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DOI: 10.4230/DFU.Vol2.SciViz.2011.160

Salient Frame Detection for Molecular Dynamics Simulations

Authors: Youngmin Kim, Robert Patro, Cheuk Yiu Ip, Dianne P. O’Leary, and Andriy Anishkin

Published in: Dagstuhl Follow-Ups, Volume 2, Scientific Visualization: Interactions, Features, Metaphors (2011)

Abstract

Recent advances in sophisticated computational techniques have facilitated simulation of incrediblydetailed time-varying trajectories and in the process have generated vast quantities of simulation data. The current tools to analyze and comprehend large-scale time-varying data, however, lag far behind our ability to produce such simulation data. Saliency-based analysis can be applied to time-varying 3D datasets for the purpose of summarization, abstraction, and motion analysis. As the sizes of time-varying datasets continue to grow, it becomes more and more difficult to comprehend vast amounts of data and information in a short period of time. In this paper, we use eigenanalysis to generate orthogonal basis functions over sliding windows to characterize regions of unusual deviations and significant trends. Our results show that motion subspaces provide an effective technique for summarization of large molecular dynamics trajectories.

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Youngmin Kim, Robert Patro, Cheuk Yiu Ip, Dianne P. O’Leary, and Andriy Anishkin. Salient Frame Detection for Molecular Dynamics Simulations. In Scientific Visualization: Interactions, Features, Metaphors. Dagstuhl Follow-Ups, Volume 2, pp. 160-175, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2011)

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@InCollection{kim_et_al:DFU.Vol2.SciViz.2011.160,
  author =	{Kim, Youngmin and Patro, Robert and Yiu Ip, Cheuk and O’Leary, Dianne P. and Anishkin, Andriy},
  title =	{{Salient Frame Detection for Molecular Dynamics Simulations}},
  booktitle =	{Scientific Visualization: Interactions, Features, Metaphors},
  pages =	{160--175},
  series =	{Dagstuhl Follow-Ups},
  ISBN =	{978-3-939897-26-2},
  ISSN =	{1868-8977},
  year =	{2011},
  volume =	{2},
  editor =	{Hagen, Hans},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DFU.Vol2.SciViz.2011.160},
  URN =		{urn:nbn:de:0030-drops-32926},
  doi =		{10.4230/DFU.Vol2.SciViz.2011.160},
  annote =	{Keywords: Saliency based analysis, Molecular Dynamics, Simulation}
}

Document

DOI: 10.4230/DFU.SciViz.2010.321

Saliency Guided Summarization of Molecular Dynamics Simulations

Authors: Robert Patro, Cheuk Yiu Ip, and Amitabh Varshney

Published in: Dagstuhl Follow-Ups, Volume 1, Scientific Visualization: Advanced Concepts (2010)

Abstract

We present a novel method to measure saliency in molecular dynamics simulation data. This saliency measure is based on a multiscale center-surround mechanism, which is fast and efficient to compute. We explore the use of the saliency function to guide the selection of representative and anomalous timesteps for summarization of simulations. To this end, we also introduce a multiscale keyframe selection procedure which automatically provides keyframes representing the simulation at varying levels of coarseness. We compare our saliency guided keyframe approach against other methods, and show that it consistently selects superior keyframes as measured by their predictive power in reconstructing the simulation.

Cite as

Robert Patro, Cheuk Yiu Ip, and Amitabh Varshney. Saliency Guided Summarization of Molecular Dynamics Simulations. In Scientific Visualization: Advanced Concepts. Dagstuhl Follow-Ups, Volume 1, pp. 321-335, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)

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@InCollection{patro_et_al:DFU.SciViz.2010.321,
  author =	{Patro, Robert and Ip, Cheuk Yiu and Varshney, Amitabh},
  title =	{{Saliency Guided Summarization of Molecular Dynamics Simulations}},
  booktitle =	{Scientific Visualization: Advanced Concepts},
  pages =	{321--335},
  series =	{Dagstuhl Follow-Ups},
  ISBN =	{978-3-939897-19-4},
  ISSN =	{1868-8977},
  year =	{2010},
  volume =	{1},
  editor =	{Hagen, Hans},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DFU.SciViz.2010.321},
  URN =		{urn:nbn:de:0030-drops-27134},
  doi =		{10.4230/DFU.SciViz.2010.321},
  annote =	{Keywords: Molecuar Dynamics, Saliency, Simulation}
}

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Salient Frame Detection for Molecular Dynamics Simulations

Abstract

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Saliency Guided Summarization of Molecular Dynamics Simulations

Abstract

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