6 Search Results for "Ebert, David S."


Document
AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction

Authors: Adam Cicherski, Anna Lisiecka, and Norbert Dojer

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)


Abstract
The success of pangenome-based approaches to genomics analysis depends largely on the existence of efficient methods for constructing pangenome graphs that are applicable to large genome collections. In the current paper we present AlfaPang, a new pangenome graph building algorithm. AlfaPang is based on a novel alignment-free approach that allows to construct pangenome graphs using significantly less computational resources than state-of-the-art tools. The code of AlfaPang is freely available at https://github.com/AdamCicherski/AlfaPang.

Cite as

Adam Cicherski, Anna Lisiecka, and Norbert Dojer. AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 23:1-23:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)


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@InProceedings{cicherski_et_al:LIPIcs.WABI.2024.23,
  author =	{Cicherski, Adam and Lisiecka, Anna and Dojer, Norbert},
  title =	{{AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{23:1--23:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.23},
  URN =		{urn:nbn:de:0030-drops-206673},
  doi =		{10.4230/LIPIcs.WABI.2024.23},
  annote =	{Keywords: pangenome, variation graph, genome alignment, population genomics}
}
Document
Interaction with Information for Visual Reasoning (Dagstuhl Seminar 13352)

Authors: David S. Ebert, Brian D. Fisher, and Petra Isenberg

Published in: Dagstuhl Reports, Volume 3, Issue 8 (2013)


Abstract
From August 26--August 30, 2013 Seminar 13352 was held at Dagstuhl on the topic of "Interaction with Information for Visual Reasoning." The seminar brought together a group of cognitive scientists, psychologists, and computer scientists in the area of scientific visualization, information visualization, and visual analytics who were carefully selected for their theoretical and methodological capabilities and history of interdisciplinary collaboration. During the workshop seven discussion groups were formed during which the role of interaction for visualization was carefully reflected on. We discussed in particular the value, structure, and different types of interaction but also how to evaluate visualization and the idea of 'narrative' as applied to visual analytics. This report documents the program and short summaries of the discussion groups for the seminar.

Cite as

David S. Ebert, Brian D. Fisher, and Petra Isenberg. Interaction with Information for Visual Reasoning (Dagstuhl Seminar 13352). In Dagstuhl Reports, Volume 3, Issue 8, pp. 151-167, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2013)


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@Article{ebert_et_al:DagRep.3.8.151,
  author =	{Ebert, David S. and Fisher, Brian D. and Isenberg, Petra},
  title =	{{Interaction with Information for Visual Reasoning (Dagstuhl Seminar 13352)}},
  pages =	{151--167},
  journal =	{Dagstuhl Reports},
  ISSN =	{2192-5283},
  year =	{2013},
  volume =	{3},
  number =	{8},
  editor =	{Ebert, David S. and Fisher, Brian D. and Isenberg, Petra},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagRep.3.8.151},
  URN =		{urn:nbn:de:0030-drops-43463},
  doi =		{10.4230/DagRep.3.8.151},
  annote =	{Keywords: Interaction, visualization, visual analytics, cognitive science, psychology}
}
Document
Abstract Feature Space Representation for Volumetric Transfer Function Exploration

Authors: Ross Maciejewski, Yun Jang, David S. Ebert, and Kelly P. Gaither

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


Abstract
The application of n-dimensional transfer functions for feature segmentation has become increasingly popular in volume rendering. Recent work has focused on the utilization of higher order dimensional transfer functions incorporating spatial dimensions (x,y, and z) along with traditional feature space dimensions (value and value gradient). However, as the dimensionality increases, it becomes exceedingly difficult to abstract the transfer function into an intuitive and interactive workspace. In this work we focus on populating the traditional two-dimensional histogram with a set of derived metrics from the spatial (x, y and z) and feature space (value, value gradient, etc.) domain to create a set of abstract feature space transfer function domains. Current two-dimensional transfer function widgets typically consist of a two-dimensional histogram where each entry in the histogram represents the number of voxels that maps to that entry. In the case of an abstract transfer function design, the amount of spatial variance at that histogram coordinate is mapped instead, thereby relating additional information about the data abstraction in the projected space. Finally, a non-parametric kernel density estimation approach for feature space clustering is applied in the abstracted space, and the resultant transfer functions are discussed with respect to the space abstraction.

Cite as

Ross Maciejewski, Yun Jang, David S. Ebert, and Kelly P. Gaither. Abstract Feature Space Representation for Volumetric Transfer Function Exploration. In Scientific Visualization: Interactions, Features, Metaphors. Dagstuhl Follow-Ups, Volume 2, pp. 212-221, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2011)


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@InCollection{maciejewski_et_al:DFU.Vol2.SciViz.2011.212,
  author =	{Maciejewski, Ross and Jang, Yun and Ebert, David S. and Gaither, Kelly P.},
  title =	{{Abstract Feature Space Representation for Volumetric Transfer Function Exploration}},
  booktitle =	{Scientific Visualization: Interactions, Features, Metaphors},
  pages =	{212--221},
  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.2011.212},
  URN =		{urn:nbn:de:0030-drops-32955},
  doi =		{10.4230/DFU.Vol2.SciViz.2011.212},
  annote =	{Keywords: Volumetric Transfer Function, Abstract Feature Space}
}
Document
09251 Abstracts Collection – Scientific Visualization

Authors: David S. Ebert, Eduard Gröller, Hans Hagen, and Arie Kaufman

Published in: Dagstuhl Seminar Proceedings, Volume 9251, Scientific Visualization (2010)


Abstract
From 06-14-2009 to 06-19-2009, the Dagstuhl Seminar 09251 ``Scientific Visualization '' was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, over 50 international participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general.

Cite as

David S. Ebert, Eduard Gröller, Hans Hagen, and Arie Kaufman. 09251 Abstracts Collection – Scientific Visualization. In Scientific Visualization. Dagstuhl Seminar Proceedings, Volume 9251, pp. 1-36, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2010)


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@InProceedings{ebert_et_al:DagSemProc.09251.1,
  author =	{Ebert, David S. and Gr\"{o}ller, Eduard and Hagen, Hans and Kaufman, Arie},
  title =	{{09251 Abstracts Collection – Scientific Visualization}},
  booktitle =	{Scientific Visualization},
  pages =	{1--36},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2010},
  volume =	{9251},
  editor =	{David S. Ebert and Eduard Gr\"{o}ller and Hans Hagen and Arie Kaufman},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09251.1},
  URN =		{urn:nbn:de:0030-drops-27436},
  doi =		{10.4230/DagSemProc.09251.1},
  annote =	{Keywords: Scientific visualization, Data analysis, Data modeling, Segmentation, Knowledge extraction, Ubiquitous visualization, Categorical visualization, Intelligent/automatic visualization, Point-based/mesh-free visualization}
}
Document
07291 Abstracts Collection – Scientific Visualization

Authors: David S. Ebert, Hans Hagen, Kenneth I. Joy, and Daniel A. Keim

Published in: Dagstuhl Seminar Proceedings, Volume 7291, Scientific Visualization (2008)


Abstract
From 15.07. to 20.07.07, the Dagstuhl Seminar 07291 ``Scientific Visualization'' was held in the International Conference and Research Center (IBFI),Schloss Dagstuhl. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.

Cite as

David S. Ebert, Hans Hagen, Kenneth I. Joy, and Daniel A. Keim. 07291 Abstracts Collection – Scientific Visualization. In Scientific Visualization. Dagstuhl Seminar Proceedings, Volume 7291, pp. 1-18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)


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@InProceedings{ebert_et_al:DagSemProc.07291.1,
  author =	{Ebert, David S. and Hagen, Hans and Joy, Kenneth I. and Keim, Daniel A.},
  title =	{{07291 Abstracts Collection – Scientific Visualization}},
  booktitle =	{Scientific Visualization},
  pages =	{1--18},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{7291},
  editor =	{David S. Ebert and Hans Hagen and Kenneth I. Joy and Daniel A. Keim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.07291.1},
  URN =		{urn:nbn:de:0030-drops-14145},
  doi =		{10.4230/DagSemProc.07291.1},
  annote =	{Keywords: Markov chains, numerical methods, web information retrieval, performance evaluation, intrusion detection, aggregation-disaggregation methods, graph-oriented decomposition}
}
Document
07291 Summary – Scientific Visualization

Authors: David S. Ebert, Hans Hagen, Kenneth I. Joy, and Daniel A. Keim

Published in: Dagstuhl Seminar Proceedings, Volume 7291, Scientific Visualization (2008)


Abstract
Scientific visualization (SV) is concerned with the use of computer-generated images to aid the understanding, analysis and manipulation of data. Since its beginning in the early 90's, the techniques of SV have aided scientists, engineers, medical practitioners, and others in the study of a wide variety of data sets including, for example, high performance computing simulations, measured data from scanners (CAT, MR, confocal microscopy), internet traffic, and financial records. One of the important themes being nurtured under the aegis of Scientific Visualization is the utilization of the broad bandwidth of the human sensory system in steering and interpreting complex processes and simulations involving voluminous data sets across diverse scientific disciplines. Since vision dominates our sensory input, strong efforts have been made to bring the mathematical abstraction and modeling to our eyes through the mediation of computer graphics. This interplay between various application areas and their specific problem solving visualization techniques was emphasized in the proposed seminar.

Cite as

David S. Ebert, Hans Hagen, Kenneth I. Joy, and Daniel A. Keim. 07291 Summary – Scientific Visualization. In Scientific Visualization. Dagstuhl Seminar Proceedings, Volume 7291, pp. 1-2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)


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@InProceedings{ebert_et_al:DagSemProc.07291.2,
  author =	{Ebert, David S. and Hagen, Hans and Joy, Kenneth I. and Keim, Daniel A.},
  title =	{{07291 Summary – Scientific Visualization}},
  booktitle =	{Scientific Visualization},
  pages =	{1--2},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{7291},
  editor =	{David S. Ebert and Hans Hagen and Kenneth I. Joy and Daniel A. Keim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.07291.2},
  URN =		{urn:nbn:de:0030-drops-14132},
  doi =		{10.4230/DagSemProc.07291.2},
  annote =	{Keywords: Markov chains, numerical methods, web information retrieval, performance evaluation, intrusion detection, aggregation-disaggregation methods graph-oriented decomposition}
}
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