo: Combat Evolved Anniversary 2.37 2012 Halo 4 9.52 2014 Halo: The Master Chief Collection 2.61 2015 Halo 5 5 Let’s construct a bar chart based on units sold. Translating frequencies into relative frequencies is an easy process. A rela- tive frequency is the frequency divided by total number of data points. Example 2 Create a relative frequency chart for Halo games. -
Principal Components Analysis (Pca)
PRINCIPAL COMPONENTS ANALYSIS (PCA) Steven M. Holand Department of Geology, University of Georgia, Athens, GA 30602-2501 3 December 2019 Introduction Suppose we had measured two variables, length and width, and plotted them as shown below. Both variables have approximately the same variance and they are highly correlated with one another. We could pass a vector through the long axis of the cloud of points and a second vec- tor at right angles to the first, with both vectors passing through the centroid of the data. Once we have made these vectors, we could find the coordinates of all of the data points rela- tive to these two perpendicular vectors and re-plot the data, as shown here (both of these figures are from Swan and Sandilands, 1995). In this new reference frame, note that variance is greater along axis 1 than it is on axis 2. Also note that the spatial relationships of the points are unchanged; this process has merely rotat- ed the data. Finally, note that our new vectors, or axes, are uncorrelated. By performing such a rotation, the new axes might have particular explanations. In this case, axis 1 could be regard- ed as a size measure, with samples on the left having both small length and width and samples on the right having large length and width. Axis 2 could be regarded as a measure of shape, with samples at any axis 1 position (that is, of a given size) having different length to width ratios. PC axes will generally not coincide exactly with any of the original variables. -
Bar Charts and Box Plots Normal Poisson Exponential Creating a Simple Yet Effective Plot Requires an 02468 C 1.0 Exponential Uniform Understanding of Data and Tasks
THIS MONTH a Uniform POINTS OF VIEW Normal Poisson Exponential 02468 b Uniform Bar charts and box plots Normal Poisson Exponential Creating a simple yet effective plot requires an 02468 c 1.0 Exponential Uniform understanding of data and tasks. λ = 1 Min = 5.5 Normal Max = 6.5 0.5 Poisson σμ= 1, = 5 μ = 2 Bar charts and box plots are omnipresent in the scientific literature. 0 02468 They are typically used to visualize quantities associated with a set of Figure 2 | Representation of four distributions with bar charts and box plots. items. Representing the data accurately, however, requires choosing (a) Bar chart showing sample means (n = 1,000) with standard-deviation the appropriate plot according to the nature of the data and the task at error bars. (b) Box plot (n = 1,000) with whiskers extending to ±1.5 × IQR. hand. Bar charts are appropriate for counts, whereas box plots should (c) Probability density functions of the distributions in a and b. λ, rate; be used to represent the characteristics of a distribution. µ, mean; σ, standard deviation. Bar charts encode quantities by length, which is a highly accurate visual encoding and preferred over the angle-based strategy used in to represent such uncertainty. However, because the bars always start pie charts (Fig. 1a). Often the counts that we want to represent are at zero, they can be misleading: for example, part of the range covered sums over multiple categories. There are several options to visualize by the bar might have never been observed in the sample.