VizRank: Data Visualization Guided by Machine Learning

Data visualization plays a crucial role in identifying interesting patterns in exploratory data analysis. Its use is, however, made difficult by the large number of possible data projections showing different attribute subsets that must be evaluated by the data analyst. In this paper, we introduce a method called VizRank, which is applied on classified data to automatically select the most useful data projections. VizRank can be used with any visualization method that maps attribute values to points in a two-dimensional visualization space. It assesses possible data projections and ranks them by their ability to visually discriminate between classes. The quality of class separation is estimated by computing the predictive accuracy of k-nearest neighbor classifier on the data set consisting of x and y positions of the projected data points and their class information. The paper introduces the method and presents experimental results which show that VizRank's ranking of projections highly agrees with subjective rankings by data analysts. The practical use of VizRank is also demonstrated by an application in the field of functional genomics

Simple and Effective Visual Models for Gene Expression Cancer Diagnostics

In the paper we show that diagnostic classes in cancer gene expression data sets, which most often include thousands of features (genes), may be effectively separated with simple two-dimensional plots such as scatterplot and radviz graph. The principal innovation proposed in the paper is a method called VizRank, which is able to score and identify the best among possibly millions of candidate projections for visualizations. Compared to recently much applied techniques in the field of cancer genomics that include neural networks, support vector machines and various ensemble-based approaches, VizRank is fast and finds visualization models that can be easily examined and interpreted by domain experts. Our experiments on a number of gene expression data sets show that VizRank was always able to find data visualizations with a small number of (two to seven) genes and excellent class separation. In addition to providing grounds for gene expression cancer diagnosis, VizRank and its visualizations also identify small sets of relevant genes, uncover interesting gene interactions and point to outliers and potential misclassifications in cancer data sets

Three-dimensional Radial Visualization of High-dimensional Datasets with Mixed Features

We develop methodology for 3D radial visualization (RadViz) of high-dimensional datasets. Our display engine is called RadViz3D and extends the classical 2D RadViz that visualizes multivariate data in the 2D plane by mapping every record to a point inside the unit circle. We show that distributing anchor points at least approximately uniformly on the 3D unit sphere provides a better visualization with minimal artificial visual correlation for data with uncorrelated variables. Our RadViz3D methodology therefore places equi-spaced anchor points, one for every feature, exactly for the five Platonic solids, and approximately via a Fibonacci grid for the other cases. Our Max-Ratio Projection (MRP) method then utilizes the group information in high dimensions to provide distinctive lower-dimensional projections that are then displayed using Radviz3D. Our methodology is extended to datasets with discrete and continuous features where a Gaussianized distributional transform is used in conjunction with copula models before applying MRP and visualizing the result using RadViz3D. A R package radviz3d implementing our complete methodology is available.Comment: 12 pages, 10 figures, 1 tabl

Application of Data Visualization and Big Data Analysis in Intelligent Agriculture

Intelligent agriculture can renovate agricultural production and management, making agricultural production truly scientific and efficient. The existing data mining technology for agricultural information is powerful and professional. But the technology is not well adapted for intelligent agriculture. Therefore, this paper introduces data visualization and big data analysis into the application scenarios of intelligent agriculture. Firstly, an intelligent agriculture data visualization system was established, and the RadViz data visualization method was detailed for intelligent agriculture. Moreover, the intelligent agriculture data were processed using dimensionality reduction through principal component analysis (PCA) and further optimized through k-means clustering (KMC). Finally, the crop yield was predicted using the multiple regression algorithm and the residual principal component regression algorithm. The crop yield prediction model was proved effective through experiments

Three-dimensional Radial Visualization of High-dimensional Continuous or Discrete Data

This paper develops methodology for 3D radial visualization of high-dimensional datasets. Our display engine is called RadViz3D and extends the classic RadViz that visualizes multivariate data in the 2D plane by mapping every record to a point inside the unit circle. The classic RadViz display has equally-spaced anchor points on the unit circle, with each of them associated with an attribute or feature of the dataset. RadViz3D obtains equi-spaced anchor points exactly for the five Platonic solids and approximately for the other cases via a Fibonacci grid. We show that distributing anchor points at least approximately uniformly on the 3D unit sphere provides a better visualization than in 2D. We also propose a Max-Ratio Projection (MRP) method that utilizes the group information in high dimensions to provide distinctive lower-dimensional projections that are then displayed using Radviz3D. Our methodology is extended to datasets with discrete and mixed features where a generalized distributional transform is used in conjuction with copula models before applying MRP and RadViz3D visualization

ICE: An Interactive Configuration Explorer for High Dimensional Categorical Parameter Spaces

There are many applications where users seek to explore the impact of the settings of several categorical variables with respect to one dependent numerical variable. For example, a computer systems analyst might want to study how the type of file system or storage device affects system performance. A usual choice is the method of Parallel Sets designed to visualize multivariate categorical variables. However, we found that the magnitude of the parameter impacts on the numerical variable cannot be easily observed here. We also attempted a dimension reduction approach based on Multiple Correspondence Analysis but found that the SVD-generated 2D layout resulted in a loss of information. We hence propose a novel approach, the Interactive Configuration Explorer (ICE), which directly addresses the need of analysts to learn how the dependent numerical variable is affected by the parameter settings given multiple optimization objectives. No information is lost as ICE shows the complete distribution and statistics of the dependent variable in context with each categorical variable. Analysts can interactively filter the variables to optimize for certain goals such as achieving a system with maximum performance, low variance, etc. Our system was developed in tight collaboration with a group of systems performance researchers and its final effectiveness was evaluated with expert interviews, a comparative user study, and two case studies.Comment: 10 pages, Published by IEEE at VIS 2019 (Vancouver, BC, Canada

Visualising Mutually Non-dominating Solution Sets in Many-objective Optimisation

Copyright © 2013 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other users, including reprinting/ republishing this material for advertising or promotional purposes, creating new collective works for resale or redistribution to servers or lists, or reuse of any copyrighted components of this work in other works.As many-objective optimization algorithms mature, the problem owner is faced with visualizing and understanding a set of mutually nondominating solutions in a high dimensional space. We review existing methods and present new techniques to address this problem. We address a common problem with the well-known heatmap visualization, since the often arbitrary ordering of rows and columns renders the heatmap unclear, by using spectral seriation to rearrange the solutions and objectives and thus enhance the clarity of the heatmap. A multiobjective evolutionary optimizer is used to further enhance the simultaneous visualization of solutions in objective and parameter space. Two methods for visualizing multiobjective solutions in the plane are introduced. First, we use RadViz and exploit interpretations of barycentric coordinates for convex polygons and simplices to map a mutually nondominating set to the interior of a regular convex polygon in the plane, providing an intuitive representation of the solutions and objectives. Second, we introduce a new measure of the similarity of solutions—the dominance distance—which captures the order relations between solutions. This metric provides an embedding in Euclidean space, which is shown to yield coherent visualizations in two dimensions. The methods are illustrated on standard test problems and data from a benchmark many-objective problem

High-dimensional Clustering onto Hamiltonian Cycle

Clustering aims to group unlabelled samples based on their similarities. It has become a significant tool for the analysis of high-dimensional data. However, most of the clustering methods merely generate pseudo labels and thus are unable to simultaneously present the similarities between different clusters and outliers. This paper proposes a new framework called High-dimensional Clustering onto Hamiltonian Cycle (HCHC) to solve the above problems. First, HCHC combines global structure with local structure in one objective function for deep clustering, improving the labels as relative probabilities, to mine the similarities between different clusters while keeping the local structure in each cluster. Then, the anchors of different clusters are sorted on the optimal Hamiltonian cycle generated by the cluster similarities and mapped on the circumference of a circle. Finally, a sample with a higher probability of a cluster will be mapped closer to the corresponding anchor. In this way, our framework allows us to appreciate three aspects visually and simultaneously - clusters (formed by samples with high probabilities), cluster similarities (represented as circular distances), and outliers (recognized as dots far away from all clusters). The experiments illustrate the superiority of HCHC