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Smoothness preserving layout for dynamic labels by hybrid optimization

ABSTRACT: Stable label movement and smooth label trajectory are critical for effective information understanding. Sudden label changes cannot be avoided by whatever forced directed methods due to the unreliability of resultant force or global optimization methods due to the complex trade-off on the different aspects. To solve this problem, we proposed a hybrid optimization method by taking advantages of the merits of both approaches. We first detect the spatial-temporal intersection regions from whole trajectories of the features, and initialize the layout by optimization in decreasing order by the number of the involved features. The label movements between the spatial-temporal intersection regions are determined by force directed methods. To cope with some features with high speed relative to neighbors, we introduced a force from future, called temporal force, so that the labels of related features can elude ahead of time and retain smooth movements. We also proposed a strategy by optimizing the label layout to predict the trajectories of features so that such global optimization method can be applied to streaming data.

Electronic Supplementary Material

Supplementary material is available in the online version of this article at 10.1007/s41095-021-0231-y.

SUBMITTER: He Y

PROVIDER: S-EPMC8549603 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundRNA visualization software tools have traditionally presented a static visualization of RNA molecules with limited ability for users to interact with the resulting image once it is complete. Only a few tools allowed for dynamic structures. One such tool is jViz.RNA. Currently, jViz.RNA employs a unique method for the creation of the RNA molecule layout by mapping the RNA nucleotides into vertexes in a graph, which we call the detailed graph, and then utilizes a Newtonian mechanics inspired system of forces to calculate a layout for the RNA molecule. The work presented here focuses on improvements to jViz.RNA that allow the drawing of RNA secondary structures according to common drawing conventions, as well as dramatic run-time performance improvements. This is done first by presenting an alternative method for mapping the RNA molecule into a graph, which we call the compressed graph, and then employing advanced numerical integration methods for the compressed graph representation.ResultsComparing the compressed graph and detailed graph implementations, we find that the compressed graph produces results more consistent with RNA drawing conventions. However, we also find that employing the compressed graph method requires a more sophisticated initial layout to produce visualizations that would require minimal user interference. Comparing the two numerical integration methods demonstrates the higher stability of the Backward Euler method, and its resulting ability to handle much larger time steps, a high priority feature for any software which entails user interaction.ConclusionThe work in this manuscript presents the preferred use of compressed graphs to detailed ones, as well as the advantages of employing the Backward Euler method over the Forward Euler method. These improvements produce more stable as well as visually aesthetic representations of the RNA secondary structures. The results presented demonstrate that both the compressed graph representation, as well as the Backward Euler integrator, greatly enhance the run-time performance and usability. The newest iteration of jViz.RNA is available at https://jviz.cs.sfu.ca/download/download.html .

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Smoothness preserving layout for dynamic labels by hybrid optimization

Electronic Supplementary Material

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