On Computationally-Enhanced Visual Analysis of Heterogeneous Data and Its Application in Biomedical Informatics

With the advance of new data acquisition and generation technologies, the biomedical domain is becoming increasingly data-driven. Thus, understanding the information in large and complex data sets has been in the focus of several research fields such as statistics, data mining, machine learning, and visualization. While the first three fields predominantly rely on computational power, visualization relies mainly on human perceptual and cognitive capabilities for extracting information. Data visualization, similar to Human–Computer Interaction, attempts an appropriate interaction between human and data to interactively exploit data sets. Specifically within the analysis of complex data sets, visualization researchers have integrated computational methods to enhance the interactive processes. In this state-of-the-art report, we investigate how such an integration is carried out. We study the related literature with respect to the underlying analytical tasks and methods of integration. In addition, we focus on how such methods are applied to the biomedical domain and present a concise overview within our taxonomy. Finally, we discuss some open problems and future challenges.

[1]  O. Rubel,et al.  Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data , 2010, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

[2]  Kwan-Liu Ma,et al.  Machine Learning to Boost the Next Generation of Visualization Technology , 2007, IEEE Computer Graphics and Applications.

[3]  Pierre Dragicevic,et al.  Rolling the Dice: Multidimensional Visual Exploration using Scatterplot Matrix Navigation , 2008, IEEE Transactions on Visualization and Computer Graphics.

[4]  Andreas Holzinger,et al.  Dynamic Media in Computer Science Education; Content Complexity and Learning Performance: Is Less More? , 2008, J. Educ. Technol. Soc..

[5]  Hanspeter Pfister,et al.  Characterizing Cancer Subtypes Using Dual Analysis in Caleydo StratomeX , 2014, IEEE Computer Graphics and Applications.

[6]  Ethem Alpaydin,et al.  Introduction to machine learning , 2004, Adaptive computation and machine learning.

[7]  Jonathan R. Karr,et al.  A Whole-Cell Computational Model Predicts Phenotype from Genotype , 2012, Cell.

[8]  Peter Filzmoser,et al.  Uncertainty‐Aware Exploration of Continuous Parameter Spaces Using Multivariate Prediction , 2011, Comput. Graph. Forum.

[9]  Helwig Hauser,et al.  Outlier-Preserving Focus+Context Visualization in Parallel Coordinates , 2006, IEEE Transactions on Visualization and Computer Graphics.

[10]  Blaz Zupan,et al.  FreeViz - An intelligent multivariate visualization approach to explorative analysis of biomedical data , 2007, J. Biomed. Informatics.

[11]  Harald Piringer,et al.  A Partition-Based Framework for Building and Validating Regression Models , 2013, IEEE Transactions on Visualization and Computer Graphics.

[12]  Andreas Holzinger,et al.  Analysis of biomedical data with multilevel glyphs , 2014, BMC Bioinformatics.

[13]  I. Dubchak,et al.  Visualizing genomes: techniques and challenges , 2010, Nature Methods.

[14]  Brad A. Myers,et al.  What to do when search fails: finding information by association , 2008, CHI.

[15]  Russell Beale,et al.  Supporting serendipity: Using ambient intelligence to augment user exploration for data mining and web browsing , 2007, Int. J. Hum. Comput. Stud..

[16]  Igor Jurisica,et al.  Visual Data Mining: Effective Exploration of the Biological Universe , 2014, Interactive Knowledge Discovery and Data Mining in Biomedical Informatics.

[17]  Andreas Holzinger,et al.  On Topological Data Mining , 2014, Interactive Knowledge Discovery and Data Mining in Biomedical Informatics.

[18]  Daniel A. Keim,et al.  Information Visualization and Visual Data Mining , 2002, IEEE Trans. Vis. Comput. Graph..

[19]  Tamara Munzner,et al.  A Multi-Level Typology of Abstract Visualization Tasks , 2013, IEEE Transactions on Visualization and Computer Graphics.

[20]  Andreas Holzinger,et al.  Usability engineering methods for software developers , 2005, CACM.

[21]  Kristin A. Cook,et al.  Illuminating the Path: The Research and Development Agenda for Visual Analytics , 2005 .

[22]  Chris Weaver,et al.  An adaptive parameter space-filling algorithm for highly interactive cluster exploration , 2012, 2012 IEEE Conference on Visual Analytics Science and Technology (VAST).

[23]  Topological Methods in Data Analysis and Visualization , 2011, Mathematics and Visualization.

[24]  Xianggui Qu,et al.  Multivariate Data Analysis , 2007, Technometrics.

[25]  Maryann E Martone,et al.  The cell centered database project: an update on building community resources for managing and sharing 3D imaging data. , 2008, Journal of structural biology.

[26]  Dieter Schmalstieg,et al.  StratomeX: Visual Analysis of Large‐Scale Heterogeneous Genomics Data for Cancer Subtype Characterization , 2012, Comput. Graph. Forum.

[27]  Tamara Munzner,et al.  MulteeSum: A Tool for Comparative Spatial and Temporal Gene Expression Data , 2010, IEEE Transactions on Visualization and Computer Graphics.

[28]  Steven J. M. Jones,et al.  An Interactive Analysis and Exploration Tool for Epigenomic Data , 2013, Comput. Graph. Forum.

[29]  Ben Shneiderman,et al.  Readings in information visualization - using vision to think , 1999 .

[30]  Denis Lalanne,et al.  Investigating and reflecting on the integration of automatic data analysis and visualization in knowledge discovery , 2010, SKDD.

[31]  John F. Roddick,et al.  Guiding knowledge discovery through interactive data mining , 2003 .

[32]  M. E. McGill,et al.  Dynamic Graphics for Statistics. , 1990 .

[33]  Tamara Munzner,et al.  Vismon: Facilitating Analysis of Trade‐Offs, Uncertainty, and Sensitivity In Fisheries Management Decision Making , 2012, Comput. Graph. Forum.

[34]  P. Filzmoser,et al.  Principal component analysis for compositional data with outliers , 2009 .

[35]  Jaegul Choo,et al.  iVisClassifier: An interactive visual analytics system for classification based on supervised dimension reduction , 2010, 2010 IEEE Symposium on Visual Analytics Science and Technology.

[36]  Matthew O. Ward,et al.  Model space visualization for multivariate linear trend discovery , 2009, 2009 IEEE Symposium on Visual Analytics Science and Technology.

[37]  Alexandru Telea,et al.  Code Flows: Visualizing Structural Evolution of Source Code , 2008, Comput. Graph. Forum.

[38]  Ben Shneiderman,et al.  Integrating Statistics and Visualization for Exploratory Power: From Long-Term Case Studies to Design Guidelines , 2009, IEEE Computer Graphics and Applications.

[39]  Reinhard Schneider,et al.  Visualizing time-related data in biology, a review , 2013, Briefings Bioinform..

[40]  Andreas Holzinger,et al.  Functional and genetic analysis of the colon cancer network , 2014, BMC Bioinformatics.

[41]  Alfredo Cuzzocrea,et al.  Availability, Reliability, and Security in Information Systems and HCI , 2013, Lecture Notes in Computer Science.

[42]  S. Johansson,et al.  Interactive Dimensionality Reduction Through User-defined Combinations of Quality Metrics , 2009, IEEE Transactions on Visualization and Computer Graphics.

[43]  George Karypis,et al.  gCLUTO – An Interactive Clustering, Visualization, and Analysis System , 2004 .

[44]  Gunnar E. Carlsson,et al.  Topology and data , 2009 .

[45]  Steven J. M. Jones,et al.  Circos: an information aesthetic for comparative genomics. , 2009, Genome research.

[46]  Peter Filzmoser,et al.  Brushing Moments in Interactive Visual Analysis , 2010, Comput. Graph. Forum.

[47]  R. Nussinov,et al.  Sequence dependence of C-end rule peptides in binding and activation of neuropilin-1 receptor. , 2013, Journal of structural biology.

[48]  Andreas Holzinger,et al.  Interactive Knowledge Discovery and Data Mining in Biomedical Informatics , 2014, Lecture Notes in Computer Science.

[49]  Helwig Hauser,et al.  Interactive Visual Analysis of Temporal Cluster Structures , 2011, Comput. Graph. Forum.

[50]  Tamara Munzner,et al.  DimStiller: Workflows for dimensional analysis and reduction , 2010, 2010 IEEE Symposium on Visual Analytics Science and Technology.

[51]  Igor Jurisica,et al.  Knowledge Discovery and Data Mining in Biomedical Informatics: State-of-the-Art and Future Challenges , 2014 .

[52]  Helwig Hauser,et al.  Parallel Sets: interactive exploration and visual analysis of categorical data , 2006, IEEE Transactions on Visualization and Computer Graphics.

[53]  Tamara Munzner,et al.  MizBee: A Multiscale Synteny Browser , 2009, IEEE Transactions on Visualization and Computer Graphics.

[54]  Matthew A. Hibbs,et al.  Visualization of omics data for systems biology , 2010, Nature Methods.

[55]  Jarke J. van Wijk,et al.  The value of visualization , 2005, VIS 05. IEEE Visualization, 2005..

[56]  Andreas Holzinger,et al.  On Knowledge Discovery and Interactive Intelligent Visualization of Biomedical Data - Challenges in Human-Computer Interaction & Biomedical Informatics , 2012, DATA.

[57]  Ivan Viola,et al.  Visual cavity analysis in molecular simulations , 2013, BMC Bioinformatics.

[58]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[59]  Daniel A. Keim,et al.  Visual Analytics: Definition, Process, and Challenges , 2008, Information Visualization.

[60]  John W. Tukey,et al.  Exploratory Data Analysis. , 1979 .

[61]  Andreas Holzinger,et al.  On Visual Analytics and Evaluation in Cell Physiology: A Case Study , 2013, CD-ARES.

[62]  Ben Shneiderman Inventing discovery tools: combining information visualization with data mining? , 2002, Inf. Vis..

[63]  Raphael Fuchs,et al.  Visual Human+Machine Learning , 2009, IEEE Transactions on Visualization and Computer Graphics.

[64]  Ben Shneiderman,et al.  The eyes have it: a task by data type taxonomy for information visualizations , 1996, Proceedings 1996 IEEE Symposium on Visual Languages.

[65]  Andreas Holzinger,et al.  Human-Computer Interaction and Knowledge Discovery (HCI-KDD): What Is the Benefit of Bringing Those Two Fields to Work Together? , 2013, CD-ARES.

[66]  Dieter Schmalstieg,et al.  enRoute: Dynamic path extraction from biological pathway maps for in-depth experimental data analysis , 2012, 2012 IEEE Symposium on Biological Data Visualization (BioVis).

[67]  Thomas Ertl,et al.  Visual Verification and Analysis of Cluster Detection for Molecular Dynamics , 2007, IEEE Transactions on Visualization and Computer Graphics.

[68]  Helwig Hauser,et al.  Visualization and Visual Analysis of Multifaceted Scientific Data: A Survey , 2013, IEEE Transactions on Visualization and Computer Graphics.

[69]  Boris G. Mirkin,et al.  Core Concepts in Data Analysis: Summarization, Correlation and Visualization , 2011, Undergraduate Topics in Computer Science.

[70]  Tobias Schreck,et al.  Visual Cluster Analysis of Trajectory Data with Interactive Kohonen Maps , 2008, 2008 IEEE Symposium on Visual Analytics Science and Technology.

[71]  Jarke J. van Wijk,et al.  BaobabView: Interactive construction and analysis of decision trees , 2011, 2011 IEEE Conference on Visual Analytics Science and Technology (VAST).

[72]  Ivica Letunic,et al.  Visualization of multiple alignments, phylogenies and gene family evolution , 2010, Nature Methods.

[73]  Andreas Kerren,et al.  Introduction to Human-Centered Visualization Environments , 2006, Human-Centered Visualization Environments.

[74]  Gerik Scheuermann,et al.  Brushing of Attribute Clouds for the Visualization of Multivariate Data , 2008, IEEE Transactions on Visualization and Computer Graphics.

[75]  Jacob Cohen,et al.  Applied multiple regression/correlation analysis for the behavioral sciences , 1979 .

[76]  Tamara Munzner,et al.  Steerable, Progressive Multidimensional Scaling , 2004, IEEE Symposium on Information Visualization.

[77]  Jörn Kohlhammer,et al.  Towards closing the analysis gap: Visual generation of decision supporting schemes from raw data , 2008, Comput. Graph. Forum.

[78]  Suzi Adams,et al.  Visual exploration of microbial populations , 2011, 2011 IEEE Symposium on Biological Data Visualization (BioVis)..

[79]  Matthew O. Ward,et al.  Interactive Data Visualization - Foundations, Techniques, and Applications , 2010 .

[80]  Klaus Mueller,et al.  TripAdvisor^{N-D}: A Tourism-Inspired High-Dimensional Space Exploration Framework with Overview and Detail , 2013, IEEE Transactions on Visualization and Computer Graphics.

[81]  Peter Filzmoser,et al.  Brushing Dimensions - A Dual Visual Analysis Model for High-Dimensional Data , 2011, IEEE Transactions on Visualization and Computer Graphics.

[82]  Hamish Carr,et al.  Topological Methods in Data Analysis and Visualization III, Theory, Algorithms, and Applications , 2011 .

[83]  Ben Shneiderman Inventing Discovery Tools: Combining Information Visualization with Data Mining1 , 2002 .

[84]  Igor Jurisica,et al.  Knowledge Discovery and Data Mining in Biomedical Informatics: The Future Is in Integrative, Interactive Machine Learning Solutions , 2014, Interactive Knowledge Discovery and Data Mining in Biomedical Informatics.

[85]  Bernd Hamann,et al.  Maximizing Adaptivity in Hierarchical Topological Models Using Cancellation Trees , 2009, Mathematical Foundations of Scientific Visualization, Computer Graphics, and Massive Data Exploration.

[86]  Kay Nieselt,et al.  Mayday-a microarray data analysis workbench , 2006, Bioinform..

[87]  Helwig Hauser,et al.  Integrating cluster formation and cluster evaluation in interactive visual analysis , 2011, SCC.

[88]  Bang Wong,et al.  Visualizing biological data—now and in the future , 2010, Nature Methods.

[89]  Matthew O. Ward,et al.  Value and Relation Display: Interactive Visual Exploration of Large Data Sets with Hundreds of Dimensions , 2007, IEEE Trans. Vis. Comput. Graph..

[90]  Bernhard Preim,et al.  Interactive Visual Analysis of Perfusion Data , 2007, IEEE Transactions on Visualization and Computer Graphics.

[91]  Igor Jurisica,et al.  Knowledge Discovery and interactive Data Mining in Bioinformatics - State-of-the-Art, future challenges and research directions , 2014, BMC Bioinformatics.

[92]  Matthew O. Ward,et al.  Interactive data visualization , 2010 .

[93]  VARUN CHANDOLA,et al.  Anomaly detection: A survey , 2009, CSUR.

[94]  Marie Loren Luong Topology-Based Methods in Visualization II , 2009, Mathematics and Visualization.

[95]  D. V. van Essen,et al.  A neurobiological model of visual attention and invariant pattern recognition based on dynamic routing of information , 1993, The Journal of neuroscience : the official journal of the Society for Neuroscience.

[96]  Matthew Berriman,et al.  Artemis: an integrated platform for visualization and analysis of high-throughput sequence-based experimental data , 2011, Bioinform..

[97]  Chaomei Chen,et al.  Top 10 Unsolved Information Visualization Problems , 2005, IEEE Computer Graphics and Applications.

[98]  Bernd Hamann,et al.  Mathematical Foundations of Scientific Visualization, Computer Graphics, and Massive Data Exploration , 2009, Mathematics and Visualization.

[99]  Ben Shneiderman,et al.  Interactively Exploring Hierarchical Clustering Results , 2003 .

[100]  Matthew O. Ward,et al.  Visual Hierarchical Dimension Reduction for Exploration of High Dimensional Datasets , 2003, VisSym.

[101]  Russ B. Altman,et al.  Bioinformatics challenges for personalized medicine , 2011, Bioinform..

[102]  R. Jordan Crouser,et al.  Online Submission ID: 200 An Affordance-Based Framework for Human Computation and Human-Computer Collaboration , 2022 .

[103]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[104]  Bang Wong,et al.  Pathline: A Tool For Comparative Functional Genomics , 2010, Comput. Graph. Forum.

[105]  Eser Kandogan,et al.  Just-in-time annotation of clusters, outliers, and trends in point-based data visualizations , 2012, 2012 IEEE Conference on Visual Analytics Science and Technology (VAST).

[106]  Daniel Weiskopf,et al.  Proceedings of the 12th Eurographics / IEEE - VGTC conference on Visualization , 2009 .

[107]  Gerik Scheuermann,et al.  Topology-based Methods in Visualization , 2007, Topology-based Methods in Visualization.

[108]  Arvid Lundervold,et al.  Representative Factor Generation for the Interactive Visual Analysis of High-Dimensional Data , 2012, IEEE Transactions on Visualization and Computer Graphics.

[109]  Leo Breiman,et al.  Classification and Regression Trees , 1984 .

[110]  Dino Pedreschi,et al.  Visually driven analysis of movement data by progressive clustering , 2008, Inf. Vis..

[111]  Chris North,et al.  Observation-level interaction with statistical models for visual analytics , 2011, 2011 IEEE Conference on Visual Analytics Science and Technology (VAST).

[112]  Wolfgang Berger,et al.  Eurographics/ Ieee-vgtc Symposium on Visualization 2010 Hypermoval: Interactive Visual Validation of Regression Models for Real-time Simulation , 2022 .

[113]  Damian Szklarczyk,et al.  STRING v9.1: protein-protein interaction networks, with increased coverage and integration , 2012, Nucleic Acids Res..

[114]  Daniel T. Larose,et al.  Discovering Knowledge in Data: An Introduction to Data Mining , 2005 .

[115]  David Haussler,et al.  The UCSC genome browser and associated tools , 2012, Briefings Bioinform..

[116]  James Davey,et al.  Guiding feature subset selection with an interactive visualization , 2011, 2011 IEEE Conference on Visual Analytics Science and Technology (VAST).

[117]  Chris North,et al.  Beyond Control Panels: Direct Manipulation for Visual Analytics , 2013, IEEE Computer Graphics and Applications.

[118]  Dieter Schmalstieg,et al.  Comparative Analysis of Multidimensional, Quantitative Data , 2010, IEEE Transactions on Visualization and Computer Graphics.

[119]  Denis Gracanin,et al.  Interactive Visual Steering - Rapid Visual Prototyping of a Common Rail Injection System , 2008, IEEE Transactions on Visualization and Computer Graphics.

[120]  Richard A. Johnson,et al.  Applied Multivariate Statistical Analysis , 1983 .

[121]  David S. Ebert,et al.  A correlative analysis process in a visual analytics environment , 2012, 2012 IEEE Conference on Visual Analytics Science and Technology (VAST).

[122]  Daniel A. Keim,et al.  Mastering the Information Age - Solving Problems with Visual Analytics , 2010 .

[123]  Herbert Edelsbrunner,et al.  Computational Topology - an Introduction , 2009 .