Interactive visual comparison of multiple trees

Abstract

Traditionally, the visual analysis of hierarchies, respectively, trees, is conducted by focusing on one given hierarchy. However, in many research areas multiple, differing hierarchies need to be analyzed simultaneously in a comparative way - in particular to highlight differences between them, which sometimes can be subtle. A prominent example is the analysis of so-called phylogenetic trees in biology, reflecting hierarchical evolutionary relationships among a set of organisms. Typically, the analysis considers multiple phylogenetic trees, either to account for statistical significance or for differences in derivation of such evolutionary hierarchies; for example, based on different input data, such as the 16S ribosomal RNA and protein sequences of highly conserved enzymes. The simultaneous analysis of a collection of such trees leads to more insight into the evolutionary process. We introduce a novel visual analytics approach for the comparison of multiple hierarchies focusing on both global and local structures. A new tree comparison score has been elaborated for the identification of interesting patterns. We developed a set of linked hierarchy views showing the results of automatic tree comparison on various levels of details. This combined approach offers detailed assessment of local and global tree similarities. The approach was developed in close cooperation with experts from the evolutionary biology domain. We apply it to a phylogenetic data set on bacterial ancestry, demonstrating its application benefit

Visualization System Requirements for Data Processing Pipeline Design and Optimization

“…Although rules of thumb exist for the parameter settings, the right parameter setting depends on the dataset at hand. Biologists wish to analyze the sensitivity of the output tree to the input parameters, datasets and algorithms that are used [29], [30]. They calculate the trees, which takes up to an hour per tree, and compare the tree structures to analyze: (1) parameter sensitivity, and (2) core structures within trees (i.e., evolutionarily stable subtrees).…”

“…Each colored cell indicates a requirement that is important for a given case study/paper, and an 'x' indicates that the requirement remains unmet by users' current tools. [25] req req req req req Chemical process models [26] x req req x Economic modelling [27] req req xx req req x req Aircraft engine design [28] req req x req req Phylogenetic trees [29,30] x req x x req req Molecular evolution [31,32] x x req x req x * Raidou et al [75] iCoCooN req req req * Ruppert et al [46] --x req x Luboshik et al [38] --x req req req Bruckner et al [10] --x req x req * Beham et al [43] Cupid req req xx Konyha et al [39] --x req x Pretorius et al [12] Paramorama req x req Afzal et al [36] RVF x req req x Bergner et al [13] ParaGlide xx req Torsney-Weir et al [33] Tuner x req x x * Padua et al [11] --x req x * Bögl et al [42] TiMoVA req req req x x req Spence et al [73] --req req Berger et al [9] --req x xx Piringer et al [40] HyperMoVal xx req req req Matkovic et al [17] --req x Coffey et al [34] --x x req Matkovic et al [50] --x Potter et al [49] Ensemble-Vis x req Booshehrian et al [19] Vismon req x req x Brecheisen et al [52] --x req x Unger et al [54] --req req req Amirkhanov et al [74] --x Marks et al [48] Design Galleries req x Waser et al [18] World Lines req x x * Martins et al [35] --x req x * Wu [53] --xx x Guo et al [41] --req…”

Facilitating Discourse Analysis with Interactive Visualization

“…A breadth of techniques have been proposed for the visual comparison of trees, that can be classified under three main categories: side-byside views [2,6,22], merged views [29,30] and animation [27]. For an exhaustive review see the survey by Graham et al [13].…”

“…Side-by-side views can leverage interaction through dynamic queries: for instance, TreeJuxtaposer [22] allows the user to interactively visualize similar subtree structures by highlighting a query pattern. A system particularly related to our work was developed by Bremm et al [2] for the comparison of phylogenic trees. In that work, several visualization techniques are combined as coordinated views, including a tabular view of the trees of interest and a similarity matrix view indicating similarity scores between the trees of the dataset.…”

“…its vice president for manufacturing resigned (2) ( 'the personnel changes were needed' 'to improve the efficiency of its manufacturing operation.'))) (Attribution [S][N]…”