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Dianne Cook

Publications and source records attributed to Dianne Cook.

At least 19 recordsLinked to original sources

Colour Blinded by the Noise

Uncertainty visualisation is important for data transparency, especially for map visualisations where data is often aggregated. Despite the importance of this area, studies evaluating uncertainty visualisation lack consensus and produce conflicting results. This work introduces a new evaluation approach for uncertainty visualisation that attempts to assess uncertainty as noise, rather than signal. We evaluate five methods of visualising uncertainty: standard choropleth maps, value/variance bivariate maps, value-suppressing uncertainty palettes, overlaid sampling, and pixelated sampling maps. Built on principles of implicit testing, we put an 'uncertainty visualisation' spin on the classic Ishihara colourblind test to create a novel test that is able to evaluate uncertainty as noise. We compare signal visibility to conventional hypothesis tests at various levels of group separation. By building our experimental design on top of established graphics theory, we isolate the plot components that facilitate successful signal suppression and establish foundational theory for the perception of uncertainty visualisation.

cs.HC

A Mathematical Framework and Software Implementation for Uncertainty Visualisation

Random variables are the bread and butter of statistics, and visualisations are one of the most versatile tools in the field, so it is a wonder why we do not have a methodology for visualising random variables. This gap is particularly evident for exploratory data analysis (EDA). We address this gap by designing a mathematical framework for visualisation, which argues that we should consider visualisations to be continuous functions. In the case of random variable inputs, this means the visualisations should obey the continuous mapping theorem (CMT). By breaking the visual function down into its components, we are able to identify which parts of the mapping are ill-defined for random variable inputs and redefine them in a way that guarantees both the flexibility required for EDA and the statistical sensibility of CMT. This formalisation represents a complete integration of uncertainty into the grammar of graphics, which we show by implementing the theory in the R package, "ggdibbler". The ggdibbler software is a "ggplot2" extension that allows users to replace the data of any plotting function with a random variable, with the guarantee that the visualisation will have the same convergence properties as its underlying data.

stat.AP

Automated Residual Plot Assessment With the R Package autovi and the Shiny Application autovi.web

Visual assessment of residual plots is a common approach for diagnosing linear models, but it relies on manual evaluation, which does not scale well and can lead to inconsistent decisions across analysts. The lineup protocol, which embeds the observed plot among null plots, can reduce subjectivity but requires even more human effort. In today's data-driven world, such tasks are well suited for automation. We present a new R package that uses a computer vision model to automate the evaluation of residual plots. An accompanying Shiny application is provided for ease of use. Given a sample of residuals, the model predicts a visual signal strength (VSS) and offers supporting information to help analysts assess model fit.

stat.ML

An Enhanced Projection Pursuit Tree Classifier with Visual Methods for Assessing Algorithmic Improvements

This paper presents enhancements to the projection pursuit tree classifier and visual diagnostic methods for assessing their impact in high dimensions. The original algorithm uses linear combinations of variables in a tree structure where depth is constrained to be less than the number of classes -- a limitation that proves too rigid for complex classification problems. Our extensions improve performance in multi-class settings with unequal variance-covariance structures and nonlinear class separations by allowing more splits and more flexible class groupings in the projection pursuit computation. Proposing algorithmic improvements is straightforward; demonstrating their actual utility is not. We therefore develop two visual diagnostic approaches to verify that the enhancements perform as intended. Using high-dimensional visualization techniques, we examine model fits on benchmark datasets to assess whether the algorithm behaves as theorized. An interactive web application enables users to explore the behavior of both the original and enhanced classifiers under controlled scenarios. The enhancements are implemented in the R package PPtreeExt.

stat.ML

quollr: An R Package for Visualizing 2-D Models from Nonlinear Dimension Reductions in High-Dimensional Space

Nonlinear dimension reduction methods provide a low-dimensional representation of high-dimensional data by applying a Nonlinear transformation. However, the complexity of the transformations and data structures can create wildly different representations depending on the method and hyper-parameter choices. It is difficult to determine whether any of these representations are accurate, which one is the best, or whether they have missed important structures. The R package quollr has been developed as a new visual tool to determine which method and which hyper-parameter choices provide the most accurate representation of high-dimensional data. The scurve data from the package is used to illustrate the algorithm. Single-cell RNA sequencing (scRNA-seq) data from mouse limb muscles are used to demonstrate the usability of the package.

stat.ME

cardinalR: Generating Interesting High-Dimensional Data Structures

Simulated high-dimensional data is useful for testing, validating, and improving algorithms used in dimension reduction, supervised and unsupervised learning. High-dimensional data is characterized by multiple variables that are dependent or associated in some way, such as linear, nonlinear, clustering or anomalies. Here we provide new methods for generating a variety of high-dimensional structures using mathematical functions and statistical distributions organized into the R package cardinalR. Several example data sets are also provided. These will be useful for researchers to better understand how different analytical methods work and can be improved, with a special focus on nonlinear dimension reduction methods. This package enriches the existing toolset of benchmark datasets for evaluating algorithms.

stat.ME

Choosing Better NLDR Layouts by Evaluating the Model in the High-dimensional Data Space

Nonlinear dimension reduction (NLDR) techniques such as tSNE, and UMAP provide a low-dimensional representation of high-dimensional data ($p\text{-}D$) by applying a nonlinear transformation. NLDR often exaggerates random patterns. But NLDR views have an important role in data analysis because, if done well, they provide a concise visual (and conceptual) summary of $p\text{-}D$ distributions. The NLDR methods and hyper-parameter choices can create wildly different representations, making it difficult to decide which is best, or whether any or all are accurate or misleading. To help assess the NLDR and decide on which, if any, is the most reasonable representation of the structure(s) present in the $p\text{-}D$ data, we have developed an algorithm to show the $2\text{-}D$ NLDR model in the $p\text{-}D$ space, viewed with a tour, a movie of linear projections. From this, one can see if the model fits everywhere, or better in some subspaces, or completely mismatches the data. Also, we can see how different methods may have similar summaries or quirks.

stat.ME

Is this normal? A new projection pursuit index to assess a sample against a multivariate null distribution

Many data problems contain some reference or normal conditions, upon which to compare newly collected data. This scenario occurs in data collected as part of clinical trials to detect adverse events, or for measuring climate change against historical norms. The data is typically multivariate, and often the normal ranges are specified by a multivariate normal distribution. The work presented in this paper develops methods to compare the new sample against the reference distribution with high-dimensional visualisation. It uses a projection pursuit guided tour to produce a sequence of low-dimensional projections steered towards those where the new sample is most different from the reference. A new projection pursuit index is defined for this purpose. The tour visualisation also includes drawing of the projected ellipse, which is computed analytically, corresponding to the reference distribution. The methods are implemented in the R package, tourr.

stat.ME

The Noisy Work of Uncertainty Visualisation Research: A Review

Better representation of the uncertainty in a data visualisation is a focus of recent research activity. A problem with the current literature is that there is a lack of clarity about the definition of uncertainty and what it means to represent it in a plot. This confusion results in a significant amount of conflicting results in the literature, especially in experiments that assess the effectiveness of different uncertainty representations. In this review, we summarise the current literature, provide workable definitions, and illustrate these definitions with examples. In doing so, we ask what it really takes to achieve transparency in statistical graphics. It is hoped that it will be useful for guiding new graphics methodology and experimental research.

cs.HC

Automated Assessment of Residual Plots with Computer Vision Models

Plotting the residuals is a recommended procedure to diagnose deviations from linear model assumptions, such as non-linearity, heteroscedasticity, and non-normality. The presence of structure in residual plots can be tested using the lineup protocol to do visual inference. There are a variety of conventional residual tests, but the lineup protocol, used as a statistical test, performs better for diagnostic purposes because it is less sensitive and applies more broadly to different types of departures. However, the lineup protocol relies on human judgment which limits its scalability. This work presents a solution by providing a computer vision model to automate the assessment of residual plots. It is trained to predict a distance measure that quantifies the disparity between the residual distribution of a fitted classical normal linear regression model and the reference distribution, based on Kullback-Leibler divergence. From extensive simulation studies, the computer vision model exhibits lower sensitivity than conventional tests but higher sensitivity than human visual tests. It is slightly less effective on non-linearity patterns. Several examples from classical papers and contemporary data illustrate the new procedures, highlighting its usefulness in automating the diagnostic process and supplementing existing methods.

stat.ML

Squintability and Other Metrics for Assessing Projection Pursuit Indexes, and Guiding Optimization Choices

The projection pursuit (PP) guided tour optimizes a criterion function, known as the PP index, to gradually reveal projections of interest from high-dimensional data through animation. Optimization of some PP indexes can be non-trivial, if they are non-smooth functions, or when the optimum has a small "squint angle", detectable only from close proximity. Here, measures for calculating the smoothness and squintability properties of the PP index are defined. These are used to investigate the performance of a recently introduced swarm-based algorithm, Jellyfish Search Optimizer (JSO), for optimizing PP indexes. The performance of JSO in detecting the target pattern (pipe shape) is compared with existing optimizers in PP. Additionally, JSO's performance on detecting the sine-wave shape is evaluated using different PP indexes (hence different smoothness and squintability) across various data dimensions (d = 4, 6, 8, 10, 12) and JSO hyper-parameters. We observe empirically that higher squintability improves the success rate of the PP index optimization, while smoothness has no significant effect. The JSO algorithm has been implemented in the R package, `tourr`, and functions to calculate smoothness and squintability measures are implemented in the `ferrn` package.

stat.CO

A Tidy Framework and Infrastructure to Systematically Assemble Spatio-temporal Indexes from Multivariate Data

Indexes are useful for summarizing multivariate information into single metrics for monitoring, communicating, and decision-making. While most work has focused on defining new indexes for specific purposes, more attention needs to be directed towards making it possible to understand index behavior in different data conditions, and to determine how their structure affects their values and variation in values. Here we discuss a modular data pipeline recommendation to assemble indexes. It is universally applicable to index computation and allows investigation of index behavior as part of the development procedure. One can compute indexes with different parameter choices, adjust steps in the index definition by adding, removing, and swapping them to experiment with various index designs, calculate uncertainty measures, and assess indexes robustness. The paper presents three examples to illustrate the pipeline framework usage: comparison of two different indexes designed to monitor the spatio-temporal distribution of drought in Queensland, Australia; the effect of dimension reduction choices on the Global Gender Gap Index (GGGI) on countries ranking; and how to calculate bootstrap confidence intervals for the Standardized Precipitation Index (SPI). The methods are supported by a new R package, called tidyindex.

stat.CO

Frame to frame interpolation for high-dimensional data visualisation using the woylier package

The woylier package implements tour interpolation paths between frames using Givens rotations. This provides an alternative to the geodesic interpolation between planes currently available in the tourr package. Tours are used to visualise high-dimensional data and models, to detect clustering, anomalies and non-linear relationships. Frame-to-frame interpolation can be useful for projection pursuit guided tours when the index is not rotationally invariant. It also provides a way to specifically reach a given target frame. We demonstrate the method for exploring non-linear relationships between currency cross-rates.

stat.ME

A Clustering Algorithm to Organize Satellite Hotspot Data for the Purpose of Tracking Bushfires Remotely

This paper proposes a spatiotemporal clustering algorithm and its implementation in the R package spotoroo. This work is motivated by the catastrophic bushfires in Australia throughout the summer of 2019-2020 and made possible by the availability of satellite hotspot data. The algorithm is inspired by two existing spatiotemporal clustering algorithms but makes enhancements to cluster points spatially in conjunction with their movement across consecutive time periods. It also allows for the adjustment of key parameters, if required, for different locations and satellite data sources. Bushfire data from Victoria, Australia, is used to illustrate the algorithm and its use within the package.

cs.LG

A Plot is Worth a Thousand Tests: Assessing Residual Diagnostics with the Lineup Protocol

Regression experts consistently recommend plotting residuals for model diagnosis, despite the availability of many numerical hypothesis test procedures designed to use residuals to assess problems with a model fit. Here we provide evidence for why this is good advice using data from a visual inference experiment. We show how conventional tests are too sensitive, which means that too often the conclusion would be that the model fit is inadequate. The experiment uses the lineup protocol which puts a residual plot in the context of null plots. This helps generate reliable and consistent reading of residual plots for better model diagnosis. It can also help in an obverse situation where a conventional test would fail to detect a problem with a model due to contaminated data. The lineup protocol also detects a range of departures from good residuals simultaneously. Supplemental materials for the article are available online.

stat.AP

Performance is not enough: the story told by a Rashomon quartet

The usual goal of supervised learning is to find the best model, the one that optimizes a particular performance measure. However, what if the explanation provided by this model is completely different from another model and different again from another model despite all having similarly good fit statistics? Is it possible that the equally effective models put the spotlight on different relationships in the data? Inspired by Anscombe's quartet, this paper introduces a Rashomon Quartet, i.e. a set of four models built on a synthetic dataset which have practically identical predictive performance. However, the visual exploration reveals distinct explanations of the relations in the data. This illustrative example aims to encourage the use of methods for model visualization to compare predictive models beyond their performance.

stat.ML

A Study on a User-Controlled Radial Tour for Variable Importance in High-Dimensional Data

Principal component analysis is a long-standing go-to method for exploring multivariate data. The principal components are linear combinations of the original variables, ordered by descending variance. The first few components typically provide a good visual summary of the data. Tours also make linear projections of the original variables but offer many different views, like examining the data from different directions. The grand tour shows a smooth sequence of projections as an animation following interpolations between random target bases. The manual radial tour rotates the selected variable's contribution into and out of a projection. This allows the importance of the variable to structure in the projection to be assessed. This work describes a mixed-design user study evaluating the radial tour's efficacy compared with principal component analysis and the grand tour. A supervised classification task is assigned to participants who evaluate variable attribution of the separation between two classes. Their accuracy in assigning the variable importance is measured across various factors. Data were collected from 108 crowdsourced participants, who performed two trials with each visual for 648 trials in total. Mixed model regression finds strong evidence that the radial tour results in a large increase in accuracy over the alternatives. Participants also reported a preference for the radial tour in comparison to the other two methods.

stat.AP

New and simplified manual controls for projection and slice tours, with application to exploring classification boundaries in high dimensions

This paper describes new user controls for examining high-dimensional data using low-dimensional linear projections and slices. A user can interactively change the contribution of a given variable to a low-dimensional projection, which is useful for exploring the sensitivity of structure to particular variables. The user can also interactively shift the center of a slice, for example, to explore how structure changes in local subspaces. The Mathematica package as well as example notebooks are provided, which contain functions enabling the user to experiment with these new manual controls, with one specifically for exploring regions and boundaries produced by classification models. The advantage of Mathematica is its linear algebra capabilities, and interactive cursor location controls. Some limited implementation has also been made available in the R package tourr.

stat.CO