Gunther H. Weber

Staff Scientist & Adjunct Associate Professor
Deputy Group Lead
Data Analytics & Visualization Group
Data Science & Technology
Email: GHWeber@lbl.gov
Phone: +1-510-486-5871
Fax: +1-510-486-4300
One Cyclotron Road, MS 59R3103
Berkeley, California 94720 US

Biography

Gunther H. Weber received a Ph.D. in computer science, with a focus on computer graphics and visualization, from the University of Kaiserslautern, Germany in 2003. He is currently a Staff Scientist in the Computational Research Division at the Lawrence Berkeley National Laboratory (LBNL), where he serves as Deputy Group Lead of the Data Analysis and Visualization Group in the Data Science and Technology Department. Gunther Weber is an Adjunct Associate Professor of Computer Science at the University of California, Davis. His research interests include computer graphics, scientific visualization, data analysis with using topological methods, parallel and distributed computing for visualization and data analysis applications, hierarchical data representation methods, and bioinformatics. He has extensive experience in working with researchers from diverse science and engineering fields, including applied numerical computing, combustion simulation, gene expression, medicine, civil engineering, cosmology, climate and particle accelerator modeling. Dr. Weber has authored or co-authored over 80 publications, five of which won best paper awards. He has served as principal investigator (PI) or Co-PI on several Department of Energy (DOE) and National Science Foundation (NSF) projects. He is a reviewer for major funding agencies (DOE, NSF), conference proceedings and journals. Dr. Weber served as co-organizer, co-chair and program committee member of more than 40 internationally recognized conferences.

Publications

Conference Articles

  1. A. Ovsyannikov, M. Romanus, B. Van Straalen, G. H. Weber, and D. Trebotich, “Scientific Workflows at DataWarp-Speed: Accelerated Data-Intensive Science using NERSC’s Burst Buffer,” in Proceedings of the 1st Joint International Workshop on Parallel Data Storage & Data Intensive Scalable Computing Systems, 2016, pp. 1–6.
  2. H. A. Carr, G. H. Weber, C. M. Sewell, and J. P. Ahrens, “Parallel Peak Pruning for Scalable SMP Contour Tree Computation,” in Proceedings of the 6th IEEE Symposium on Large Data Analysis and Visualization (LDAV), 2016, pp. 75–84. Best paper award.
  3. G. H. Weber, H. Childs, and J. S. Meredith, “Efficient Parallel Extraction of Crack-free Isosurfaces from Adaptive Mesh Refinement (AMR) Data,” in Proceedings of IEEE Symposium on Large Data Analysis and Visualization (LDAV), 2012, pp. 31–38.
  4. A. R. Sanderson, B. Whitlock, O. Rübel, H. Childs, G. H. Weber, Prabhat, and K. Wu, “A System for Query Based Analysis and Visualization,” in Third International EuroVis Workshop on Visual Analytics EuroVA 2012, Vienna, Austria, 2012, pp. 25–29.
  5. S. Murugesan, K. Bouchard, E. Chang, M. Dougherty, B. Hamann, and G. H. Weber, “Hierarchical Spatio-temporal Visual Analysis of Cluster Evolution in Electrocorticography Data,” in Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, New York, NY, USA, 2016, pp. 630–639. Best paper award.
  6. U. Ayachit, A. Bauer, E. P. N. Duque, G. Eisenhauer, N. Ferrier, J. Gu, K. E. Jansen, B. Loring, Z. Lukić, S. Menon, D. Morozov, P. O’Leary, R. Ranjan, M. Rasquin, C. P. Stone, V. Vishwanath, G. H. Weber, B. Whitlock, M. Wolf, K. J. Wu, and E. W. Bethel, “Performance Analysis, Design Considerations, and Applications of Extreme-scale In Situ Infrastructures,” in SC ’16: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, 2016.
  7. W. Bhimji, D. Bard, M. Romanus, D. Paul, A. Ovsyannikov, B. Friesen, M. Bryson, J. Correa, G. K. Lockwood, V. Tsulaia, S. Byna, S. Farrell, D. Gursoy, C. Daley, V. Beckner, B. Van Straalen, D. Trebotich, C. Tull, G. H. Weber, N. J. Wright, K. Antypas, and Prabhat, “Accelerating Science with the NERSC Burst Buffer Early User Program,” in CUG2016 Proceedings, 2016. Best paper award, in press.
  8. G. H. Weber, H. Johansen, D. T. Graves, and T. J. Ligocki, “Simulating Urban Environments for Energy Analysis,” in Proceedings Visualization in Environmental Sciences (EnvirVis), 2014.
  9. G. H. Weber, H. Childs, and J. S. Meredith, “Recent Advances in VisIt: Parallel Crack-free Isosurface Extraction,” in Numerical Modeling of Space Plasma Flows: Astronum-2012 (Astronomical Society of the Pacific Conference Series), 2013.
  10. D. Morozov and G. H. Weber, “Distributed Merge Trees,” in Proceedings of the 18th ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (PPoPP’13), New York, NY, USA, 2013, pp. 93–102.
  11. K. Beketayev, G. H. Weber, D. Morozov, A. Abzhanov, and B. Hamann, “Geometry-Preserving Topological Landscapes,” in Proceedings of the Workshop at SIGGRAPH Asia 2012, New York, NY, USA, 2012, pp. 155–160.
  12. D. Demir, K. Beketayev, G. H. Weber, P.-T. Bremer, V. Pascucci, and B. Hamann, “Topology Exploration with Hierarchical Landscapes,” in Proceedings of the Workshop at SIGGRAPH Asia 2012, New York, NY, USA, 2012, pp. 147–154.

Journal Articles

  1. G. H. Weber, M. S. Bandstra, D. Chivers, H. H. Elgammal, V. Hendrix, J. Kua, J. Maltz, K. Muriki, Y. Ong, K. Song, M. Quinlan, L. Ramakrishnan, and B. J. Quiter, “Web-based Visual Data Exploration for Improved Radiological Source Detection,” Concurrency and Computation: Practice and Experience, vol. 29, no. 18, p. e4203, Sep. 2017.
  2. B. Friesen, A. Almgren, Z. Lukić, G. H. Weber, D. Morozov, V. Beckner, and M. Day, “In Situ and In-transit Analysis of Cosmological Simulations,” Computational Astrophysics and Cosmology, vol. 3, no. 4, pp. 1–18, Aug. 2016.
  3. S. Murugesan, K. Bouchard, J. A. Brown, B. Hamann, W. W. Seeley, A. Trujillo, and G. H. Weber, “Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity,” IEEE Transactions on Computational Biology and Bioinformatics, vol. 14, no. 4, pp. 805–818, Jul. 2017.
  4. K. Beketayev, D. Yeliussizov, D. Morozov, G. H. Weber, and B. Hamann, “Measuring the Error in Approximating the Sub-level Set Topology of Sampled Scalar Data,” International Journal of Computational Geometry & Applications, vol. 28, no. 1, pp. 57–77, Mar. 2018.
  5. S. Murugesan, K. Bouchard, J. Brown, D. Lurie, B. Hamann, and G. H. Weber, “Summarization and Difference Visualization of Dynamic Networks,” IEEE Transactions on Visualization and Computer Graphics, 2018. In preparation.
  6. T. Liebmann, G. H. Weber, and G. Scheuermann, “Hierarchical Correlation Clustering in Multiple 2D Scalar Fields,” Computer Graphics Forum (Special Issue, Proceedings Eurographics/IEEE Symposium on Visualization), vol. 37, no. 3, 2018.
  7. J. Lukasczyk, R. Maciejewski, G. H. Weber, C. Garth, and H. Leitte, “Nested Tracking Graphs,” Computer Graphics Forum (Special Issue, Proceedings Eurographics/IEEE Symposium on Visualization), vol. 36, no. 3, pp. 12–22, 2017. Best paper award.
  8. G. H. Weber, S. Carpendale, D. Ebert, B. Fisher, H. Hagen, B. Shneiderman, and A. Ynnerman, “Apply or Die: On the Role and Assessment of Application Papers in Visualization,” IEEE Computer Graphics & Applications, vol. 37, no. 3, pp. 96–104, 2017.
  9. S. Murugesan, K. Bouchard, E. Chang, M. Dougherty, B. Hamann, and G. H. Weber, “Multi-scale Visual Analysis of Time-varying Electrocorticography Data via Clustering of Brain Regions,” BMC Bioinformatics, vol. 18, no. Suppl 6, p. 236, 2017.
  10. P. Oesterling, C. Heine, G. H. Weber, and G. Scheuermann, “Visualizing nD Point Clouds as Topological Landscape Profiles to Guide Local Data Analysis,” IEEE Transactions on Visualization and Computer Graphics, vol. 19, no. 3, pp. 514–526, 2013.
  11. D. M. Ushizima, D. Morozov, G. H. Weber, A. G. C. Bianchi, J. A. Sethian, and E. W. Bethel, “Augmented Topological Descriptors of Pore Networks for Material Science,” IEEE Transactions on Visualization and Computer Graphics (Proceedings IEEE Vis 2012), vol. 18, no. 12, pp. 2041–2050, 2012.
  12. K. Beketayev, G. H. Weber, M. Haranczyk, P.-T. Bremer, M. Hlawitschka, and B. Hamann, “Topology-based Visualization of Transformation Pathways in Complex Chemical Systems,” Computer Graphics Forum (Special Issue, Proceedings Eurographics/IEEE Symposium on Visualization), vol. 30, no. 3, pp. 663–672, 2011.
  13. P.-T. Bremer, G. H. Weber, J. Tierny, V. Pascucci, M. S. Day, and J. B. Bell, “Interactive Exploration and Analysis of Large Scale Turbulent Combustion Using Topology-based Data Segmentation,” IEEE Transactions on Visualization and Computer Graphics, vol. 17, no. 9, pp. 1307–1324, 2011.
  14. H. Childs, D. Pugmire, S. Ahern, B. Whitlock, M. Howison, Prabhat, G. H. Weber, and E. W. Bethel, “Extreme Scaling of Production Visualization Software on Diverse Architectures,” IEEE Computer Graphics and Applications, vol. 30, no. 3, pp. 22–31, 2010.
  15. O. Rübel, G. H. Weber, M.-Y. Huang, E. W. Bethel, M. D. Biggin, C. C. Fowlkes, C. L. Hendriks, S. V. E. Keränen, M. B. Eisen, D. W. Knowles, J. Malik, H. Hagen, and B. Hamann, “Integrating Data Clustering and Visualization for the Analysis of 3D Gene Expression Data,” IEEE Transactions on Computational Biology and Bioinformatics, vol. 7, no. 1, pp. 64–79, 2010.
  16. P.-T. Bremer, G. H. Weber, V. Pascucci, M. S. Day, and J. B. Bell, “Analyzing and Tracking Burning Structures in Lean Premixed Hydrogen Flames,” IEEE Transactions on Visualization and Computer Graphics, vol. 16, no. 2, pp. 248–260, 2010.
  17. O. Rübel, C. G. R. Geddes, E. Cormier-Michel, K. Wu, Prabhat, G. H. Weber, D. M. Ushizima, P. Messmer, H. Hagen, B. Hamann, and E. W. Bethel, “Automatic beam path analysis of laser wakefield particle acceleration data,” Computational Science & Discovery, vol. 2, no. 1, p. 015005, 2009.
  18. G. H. Weber, O. Rübel, M.-Y. Huang, A. DePace, C. C. Fowlkes, S. V. E. Keränen, C. L. Luengo Hendriks, H. Hagen, D. W. Knowles, J. Malik, M. D. Biggin, and B. Hamann, “Visual exploration of three-dimensional gene expression using physical views and linked abstract views,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, no. 2, pp. 296–309, 2009.
  19. S. E. Dillard, V. Natarajan, G. H. Weber, V. Pascucci, and B. Hamann, “Topology-guided tessellation of quadratic elements,” International Journal of Computational Geometry & Applications, vol. 19, no. 2, pp. 195–211, 2009.
  20. C. C. Fowlkes, C. L. Luengo Hendriks, S. V. E. Keränen, G. H. Weber, O. Rübel, M.-Y. Huang, S. Chatoor, A. H. DePace, L. Simirenko, C. Henriquez, A. Beaton, R. Weiszmann, S. Celniker, B. Hamann, D. W. Knowles, M. D. Biggin, M. B. Eisen, and J. Malik, “A Quantitative Spatiotemporal Atlas of Gene Expression in the \textslDrosophila Blastoderm,” Cell, vol. 133, no. 2, pp. 364–374, 2008.
  21. G. H. Weber, P.-T. Bremer, and V. Pascucci, “Topological Landscapes: A Terrain Metaphor for Scientific Data,” IEEE Transactions on Visualization and Computer Graphics (Special Issue: Proceedings of IEEE Visualization 2007), vol. 13, no. 6, pp. 1416–1423, 2007.
  22. O. G. Staadt, V. Natarjan, G. H. Weber, D. F. Wiley, and B. Hamann, “Interactive Processing and Visualization of Image Data for Biomedical and Life Science Applications,” BMC Cell Biology, vol. 8, no. Suppl 1, p. S10, 2007.
  23. G. H. Weber, S. E. Dillard, H. Carr, V. Pascucci, and B. Hamann, “Topology-Controlled Volume Rendering,” IEEE Transactions on Visualization and Computer Graphics, vol. 13, no. 2, pp. 330–341, 2007.
  24. S. Gu, I. Anderson, V. Kunin, M. Cipriano, S. Minovitsky, G. H. Weber, N. Amenta, B. Hamann, and I. Dubchak, “TreeQ-VISTA: An Interactive Tree Visualization Tool with Functional Annotation Query Capabilities,” Bioinformatics, vol. 23, no. 6, pp. 764–766, 2007.
  25. C. L. Luengo Hendriks, S. V. E. Keränen, C. C. Fowlkes, L. Simirenko, G. H. Weber, A. H. DePace, C. Henriquez, D. W. Kaszuba, B. Hamann, M. B. Eisen, J. Malik, D. Sudar, M. D. Biggin, and D. W. Knowles, “Three-dimensional Morphology and Gene Expression in the \textslDrosophila Blastoderm at Cellular Resolution I: Data Acquisition Pipeline,” Genome Biology, vol. 7, no. 12, p. R123, 2006.

Book Chapters

  1. P. Oesterling, C. Heine, G. H. Weber, D. Morozov, and G. Scheuermann, “Computing and Visualizing Time-Varying Merge Trees for High-Dimensional Data,” in Topological Methods in Data Analysis and Visualization IV: Theory, Algorithms, and Applications, H. Carr, C. Garth, and T. Weinkauf, Eds. Springer International Publishing, 2017, pp. 87–101. Best paper award.
  2. H. A. Carr, J. Tierney, and G. H. Weber, “Pathological and Test Cases For Reeb Analysis,” in Topological Methods in Data Analysis and Visualization V: Theory, Algorithms, and Applications, H. Carr, I. Fujishiro, F. Sadlo, and S. Takahashi, Eds. Springer International Publishing, 2018. In review.
  3. P. Oesterling, C. Heine, G. H. Weber, and G. Scheuermann, “A Topology-Based Approach to Visualize the Thematic Composition of Document Collections,” in Text Mining, C. Biemann and A. Mehler, Eds. Springer International Publishing, 2014, pp. 63–85.
  4. K. Beketayev, D. Yeliussizov, D. Morozov, G. H. Weber, and B. Hamann, “Measuring the Distance Between Merge Trees,” in Topological Methods in Data Analysis and Visualization III: Theory, Algorithms, and Applications, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Springer-Verlag, 2014, pp. 151–166.
  5. D. Morozov and G. H. Weber, “Distributed Contour Trees,” in Topological Methods in Data Analysis and Visualization III: Theory, Algorithms, and Applications, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Springer-Verlag, 2014, pp. 89–102.
  6. G. H. Weber and H. Hauser, “Interactive Visual Exploration and Analysis,” in Scientific Visualization: Uncertainty, Multifield, Bio-Medical and Scalable Visualization, C. D. Hansen, M. Chen, C. R. Johnson, A. E. Kaufman, and H. Hagen, Eds. Springer-Verlag, 2014, pp. 161–174.
  7. H. Childs, E. Brugger, B. Whitlock, J. Meredith, S. Ahern, D. Pugmire, K. Biagas, M. Miller, C. Harrison, G. H. Weber, H. Krishnan, T. Fogal, A. Sanderson, C. Garth, E. W. Bethel, D. Camp, O. Rübel, M. Durant, J. M. Favre, and P. Navratil, “VisIt: An End-User Tool for Visualizing and Analyzing Very Large Data,” in High Performance Visualization: Enabling Extreme-Scale Scientific Insight, E. W. Bethel, H. Childs, and C. Hansen, Eds. Boca Raton, FL: CRC Press, 2012, pp. 357–371.
  8. H. Childs, D. Pugmire, S. Ahern, B. Whitlock, M. Howison, Prabhat, G. H. Weber, and E. W. Bethel, “Visualization at Extreme-Scale Concurrency,” in High Performance Visualization: Enabling Extreme-Scale Scientific Insight, E. W. Bethel, H. Childs, and C. Hansen, Eds. Boca Raton, FL: CRC Press, 2012, pp. 291–306.
  9. G. H. Weber, P.-T. Bremer, and V. Pascucci, “ Topological Cacti: Visualizing Contour-based Statistics,” in Topological Methods in Data Analysis and Visualization II: Theory, Algorithms, and Applications, R. Peikert, H. Hauser, H. Carr, and R. Fuchs, Eds. Heidelberg, Germany: Springer-Verlag, 2012, pp. 63–76.
  10. O. Rübel, S. V. E. Keränen, M. D. Biggin, D. W. Knowles, G. H. Weber, H. Hagen, B. Hamann, and E. W. Bethel, “Linking Advanced Visualization and MATLAB for the Analysis of 3D Gene Expression Data,” in Mathematical Methods for Visualization in Medicine and Life Sciences II, L. Linsen, H. Hagen, B. Hamann, and H.-C. Hege, Eds. Heidelberg, Germany: Springer-Verlag, 2012, pp. 267–286.
  11. G. H. Weber, P.-T. Bremer, M. S. Day, J. B. Bell, and V. Pascucci, “Feature Tracking Using Reeb Graphs,” in Topological Methods in Data Analysis and Visualization: Theory, Algorithms, and Applications, V. Pascucci, X. Tricoche, H. Hagen, and J. Tierny, Eds. Heidelberg, Germany: Springer-Verlag, 2011, pp. 241–253.

Technical Reports

  1. E. W. Bethel, D. Camp, H. Childs, M. Howison, H. Krishnan, B. Loring, J. Meyer, Prabhat, O. Rübel, D. Ushizima, and G. Weber, “Towards Exascale: High Performance Visualization and Analytics – Project Status Report,” Lawrence Berkeley National Laboratory, Berkeley, CA, USA, 94720, LBNL-5767E, Apr. 2012. Status report for DOE Exascale Research Conference in Portland, OR.
  2. G. H. Weber and P.-T. Bremer, “In-situ Analysis: Challenges and Opportunities,” Lawrence Berkeley National Laboratory, Berkeley, CA, USA, 94720, LBNL-5692E, Apr. 2012. Position paper for DOE Exascale Research Conference in Portland, OR.
  3. G. H. Weber, K. Beketayev, P.-T. Bremer, B. Hamann, M. Haranczyk, M. Hlawitschka, and V. Pascucci, “Comprehensible Presentation of Topological Information,” Lawrence Berkeley National Laboratory, Berkeley, CA, USA, 94720, LBNL-5693E, Apr. 2012. Status report for DOE Exascale Research Conference in Portland, OR.
  4. B. MacCarthy, H. Carr, and G. H. Weber, “Topological Galleries: A High Level User Interface for Topology Controlled Volume Rendering,” Lawerence Berkeley National Laboratory, Berkeley, California, U.S.A., LBNL-5019E, 2011.
  5. O. Kreylos, G. H. Weber, E. W. Bethel, J. M. Shalf, B. Hamann, and K. I. Joy, “Remote Interactive Direct Volume Rendering of AMR Data,” Lawerence Berkeley National Laboratory, Berkeley, California, U.S.A., LBNL-49954, 2006.