Statistical Graphics in QUAIL: An Overview

It has been suggested (Wainer, 1989) that the system first proposed by C.S. Peirce to organise knowledge is particularly suited to describing statistical graphics. Peirce felt that all information could be broken down into three different types { monadic information, which describes something in and of itself, dyadic information, which describes a relationship between two things, and triadic information, which describes the relation between two things mediated by a third. We can see how this applies in statistical graphics by considering the scatterplot. There, each case in a dataset is represented in the display by a glyph, which is monadic in nature. The scatterplot is a dyad; by positioning the case glyphs in the plane according to the values each case has on two variates X and Y , any empirical relationship between the variates can be seen. Triadic information is available by linking the scatterplot with another plot, say a dot-plot of a third variate, Z. Colouring the glyphs in the dot-plot within a given range of Z values, causes the corresponding glyphs in the scatterplot to be coloured in the same way. Here the relationship between X and Y is seen mediated by the third variate Z. This description of information is reflected in the design and implementation of our graphics software, which is part of the QUAIL system (Oldford et al). Quail (for QUantitative Analysis in Lisp) is a programming environment for statistical and quantitative computing. It has extensive arithmetical, mathematical, statistical and display facilities. This paper gives a brief overview of the principles underlying the statistical graphics facilities. The original software model was first illustrated in a video (Hurley and Oldford, 1988), and was described in Hurley and Oldford (1991). Perhaps surprisingly, we have not altered the original software model, rather we have extended and enriched its scope over the intervening years. The statistical graphics system in Quail has an object-oriented design, which we outline in Section 2. In the language of Peirce, individual objects have a monadic nature. We provide basic building blocks consisting of simple graphical objects such as point symbols and lines and container objects within which the simple objects are positioned to display relationships, ultimately forming plots. Container objects present dyadic information; Section 3 describes some such objects available in Quail. In Section 4, we outline a few of the ways triadic information is available; generally this involves comparison of plots, and, if the plots are displayed over time, interactive graphics

A New Flexible Dendrogram Seriation Algorithm for Data Visualisation

Seriation is a data analytic tool for obtaining a permutation of a set of objects with the goal of revealing structural information within the set of objects. Seriating variables, cases or categories generally improves visualisations of statistical data, for example, by revealing hidden patterns in data or by making large datasets easier to understand. In this paper we present a new algorithm for seriation based on dendrograms. Dendrogram seriation algorithms rearrange the nodes in a dendrogram in order to obtain a permutation of the leaves (i.e. objects) that optimises a given criterion. Our algorithm is more flexible than currently available seriation algorithms because it allows the user to either choose from a variety of seriation criteria or to input their own criteria. This choice of seriation criteria is an important feature because different criteria are suitable for different visualisation settings. Common seriation criteria include measurements of the path length through a set of objects and measurements of anti-Robinson form in a symmetric matrix. We propose new seriation criteria called lazy path length and banded anti-Robinson form, and demonstrate their effectiveness in a variety of visualisation settings

A New Flexible Dendrogram Seriation Algorithm for Data Visualisation

Seriation is a data analytic tool for obtaining a permutation of a set of objects with the goal of revealing structural information within the set of objects. Seriating variables, cases or categories generally improves visualisations of statistical data, for example, by revealing hidden patterns in data or by making large datasets easier to understand. In this paper we present a new algorithm for seriation based on dendrograms. Dendrogram seriation algorithms rearrange the nodes in a dendrogram in order to obtain a permutation of the leaves (i.e. objects) that optimises a given criterion. Our algorithm is more flexible than currently available seriation algorithms because it allows the user to either choose from a variety of seriation criteria or to input their own criteria. This choice of seriation criteria is an important feature because different criteria are suitable for different visualisation settings. Common seriation criteria include measurements of the path length through a set of objects and measurements of anti-Robinson form in a symmetric matrix. We propose new seriation criteria called lazy path length and banded anti-Robinson form, and demonstrate their effectiveness in a variety of visualisation settings

Low-Storage Quantile Estimation

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On OMEGA (Online Multivariate Exploratory Graphical Analysis): Routine Searching for Structure: Comment

Abstract included in text

On OMEGA (Online Multivariate Exploratory Graphical Analysis): Routine Searching for Structure: Comment

Abstract included in text

Visualizing Variable Importance and Variable Interaction Effects in Machine Learning Models

Variable importance, interaction measures, and partial dependence plots are important summaries in the interpretation of statistical and machine learning models. In this article, we describe new visualization techniques for exploring these model summaries. We construct heatmap and graph-based displays showing variable importance and interaction jointly, which are carefully designed to highlight important aspects of the fit. We describe a new matrix-type layout showing all single and bivariate partial dependence plots, and an alternative layout based on graph Eulerians focusing on key subsets. Our new visualizations are model-agnostic and are applicable to regression and classification supervised learning settings. They enhance interpretation even in situations where the number of variables is large. Our R package vivid (variable importance and variable interaction displays) provides an implementation. Supplementary files for this article are available online

Trisubstituted thiazoles as potent and selective inhibitors of Plasmodium falciparum protein kinase G (PfPKG).

A series of trisubstituted thiazoles have been identified as potent inhibitors of Plasmodium falciparum (Pf) cGMP-dependent protein kinase (PfPKG) through template hopping from known Eimeria PKG (EtPKG) inhibitors. The thiazole series has yielded compounds with improved potency, kinase selectivity and good in vitro ADME properties. These compounds could be useful tools in the development of new anti-malarial drugs in the fight against drug resistant malaria

Loss of the Synaptic Vesicle Protein SV2B Results in Reduced Neurotransmission and Altered Synaptic Vesicle Protein Expression in the Retina

The Synaptic Vesicle Protein 2 (SV2) family of transporter-like proteins is expressed exclusively in vesicles that undergo calcium-regulated exocytosis. Of the three isoforms expressed in mammals, SV2B is the most divergent. Here we report studies of SV2B location and function in the retina. Immunolabeling studies revealed that SV2B is detected in rod photoreceptor synaptic terminals where it is the primary isoform. In mice lacking SV2B, synaptic transmission at the synapse between photoreceptors and bipolar neurons was decreased, as evidenced by a significant reduction in the amplitude of the b-wave in electroretinogram recordings. Quantitative immunoblot analyses of whole eyes revealed that loss of SV2B was associated with reduced levels of synaptic vesicle proteins including synaptotagmin, VAMP, synaptophysin and the vesicular glutamate transporter V-GLUT1. Immunolabeling studies revealed that SV2B is detected in rod photoreceptor synaptic terminals where it is the primary isoform. Thus, SV2B contributes to the modulation of synaptic vesicle exocytosis and plays a significant role in regulating synaptic protein content