A five-level design framework for bicluster visualizations

IEEE Transactions on Visualization and Computer Graphics

Volumn 20, Issue 12, 2014, Pages 1713-1722

  Sun, Maoyuan ^a   North, Chris ^a   Ramakrishnan, Naren ^a  

^a VIRGINIA POLYTECHNIC INSTITUTE AND STATE UNIVERSITY   (United States)

Author keywords

Biclusters; Coordinated relationships; Design framework; Interactive visual analytics

Indexed keywords

BICLUSTERS; COORDINATED RELATIONSHIPS; DESIGN FRAMEWORKS; LEVEL DESIGN; VISUAL ANALYTICS;

ALGORITHM; CLUSTER ANALYSIS; COMPUTER GRAPHICS; GENE EXPRESSION PROFILING; HUMAN; INFORMATION SCIENCE; PROCEDURES; THEORETICAL MODEL;

ALGORITHMS; CLUSTER ANALYSIS; COMPUTER GRAPHICS; GENE EXPRESSION PROFILING; HUMANS; INFORMATICS; MODELS, THEORETICAL;

EID: 84909629503     PISSN: 10772626     EISSN: None     Source Type: Journal    
DOI: 10.1109/TVCG.2014.2346665     Document Type: Article

References (93)

1. D. B. Allison, X. Cui, G. P. Page, and M. Sabripour. Microarray data analysis: from disarray to consolidation and consensus. Nature Reviews Genetics, 7(1):55-65, 2006.
2. J. Alsakran, Y. Zhao, and X. Zhao. Tile-based parallel coordinates and its application in financial visualization. IS&T/SPIE Electro Imaging, 2010.
3. G. Andrienko and N. Andrienko. Blending Aggregation and Selection: Adapting Parallel Coordinates for the Visualization of Large Datasets. The Cartographic Journal, 42(1):49-60, June 2005.
4. Anil K. Jain. Data clustering: 50 years beyond K-means. Pattern Recognition Letters, 31(8):651-666, June 2010.
5. M. H. Asyali, D. Colak, and O. Demirkaya. Gene expression profile classification: a review. Current Bioinformatics, 1(1):55-73, 2006.
6. S. Barkow, S. Bleuler, A. Prelic, P. Zimmermann, and E. Zitzler. BicAT: a biclustering analysis toolbox. Bioinformatics, 22(10):1282-1283, 2006.
7. V. Batagelj, F. J. Brandenburg, W. Didimo, G. Liotta, P. Palladino, and M. Patrignani. Visual Analysis of Large Graphs Using (X,Y)-Clustering and Hybrid Visualizations. Visualization and Computer Graphics, IEEE Transactions on, 17(11):1587-1598, 2011.
8. A. Beygelzimer, S. Kakade, and J. Langford. Cover trees for nearest neighbor. In ICML '06: Proceedings of the 23rd international conference on Machine learning. ACM, June 2006.
9. E. A. Bier, E. W. Ishak, and E. Chi. Entity workspace: an evidence file that aids memory, inference, and reading. In ISI'06: Proceedings of the 4th IEEE international conference on Intelligence and Security Informatics, pages 466-472, Berlin, Heidelberg, May 2006. Springer-Verlag.
10. 3 Data-Driven Documents. Visualization and Computer Graphics, IEEE Transactions on, 17(12):2301-2309, Dec. 2011.
11. N. Boukhelifa, W. Cancino, A. Bezerianos, and E. Lutton. Evolutionary visual exploration: evaluation with expert users. In Computer Graphics Forum, volume 32, pages 31-40. Wiley Online Library, 2013.
12. A. Brazma and J. Vilo. Gene expression data analysis. FEBS letters, 480(1):17-24, Aug. 2000.
13. R. Byrne and P. N. Johnson-Laird. Spatial reasoning. Journal of memory and language, 28(5):564-575, 1989.
14. W. Cancino, N. Boukhelifa, A. Bezerianos, and E. Lutton. Evolutionary visual exploration: experimental analysis of algorithm behaviour. experimental analysis of algorithm behaviour. ACM, New York, USA, 2013.
15. B. Carpenter. Phrasal Queries with LingPipe and Lucene: Ad Hoc Genomics Text Retrieval. TREC, 2004.
16. R. M. Chapman, J. W. McCrary, and J. A. Chapman. Brain responses related to semantic meaning. Brain and Language, 5(2):195-205, 1978.
17. K. O. Cheng, N. F. Law, W. C. Siu, and T. H. Lau. BiVisu: software tool for bicluster detection and visualization. Bioinformatics, 23(17):2342-2344, Sept. 2007.
18. Y. Cheng and G. M. Church. Biclustering of expression data. Ismb, 2000.
19. C. Collins, G. Penn, and S. Carpendale. Bubble Sets: Revealing Set Relations with Isocontours over Existing Visualizations. Visualization and Computer Graphics, IEEE Transactions on, 15(6):1009-1016, 2009.
20. L. F. Cranor. A framework for reasoning about the human in the loop. UPSEC, 8:1-15, 2008.
21. A. Dasgupta, M. Chen, and R. Kosara. Conceptualizing visual uncertainty in parallel coordinates. Computer Graphics Forum, 31:1015-1024, 2012.
22. M. C. F. de Oliveira and H. Levkowitz. From visual data exploration to visual data mining: a survey. Visualization and Computer Graphics, IEEE Transactions on, 9(3):378-394, 2003.
23. I. S. Dhillon. Co-clustering documents and words using bipartite spectral graph partitioning. In Proceedings of the seventh ACM SIGKDD, pages 269-274. ACM, 2001.
24. A. Endert, P. Fiaux, and C. North. Semantic interaction for visual text analytics. In CHI '12: Proceedings of the SIGCHI Conference on Human Factors in Computing Systems, pages 473-482, New York, USA, 2012.
25. A. Endert, C. Han, D. Maiti, L. House, S. Leman, and C. North. Observation-level interaction with statistical models for visual analytics. In Visual Analytics Science and Technology (VAST), 2011 IEEE Conference on, pages 121-130. IEEE, 2011.
26. T. D. Erickson and M. E. Mattson. From words to meaning: A semantic illusion. Jour of Verb Learning and Verb Behavior, 20(5):540-551, 1981.
27. S. J. Fernstad, J. Johansson, S. Adams, J. Shaw, and D. Taylor. Visual exploration of microbial populations. Biological Data Visualization (Bio-Vis), 2011 IEEE Symposium on, pages 127-134, 2011.
28. P. Fiaux, M. Sun, L. Bradel, C. North, N. Ramakrishnan, and A. Endert. Bixplorer: Visual Analytics with Biclusters. Computer, 46(8):90-94, 2013.
29. C. Fluit, M. Sabou, and F. Van Harmelen. Ontology-based information visualization: toward semantic web applications. In Visualizing the semantic web, pages 45-58. Springer, 2006.
30. T. M. J. Fruchterman and E. M. Reingold. Graph drawing by force-directed placement. Software: Practice and Experience, 21(11):1129-1164, 1991.
31. Y.-H. Fua, M. O. Ward, and E. A. Rundensteiner. Hierarchical parallel coordinates for exploration of large datasets. In Visualization '99. Proceedings, pages 43-508. IEEE, 1999.
32. M. Ghoniem, J. Fekete, and P. Castagliola. A Comparison of the Readability of Graphs Using Node-Link and Matrix-Based Representations. Information Visualization, 2004. INFOVIS 2004. IEEE Symposium on, pages 17-24, 2004.
33. M. Ghoniem, J. D. Fekete, and P. Castagliola. On the readability of graphs using node-link and matrix-based representations: a controlled experiment and statistical analysis. InfoVis, 4(2):114-135, 2005.
34. J. P. Gonc¸alves, S. C. Madeira, and A. L. Oliveira. BiGGEsTS: integrated environment for biclustering analysis of time series gene expression data. BMC Research Notes, 2(1):124, 2009.
35. C. Görg, Z. Liu, J. Kihm, J. Choo, H. Park, and J. Stasko. Combining Computational Analyses and Interactive Visualization for Document Exploration and Sensemaking in Jigsaw. Visualization and Computer Graphics, IEEE Transactions on, 19(10):1646-1663, 2013.
36. M. Graham and J. Kennedy. Using curves to enhance parallel coordinate visualisations. In Information Visualization, 2003. Proceedings. Seventh International Conference on, pages 10-16. IEEE Comput. Soc, 2003.
37. G. A. Grothaus, A. Mufti, and T. M. Murali. Automatic layout and visualization of biclusters. Algorithms for Molecular Biology, 2006.
38. J. A. Hartigan. Direct Clustering of a Data Matrix. Journal of the American Statistical Association, 67(337):123-129, Mar. 1972.
39. J. Heer and D. Boyd. Vizster: visualizing online social networks. INFOVIS 2005. IEEE Symposium on, pages 32-39, 2005.
40. J. Heinrich, R. Seifert, M. Burch, and D. Weiskopf. BiCluster viewer: a visualization tool for analyzing gene expression data. In ISVC'11: Proceedings of the 7th international conference on Advances in visual computing. Springer-Verlag, Sept. 2011.
41. N. Henry and J. Fekete. MatrixExplorer: a Dual-Representation System to Explore Social Networks. Visualization and Computer Graphics, IEEE Transactions on, 12(5):677-684, 2006.
42. N. Henry, J. Fekete, and M. J. McGuffin. NodeTrix: a Hybrid Visualization of Social Networks. Visualization and Computer Graphics, IEEE Transactions on, 13(6):1302-1309, 2007.
43. I. Herman, G. Melancon, and M. S. Marshall. Graph visualization and navigation in information visualization: A survey. Visualization and Computer Graphics, IEEE Transactions on, 6(1):24-43, 2000.
44. P. E. Hoffman and G. G. Grinstein. A survey of visualizations for high-dimensional data mining. Information visualization in data mining and knowledge discovery, pages 47-82, 2002.
45. D. Holten. Hierarchical Edge Bundles: Visualization of Adjacency Relations in Hierarchical Data. Visualization and Computer Graphics, IEEE Transactions on, 12(5):741-748, 2006.
46. M. S. Hossain, C. Andrews, N. Ramakrishnan, and C. North. Helping intelligence analysts make connections. In Scalable Integration of Analytics and Visualization, 2011.
47. F. Hughes and D. Schum. Discovery-proof-choice, the art and science of the process of intelligence analysis-preparing for the future of intelligence analysis. Washington, DC: Joint Military Intelligence College, 2003.
48. A. Inselberg and B. Dimsdale. Parallel coordinates: A tool for visualizing multi-dimensional geometry. In Proceedings of the 1st Conference on Visualization '90, pages 361-378. IEEE Computer Society Press, 1990.
49. D. H. Jeong, C. Ziemkiewicz, B. Fisher, W. Ribarsky, and R. Chang. iPCA: an interactive system for PCA-based visual analytics. In Euro-Vis'09: Proceedings of the 11th Eurographics / IEEE - VGTC conference on Visualization, pages 767-774. Eurographics Association, June 2009.
50. Y. Jin, T. M. Murali, and N. Ramakrishnan. Compositional mining of multirelational biological datasets. ACM Transactions on Knowledge Discovery from Data, 2(1):1-35, Mar. 2008.
51. J. Johansson, C. Forsell, M. Lind, and M. Cooper. Perceiving Patterns in Parallel Coordinates: Determining Thresholds for Identification of Relationships. Information Visualization, 7(2):152-162, June 2008.
52. S. Johansson and J. Johansson. Interactive Dimensionality Reduction Through User-defined Combinations of Quality Metrics. Visualization and Computer Graphics, IEEE Transactions on, 15(6):993-1000, 2009.
53. H. Kang, C. Plaisant, B. Lee, and B. B. Bederson. NetLens: Iterative Exploration of Content-Actor Network Data. Visual Analytics Science And Technology, 2006 IEEE Symposium On, pages 91-98, 2006.
54. M. Kapushesky, P. Kemmeren, A. C. Culhane, S. Durinck, J. Ihmels, C. Korner, M. Kull, A. Torrente, U. Sarkans, J. Vilo, and A. Brazma. Expression Profiler: next generation-an online platform for analysis of microarray data. Nucleic Acids Research, 32:W465-W470, July 2004.
55. R. Kosara, F. Bendix, and H. Hauser. Parallel Sets: interactive exploration and visual analysis of categorical data. Visualization and Computer Graphics, IEEE Transactions on, 12(4):558-568, 2006.
56. M. Krzywinski, J. Schein, I. Birol, J. Connors, R. Gascoyne, D. Horsman, S. J. Jones, and M. A. Marra. Circos: An information aesthetic for comparative genomics. Genome Research, 19(9):1639-1645, Sept. 2009.
57. J. Lamping, R. Rao, and P. Pirolli. A focus+context technique based on hyperbolic geometry for visualizing large hierarchies. ACM Press/Addison-Wesley Publishing Co., New York, USA, May 1995.
58. A. Lex, H. Schulz, M. Streit, C. Partl, and D. Schmalstieg. Vis-Bricks: Multiform Visualization of Large, Inhomogeneous Data. TVCG, 17(12):2291-2300, 2011.
59. A. Lex, M. Streit, C. Partl, K. Kashofer, and D. Schmalstieg. Comparative Analysis of Multidimensional, Quantitative Data. Visualization and Computer Graphics, IEEE Transactions on, 16(6):1027-1035, 2010.
60. J. Liu, J. Yang, and W. Wang. Biclustering in gene expression data by tendency. In Computational Systems Bioinformatics Conference, 2004. CSB 2004. Proceedings. 2004 IEEE, pages 182-193. IEEE, 2004.
61. S. C. Madeira and A. L. Oliveira. Biclustering algorithms for biological data analysis: a survey. Computational Biology and Bioinformatics, IEEE/ACM Transactions on, 1(1):24-45, 2004.
62. S. Mitra and H. Banka. Multi-objective evolutionary biclustering of gene expression data. Pattern Recognition, 39(12):2464-2477, Dec. 2006.
63. A. Noack. An energy model for visual graph clustering. Graph Drawing, 2004.
64. C. North and B. Shneiderman. Snap-together visualization: a user interface for coordinating visualizations via relational schemata. ACM, New York, New York, USA, May 2000.
65. M. Novotny and H. Hauser. Outlier-Preserving Focus+Context Visualization in Parallel Coordinates. Visualization and Computer Graphics, IEEE Transactions on, 12(5):893-900, 2006.
66. C. Partl, A. Lex, M. Streit, D. Kalkofen, K. Kashofer, and D. Schmalstieg. enRoute: Dynamic path extraction from biological pathway maps for indepth experimental data analysis. Biological Data Visualization (BioVis), 2012 IEEE Symposium on, pages 107-114, 2012.
67. G. A. Pavlopoulos, A.-L. Wegener, and R. Schn. A survey of visualization tools for biological network analysis. BioData Mining, 1(1):12, 2008.
68. P. Pirolli and S. Card. The sensemaking process and leverage points for analyst technology as identified through cognitive task analysis. Proceedings of International Conference on Intelligence Analysis, 2005.
69. A. Prelic, S. Bleuler, P. Zimmermann, A. Wille, P. Buhlmann, W. Gruissem, L. Hennig, L. Thiele, and E. Zitzler. A systematic comparison and evaluation of biclustering methods for gene expression data. Bioinformatics, 22(9):1122-1129, Apr. 2006.
70. J. Quackenbush. Computational analysis of microarray data. Nature reviews genetics, 2(6):418-427, 2001.
71. R. Rosenholtz, Y. Li, and L. Nakano. Measuring visual clutter. Journal of Vision, 7(2):17-17, Aug. 2007.
72. R. Santamaría, R. Therón, and L. Quintales. A Framework to Analyze Biclustering Results on Microarray Experiments. Intelligent Data Engineering and Automated Learning - IDEAL 2007, 4881:770-779, 2007.
73. R. Santamaría, R. Therón, and L. Quintales. A visual analytics approach for understanding biclustering results from microarray data. BMC Bioinformatics, 9(1):247, 2008.
74. R. Santamaria, R. Theron, and L. Quintales. BicOverlapper: A tool for bicluster visualization. Bioinformatics, 24(9):1212-1213, Apr. 2008.
75. R. Santamaria, R. Theron, and L. Quintales. BicOverlapper 2.0: visual analysis for gene expression. Bioinformatics, 2014.
76. J. Seo and B. Shneiderman. Interactively exploring hierarchical clustering results [gene identification]. Computer, 35(7):80-86, 2002.
77. B. Shneiderman. The eyes have it: a task by data type taxonomy for information visualizations. In Visual Languages, 1996. Proceedings., IEEE Symposium on, pages 336-343, 1996.
78. H. Siirtola and K.-J. Räihä. Interacting with parallel coordinates. Interacting with Computers, 18(6):1278-1309, Dec. 2006.
79. C. A. Steed, P. J. Fitzpatrick, T. J. Jankun-Kelly, A. N. Yancey, and J. E. Swan II. ARTICLE IN PRESS. Computers and Geosciences, 35(7):1529-1539, May 2009.
80. M. Sun, L. Bradel, C. L. North, and N. Ramakrishnan. The role of interactive biclusters in sensemaking. In Proceedings of the 32nd annual ACM CHI, pages 1559-1562, 2014.
81. A. Tanay, R. Sharan, and R. Shamir. Biclustering algorithms: A survey. Handbook of computational molecular biology, 2005.
82. J. J. Thomas and K. A. Cook. Illuminating the path: The research and development agenda for visual analytics. IEEE Comp Society Press, 2005.
83. T. Uno, T. Asai, Y. Uchida, and H. Arimura. LCM: An Efficient Algorithm for Enumerating Frequent Closed Item Sets. FIMI, 2003.
84. T. von Landesberger, A. Kuijper, T. Schreck, J. Kohlhammer, J. J. van Wijk, J. D. Fekete, and D. W. Fellner. Visual Analysis of Large Graphs: State-of-the-Art and Future Research Challenges. Computer Graphics Forum, 30(6):1719-1749, Apr. 2011.
85. M. Wattenberg. Visual exploration of multivariate graphs. In Proceedings of the SIGCHI, pages 811-819. ACM, 2006.
86. E. J. Wegman. Hyperdimensional Data Analysis Using Parallel Coordinates. Journal of the American Statistical Assoc, 85(411):664-675, 1990.
87. P. C. Wong, B. Hetzler, C. Posse, M. Whiting, S. Havre, N. Cramer, A. Shah, M. Singhal, A. Turner, and J. Thomas. IN-SPIRE InfoVis 2004 Contest Entry. INFOVIS 2004., pages 51-52, 2004.
88. H.-M. Wu, Y.-J. Tien, and C.-h. Chen. Computational Statistics and Data Analysis. Computational Stat and Data Analysis, 54(3):767-778, 2010.
89. M. J. Zaki and C. J. Hsiao. CHARM: An Efficient Algorithm for Closed Itemset Mining. SDM, pages 457-473, 2002.
90. J. Zhao, C. Collins, F. Chevalier, and R. Balakrishnan. Interactive Exploration of Implicit and Explicit Relations in Faceted Datasets. IEEE TVCG, 19(12):2080-2089, 2013.
91. C. V. Zhou, C. Leckie, and S. Karunasekera. A survey of coordinated attacks and collaborative intrusion detection. Computers & Security, 29(1):124-140, 2010.
92. H. Zhou, W. Cui, H. Qu, and et al. Splatting the Lines in Parallel Coordinates. Computer Graphics Forum, 28(3):759-766, 2009.
93. H. Zhou, X. Yuan, H. Qu, W. Cui, and B. Chen. Visual Clustering in Parallel Coordinates. Computer Graphics Forum, 27(3):1047-1054, 2008.