Publications

Jordan A. Welsman, Gunther H. Weber, Oluwamayowa O. Amusat, Anna Giannakou, Lavanya Ramakrishnan, "Enhancing Electron Microscopy Image Classification Using Data Augmentation", SC24-W: Workshops of the International Conference for High Performance Computing, Networking, Storage and Analysis, IEEE, November 17, 2024, 64-71, doi: 10.1109/SCW63240.2024.00016

Á Sánchez-Villar, Z Bai, N Bertelli, EW Bethel, J Hillairet, T Perciano, S Shiraiwa, GM Wallace, JC Wright, "Real-time capable modeling of ICRF heating on NSTX and WEST via machine learning approaches", Nuclear Fusion, August 12, 2024, 64:9, doi: 10.1088/1741-4326/ad645d

Zhe Bai, Abdelilah Essiari, Talita Perciano, Kristofer E Bouchard, "AutoCT: Automated CT registration, segmentation, and quantification", Software X, February 28, 2024, 26, doi: 10.1016/j.softx.2024.101673

Jan Balewski, Mercy G Amankwah, Roel Van Beeumen, E Wes Bethel, Talita Perciano, Daan Camps, "Quantum-parallel vectorized data encodings and computations on trapped-ion and transmon QPUs", Journal, February 10, 2024, 14, doi: https://doi.org/10.1038/s41598-024-53720-x

E Wes Bethel, Mercy G Amankwah, Jan Balewski, Roel Van Beeumen, Daan Camps, Daniel Huang, Talita Perciano, "Quantum computing and visualization: A disruptive technological change ahead", Journal, November 6, 2023, 43, doi: https://doi.org/10.1109/MCG.2023.3316932

GM Wallace, Z Bai, N Bertelli, EW Bethel, T Perciano, S Shiraiwa, JC Wright, "Towards Fast, Accurate Predictions of RF Simulations via Data-driven Modeling: Forward and Lateral Models", Conference, AIP Publishing, August 1, 2023, 2984, doi: https://doi.org/10.1063/5.0162422

Li Zhou, Chao Yang, Weiguo Gao, Talita Perciano, Karen M Davies, Nicholas K Sauter, "A machine learning pipeline for membrane segmentation of cryo-electron tomograms", Journal of Computational Science, January 30, 2023, 66:101904, doi: 10.1016/j.jocs.2022.101904 Get rights and content Under a Creative Commons license

Gregory Wallace, Zhe Bai, Robbie Sadre, Talita Perciano, Nicola Bertelli, Syun'ichi Shiraiwa, Wes Bethel, John Wright, "Towards fast and accurate predictions of radio frequency power deposition and current profile via data-driven modelling: applications to lower hybrid current drive", Journal of Plasma Physics, August 18, 2022, 88:4, doi: 10.1017/S0022377822000708

M. G. Amankwah, D. Camps, E. W. Bethel, R. Van Beeumen, T. Perciano, "Quantum pixel representations and compression for N-dimensional images", Nature Scientific Reports, May 11, 2022, 12:7712, doi: 10.1038/s41598-022-11024-y

S. Zhang, R. Sadre, B. A. Legg, H. Pyles, T. Perciano, E. W. Bethel, D. Baker, O. Rübel, J. J. D. Yoreo, "Rotational dynamics and transition mechanisms of surface-adsorbed proteins", Proceedings of the National Academy of Sciences, April 11, 2022, 119:e202024211, doi: 10.1073/pnas.2020242119

M. Avaylon, R. Sadre, Z. Bai, T. Perciano, "Adaptable Deep Learning and Probabilistic Graphical Model System for Semantic Segmentation", Advances in Artificial Intelligence and Machine Learnin, March 31, 2022, 2:288--302, doi: 10.54364/AAIML.2022.1119

E. Wes Bethel, Burlen Loring, Utkarsh Ayachit, P. N. Duque, Nicola Ferrier, Joseph Insley, Junmin Gu, Kress, Patrick O’Leary, Dave Pugmire, Silvio Rizzi, Thompson, Will Usher, Gunther H. Weber, Brad Whitlock, Wolf, Kesheng Wu, "Proximity Portability and In Transit, M-to-N Data Partitioning and Movement in SENSEI", In Situ Visualization for Computational Science, ( 2022) doi: 10.1007/978-3-030-81627-8_20

E. Wes Bethel, Burlen Loring, Utkarsh Ayatchit, David Camp, P. N. Duque, Nicola Ferrier, Joseph Insley, Junmin Gu, Kress, Patrick O’Leary, David Pugmire, Silvio Rizzi, Thompson, Gunther H. Weber, Brad Whitlock, Matthew Wolf, Kesheng Wu, "The SENSEI Generic In Situ Interface: Tool and Processing Portability at Scale", In Situ Visualization for Computational Science, ( 2022) doi: 10.1007/978-3-030-81627-8_13

Sugeerth Murugesan, Mariam Kiran, Bernd Hamann, Gunther H. Weber, "Netostat: Analyzing Dynamic Flow Patterns in High-Speed Networks", Cluster Computing, 2022, doi: 10.1007/s10586-022-03543-0

C Varadharajan, AP Appling, B Arora, DS Christianson, VC Hendrix, V Kumar, AR Lima, J Müller, S Oliver, M Ombadi, T Perciano, JM Sadler, H Weierbach, JD Willard, Z Xu, J Zwart, "Can machine learning accelerate process understanding and decision-relevant predictions of river water quality?", Hydrological Processes, January 1, 2022, 36, doi: 10.1002/hyp.14565

V. Dumont, C. Garner, A. Trivedi, C. Jones, V. Ganapati, J. Mueller, T. Perciano, M. Kiran, and M. Day, "HYPPO: A Surrogate-Based Multi-Level Parallelism Tool for Hyperparameter Optimization", 2021 IEEE/ACM Workshop on Machine Learning in High Performance Computing Environments (MLHPC), November 15, 2021,

E. W. Bethel, C. Heinemann, and T. Perciano, "Performance Tradeoffs in Shared-memory Platform Portable Implementations of a Stencil Kernel", Eurographics Symposium on Parallel Graphics and Visualization, June 14, 2021,

Hamish A. Carr, Gunther H. Weber, Christopher M. Sewell, Oliver R\ ubel, Patricia Fasel, James P. Ahrens, "Scalable Contour Tree Computation by Data Parallel Peak Pruning", Transactions on Visualization and Computer Graphics, 2021, 27:2437--2454, doi: 10.1109/TVCG.2019.2948616

Hamish Carr, Oliver Rübel, Gunther H. Weber, James Ahrens, "Optimization and Augmentation for Data Parallel Contour Trees", IEEE Transactions on Visualization and Computer Graphics, 2021, doi: 10.1109/TVCG.2021.3064385

Robbie Sadre, Colin Ophus, Anstasiia Butko, Gunther H Weber, "Deep Learning Segmentation of Complex Features in Atomic-Resolution Phase Contrast Transmission Electron Microscopy Images", Microscopy and Microanalysis, 2021, doi: 10.1017/S1431927621000167

Jan-Tobias Sohns, Gunther H. Weber, Christoph Garth, "Distributed Task-Parallel Topology-Controlled Volume Rendering", Topological Methods in Data Analysis and Visualization VI: Theory, Algorithms, and Applications, (Springer International Publishing: 2021) Pages: 55-69 doi: 10.1007/978-3-030-83500-2_4

Li Zhou, Chao Yang, Weiguo Gao, Talita Perciano, Karen M. Davies, Nicholas K. Sauter, "Subcellular structure segmentation from cryo-electron tomograms via machine learning", PLOS Journal of Computational Biology, April 2, 2020, submitte, doi: doi: https://doi.org/10.1101/2020.04.09.034025

Stefano Marchesini, Anuradha Trivedi, Pablo Enfedaque, Talita Perciano, Dilworth Parkinson, "Sparse Matrix-Based HPC Tomography", Computational Science -- ICCS 2020, Cham, Springer International Publishing, 2020, 248--261, doi: 10.1007/978-3-030-50371-0_18

E. Wes Bethel, David Camp, Talita Perciano, Colleen Heinemann, "Performance Analysis of Traditional and Data-Parallel Primitive Implementations of Visualization and Analysis Kernels", Berkeley, CA, USA, 94720, 2020,

H. Childs, S. Ahern, J. Ahrens, A. C. Bauer, J. Bennett, E. W. Bethel, P.-T. Bremer, E. Brugger, J. Cottam, M. Dorier, S. Dutta, J. Favre, T. Fogal, S. Frey, C. Garth, B. Geveci, W. F. Godoy, C. D. Hansen, C. Harrison, B. Hentschel, J. Insley, C. Johnson, S. Klasky, A. Knoll, J. Kress, M. Larsen, J. Lofstead, K.-L. Ma, P. Malakar, J. Meredith, K. Moreland, P. Navratil, P. O Leary, M. Parashar, V. Pascucci, J. Patchett, T. Peterka, S. Petruzza, N. Podhorszki, D. Pugmire, M. Rasquin, S. Rizzi, D. H. Rogers, S. Sane, F. Sauer, R. Sisneros, H.-W. Shen, W. Usher, R. Vickery, V. Vishwanath, I. Wald, R. Wang, G. H. Weber, B. Whitlock, M. Wolf, H. Yu, S. B. Ziegler, "A Terminology for In Situ Visualization and Analysis Systems", International Journal of High Performance Computing Applications, 2020, 34:676--691, doi: 10.1177/1094342020935991

Petar Hristov, Gunther H. Weber, Hamish A. Carr, Oliver R\ ubel, James P. Ahrens, "Data Parallel Hypersweeps for In Situ Topological Analysis", Proceedings of the 10th IEEE Symposium on Large Data Analysis and Visualization (LDAV), 2020, 12--21, doi: 10.1109/LDAV51489.2020.00008

Jonas Lukasczyk, Christoph Garth, Gunther H. Weber, Tim Biedert, Ross Maciejewski, Heike Leitte, "Dynamic Nested Tracking Graphs", IEEE Transactions on Visualization and Computer Graphics (Proceedings IEEE VIS 2019), 2020, 26:249--258, doi: 10.1109/TVCG.2019.2934368

Sugeerth Murugesan, Kristofer Bouchard, Jesse Brown, Mariam Kiran, Dan Lurie, Bernd Hamann, Gunther H. Weber, "State-based Network Similarity Visualization", Information Visualization, 2020, 19:96--113, doi: 10.1177/1473871619882019

Anna-Pia Lohfink, Florian Wetzels, Jonas Lukasczyk, Gunther H. Weber, Christoph Garth, "Fuzzy Contour Trees: Alignment and Joint Layout of Multiple Contour Trees", Computer Graphics Forum (Special Issue, Proceedings Eurographics/IEEE Symposium on Visualization), 2020, 39:343--355, doi: 10.1111/cgf.13985

Hamish A. Carr, Julien Tierney, Gunther H. Weber, "Pathological and Test Cases For Reeb Analysis", Topological Methods in Data Analysis and Visualization V: Theory, Algorithms, and Applications", (Springer International Publishing: 2020) Pages: 103--120 doi: 10.1007/978-3-030-43036-8_7

H Chang, J J Donatelli, P Enfedaque, G Freychet, M Haranczyk, A Hexemer, Z Hu, O Jain, H Krishnan, D Kumar, X Li, L Lin, M MacNeil, S Marchesini, X Mo, M Noack, K Pande, R Pandolfi, D Parkinson, D M Pelt, T Perciano, D A Shapiro, D Ushizima, C Yang, P H Zwart, J A Sethian, "Building Mathematics, Algorithms, and Software for Experimental Facilities", Handbook on Big Data and Machine Learning in the Physical Sciences, ( 2020) Pages: 189--240 doi: 10.1142/9789811204579_0012

Talita Perciano, Colleen Heinemann, David Camp, Brenton Lessley, E Wes Bethel, "Shared-Memory Parallel Probabilistic Graphical Modeling Optimization: Comparison of Threads, OpenMP, and Data-Parallel Primitives", High Performance Computing, Cham, Springer International Publishing, 2020, 127--145, doi: 10.1007/978-3-030-50743-5_7

Donghe Kang, Oliver Rübel, Suren Byna, Spyros Blanas, "Comparison of Array Management Library Performance - A Neuroscience Use Case", SC19 Poster, November 20, 2019,

Babak Behzad, Suren Byna, Prabhat, and Marc Snir, "Optimizing I/O Performance of HPC Applications with Autotuning", ACM Transactions on Parallel Computing (TOPC), February 28, 2019,

Oliver Rübel, Andrew Tritt, Benjamin Dichter, Thomas Braun, Nicholas Cain, Nathan Clack, Thomas J. Davidson, Max Dougherty, Jean-Christophe Fillion-Robin, Nile Graddis, Michael Grauer, Justin T. Kiggins, Lawrence Niu, Doruk Ozturk, William Schroeder, Ivan Soltesz, Friedrich T. Sommer, Karel Svoboda, Lydia Ng, Loren M. Frank, Kristofer Bouchard, "NWB:N 2.0: An Accessible Data Standard for Neurophysiology", bioRxiv, January 17, 2019, doi: https://doi.org/10.1101/523035

Junmin Gu, Burlen Loring, Kesheng Wu, E Wes Bethel, "HDF5 as a vehicle for in transit data movement", Proceedings of the Workshop on In Situ Infrastructures for Enabling Extreme-Scale Analysis and Visualization, 2019, 39--43,

O. Erbilgin, O. Rübel, K. B. Louie, M. Trinh, M. de Raad, T. Wildish, D. W. Udwary, C. A. Hoover,, "MAGI: A Bayesian-like method for metabolite, annotation, and gene integration", bioRxiv, December 19, 2018, doi: 10.1101/204362

R. Van Beeumen, O. Marques, E.G. Ng, C. Yang, Z. Bai, L. Ge, O. Kononenko, Z. Li, C.-K. Ng, L. Xiao, "Computing resonant modes of accelerator cavities by solving nonlinear eigenvalue problems via rational approximation", Journal of Computational Physics, 2018, 374:1031-1043, doi: 10.1016/j.jcp.2018.08.017

T. Ke, A. S. Brewster, S. X. Yu, D. Ushizima, C. Yang, N. K. Sauter, "A convolutional neural network-based screening tool for X-ray serial crystallography", JOURNAL OF SYNCHROTRON RADIATION, April 24, 2018, 25:665-670, doi: 10.1107/S1600577518004873

Haoyuan Xing, Sofoklis Floratos, Spyros Blanas, Suren Byna, Prabhat, Kesheng Wu, and Paul Brown,, "ArrayBridge: Interweaving declarative array processing with imperative high-performance computing", 34th IEEE International Conference on Data Engineering (ICDE) 2018, April 17, 2018,

K. E. Bouchard, J.B. Aimone, M. Chun, T. Dean, M. Denker, M. Diesmann, D. Donofrio, L.M. Frank, N. Kasthuri, C. Koch, O. Rübel, H. Simon, F. T. Sommer, Prabhat, "International Neuroscience Initiatives Through the Lens of High-Performance Computing", IEEE Computer, April 12, 2018, 51(4):50-59, doi: doi 10.1109/MC.2018.2141039

O. Rübel, B. P. Bowen, "BASTet: Shareable and reproducible analysis and visualization of mass spectrometry imaging data via OpenMSI", IEEE Transactions on Visualization and Computer Graphics, January 12, 2018, 24,no. 1, doi: 10.1109/TVCG.2017.2744479

B Loring, A Myers, D Camp, EW Bethel, "Python-based in situ analysis and visualization", Proceedings of the Workshop on In Situ Infrastructures for Enabling Extreme-Scale Analysis and Visualization - ISAV 18, ACM Press, 2018, doi: 10.1145/3281464.3281465

B Lessley, T Perciano, C Heinemann, D Camp, H Childs, EW Bethel, "DPP-PMRF: Rethinking Optimization for a Probabilistic Graphical Model Using Data-Parallel Primitives", The 8th IEEE Symposium on Large Data Analysis and Visualization - LDAV 2018, 2018,

C Heinemann, T Perciano, D Ushizima, EW Bethel, "Distributed memory parallel Markov random fields using graph partitioning", Proceedings - 2017 IEEE International Conference on Big Data, Big Data 2017, 2018, 2018-Jan:3332--3341, doi: 10.1109/BigData.2017.8258318

Dáithí A Stone, Mark D Risser, Oliver M Angélil, Michael F Wehner, Shreyas Cholia, Noel Keen, Harinarayan Krishnan, Travis A O Brien, William D Collins, "A basis set for exploration of sensitivity to prescribed ocean conditions for estimating human contributions to extreme weather in CAM5. 1-1degree", Weather and climate extremes, 2018, 19:10--19,

S Swaid, M Maat, H Krishnan, D Ghoshal, L Ramakrishnan, "Usability heuristic evaluation of scientific data analysis and visualization tools", Advances in Intelligent Systems and Computing, 2018, 607:471--482, doi: 10.1007/978-3-319-60492-3_45

P Enfedaque, H Chang, H Krishnan, S Marchesini, "GPU-based implementation of ptycho-ADMM for high performance x-ray imaging", Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2018, 10860 LN:540--553, doi: 10.1007/978-3-319-93698-7_41

RJ Pandolfi, DB Allan, E Arenholz, L Barroso-Luque, SI Campbell, TA Caswell, A Blair, F De Carlo, S Fackler, AP Fournier, G Freychet, M Fukuto, D Gürsoy, Z Jiang, H Krishnan, D Kumar, RJ Kline, R Li, C Liman, S Marchesini, A Mehta, AT N Diaye, DY Parkinson, H Parks, LA Pellouchoud, T Perciano, F Ren, S Sahoo, J Strzalka, D Sunday, CJ Tassone, D Ushizima, S Venkatakrishnan, KG Yager, P Zwart, JA Sethian, A Hexemer, "Xi-cam: a versatile interface for data visualization and analysis", Journal of Synchrotron Radiation, 2018, 25:1261--1270, doi: 10.1107/S1600577518005787

C Li, C Michel, L Seland Graff, I Bethke, G Zappa, TJ Bracegirdle, E Fischer, BJ Harvey, T Iversen, MP King, H Krishnan, L Lierhammer, D Mitchell, J Scinocca, H Shiogama, DA Stone, JJ Wettstein, Midlatitude atmospheric circulation responses under 1.5 and 2.0g°C warming and implications for regional impacts, Earth System Dynamics, Pages: 359--382 2018, doi: 10.5194/esd-9-359-2018

M Wehner, D Stone, D Mitchell, H Shiogama, E Fischer, LS Graff, VV Kharin, L Lierhammer, B Sanderson, H Krishnan, Changes in extremely hot days under stabilized 1.5 and 2.0 °c global warming scenarios as simulated by the HAPPI multi-model ensemble, Earth System Dynamics, Pages: 299--311 2018, doi: 10.5194/esd-9-299-2018

MF Wehner, KA Reed, B Loring, D Stone, H Krishnan, "Changes in tropical cyclones under stabilized 1.5 and 2.0°C global warming scenarios as simulated by the Community Atmospheric Model under the HAPPI protocols", Earth System Dynamics, 2018, 9:187--195, doi: 10.5194/esd-9-187-2018

JJ Billings, AR Bennett, J Deyton, K Gammeltoft, J Graham, D Gorin, H Krishnan, M Li, AJ McCaskey, T Patterson, R Smith, GR Watson, A Wojtowicz, The eclipse integrated computational environment, SoftwareX, Pages: 234--244 2018, doi: 10.1016/j.softx.2018.07.004

M Wehner, D Stone, H Shiogama, P Wolski, A Ciavarella, N Christidis, H Krishnan, Early 21st century anthropogenic changes in extremely hot days as simulated by the C20C+ detection and attribution multi-model ensemble, Weather and Climate Extremes, Pages: 1--8 2018, doi: 10.1016/j.wace.2018.03.001

DA Stone, MD Risser, OM Angélil, MF Wehner, S Cholia, N Keen, H Krishnan, TA O Brien, WD Collins, A basis set for exploration of sensitivity to prescribed ocean conditions for estimating human contributions to extreme weather in CAM5.1-1degree, Weather and Climate Extremes, Pages: 10--19 2018, doi: 10.1016/j.wace.2017.12.003

YS Yu, M Farmand, C Kim, Y Liu, CP Grey, FC Strobridge, T Tyliszczak, R Celestre, P Denes, J Joseph, H Krishnan, FRNC Maia, ALD Kilcoyne, S Marchesini, TPC Leite, T Warwick, H Padmore, J Cabana, DA Shapiro, Three-dimensional localization of nanoscale battery reactions using soft X-ray tomography, Nature Communications, 2018, doi: 10.1038/s41467-018-03401-x

DA Shapiro, R Celestre, B Enders, J Joseph, H Krishnan, MA Marcus, K Nowrouzi, H Padmore, J Park, A Warwick, Y-S Yu, The COSMIC Imaging Beamline at the Advanced Light Source: a new facility for spectro-microscopy of nano-materials, Microscopy and Microanalysis, Pages: 8--11 2018, doi: 10.1017/s1431927618012485

B Enders, K Nowrouzi, H Krishnan, S Marchesini, J Park, Y-S Yu, DA Shapiro, Dataflow at the COSMIC Beamline - Stream Processing and Supercomputing, Microscopy and Microanalysis, Pages: 58--59 2018, doi: 10.1017/s1431927618012710

GP Rodrigo, M Henderson, GH Weber, C Ophus, K Antypas, L Ramakrishnan, "ScienceSearch: Enabling Search through Automatic Metadata Generation", 2018 IEEE 14th International Conference on e-Science (e-Science), IEEE, 2018, doi: 10.1109/escience.2018.00025

Tom Liebmann, Gunther H. Weber, Gerik Scheuermann, "Hierarchical Correlation Clustering in Multiple 2D Scalar Fields", Computer Graphics Forum (Special Issue, Proceedings Symposium on Visualization), 2018, 37, doi: 10.1111/cgf.13396

K Beketayev, D Yeliussizov, D Morozov, GH Weber, B Hamann, "Measuring the Error in Approximating the Sub-Level Set Topology of Sampled Scalar Data", International Journal of Computational Geometry and Applications, 2018, 28:57--77, doi: 10.1142/S0218195918500036

Gunther H. Weber, Colin Ophus, Lavanya Ramakrishnan, "Automated Labeling of Electron Microscopy Images Using Deep Learning", Proc. IEEE/ACM Machine Learning in HPC Environments (MLHPC), 2018, 26--36, doi: 10.1109/MLHPC.2018.8638633

Sugeerth Murugesan, Kristofer Bouchard, Jesse A. Brown, Bernd Hamann, William W. Seeley, Andrew Trujillo, Gunther H. Weber, "Brain Modulyzer: Interactive Visual Analysis of Functional Brain Connectivity", IEEE Transactions on Computational Biology and Bioinformatics, 2017, 14(4):805-818, LBNL 1005732, doi: 10.1109/TCBB.2016.2564970

Sugeerth Murugesan, Kristofer Bouchard, Edward Chang, Dougherty, Bernd Hamann, Gunther H. Weber, "Multi-scale Visual Analysis of Time-varying Electrocorticography Data Clustering of Brain Regions", BMC Bioinformatics, 2017, 18:236, doi: 10.1186/s12859-017-1633-9

Jonas Lukasczyk, Ross Maciejewski, Gunther H. Weber, Garth, Heike Leitte, "Nested Tracking Graphs", Computer Graphics Forum (Special Issue, Proceedings Symposium on Visualization), 2017, 36 (3):12--22, doi: 10.1111/cgf.13164

M. de Raad, T. de Rond, O. Rübel, J. D. Keasling, T. R. Northen, B. P. Bowen, "OpenMSI Arrayed Analysis Toolkit: Analyzing Spatially Defined Samples Using Mass Spectrometry Imaging", ACS Analytical Chemistry, May 3, 2017, doi: 10.1021/acs.analchem.6b05004

Gunther H. Weber, Sheelagh Carpendale, David Ebert, Brian Fisher Hans Hagen, Ben Shneiderman, Anders Ynnerman, "Apply or Die: On the Role and Assessment of Application Papers in", IEEE Computer Graphics \& Applications, 2017, 37 (3):96--104, doi: 10.1109/MCG.2017.51

Stone, D. A., H. Krishnan, R. Lance, S. Sippel, and M. F. Wehner, "The First and Second Hackathons of the International CLIVAR C20C+ Detection and Attribution Project", CLIVAR Exchanges, 2017,

Download File: StoneDA-KrishnanH-etalii-2017.pdf (pdf: 636 KB)

Timmermans, B., D. Stone, M. Wehner, and H. Krishnan, "Impact of tropical cyclones on modeled wind-wave climate", Geophysical Research Letters, 2017, 44:1393-1401, doi: 10.1002/2016GL071681

E. Wes Bethel, In Situ Processing Overview and Relevance to the HPC Community, SIAM Conference on Computational Science and Engineering, MS74: In Situ Methods and Infrastructures: Faster Insight Through Smarter Computing, 2017,

U Ayachit, B Whitlock, M Wolf, B Loring, B Geveci, D Lonie, EW Bethel, "The SENSEI generic in situ interface", Proceedings of ISAV 2016: 2nd Workshop on In Situ Infrastructures for Enabling Extreme-Scale Analysis and Visualization - Held in conjunction with SC 2016: The International Conference for High Performance Computing, Networking, Storage and Analysis, 2017, 40--44, doi: 10.1109/ISAV.2016.13

B Lessley, T Perciano, M Mathai, H Childs, EW Bethel, "Maximal clique enumeration with data-parallel primitives", 2017 IEEE 7th Symposium on Large Data Analysis and Visualization, LDAV 2017, 2017, 2017-Dec:16--25, doi: 10.1109/LDAV.2017.8231847

T Perciano, D Ushizima, H Krishnan, D Parkinson, N Larson, DM Pelt, W Bethel, F Zok, J Sethian, "Insight into 3D micro-CT data: Exploring segmentation algorithms through performance metrics", Journal of Synchrotron Radiation, 2017, 24:1065--1077, doi: 10.1107/S1600577517010955

E Bethel, zorder-lib: Library API for Z-Order Memory Layout:, 2017,

EW Bethel, Towards a data-centric research and development roadmap for large-scale science user facilities, Proceedings - 13th IEEE International Conference on eScience, eScience 2017, Pages: 462--464 2017, doi: 10.1109/eScience.2017.72

O Angélil, D Stone, M Wehner, CJ Paciorek, H Krishnan, W Collins, "An independent assessment of anthropogenic attribution statements for recent extreme temperature and rainfall events", Journal of Climate, 2017, 30:5--16, doi: 10.1175/JCLI-D-16-0077.1

Benedikt J Daurer, Hari Krishnan, Talita Perciano, Filipe RNC Maia, David A Shapiro, James A Sethian, Stefano Marchesini, "Nanosurveyor: a framework for real-time data processing", Advanced structural and chemical imaging, 2017, 3:7,

T Perciano, D Ushizima, H Krishnan, D Parkinson, J Sethian, "FibriPy: A software environment for fiber analysis from 3D micro-computed tomography data", Advanced Materials - TechConnect Briefs 2017, 2017, 1:25--28,

DY Parkinson, DM Pelt, T Perciano, D Ushizima, H Krishnan, HS Barnard, AA MacDowell, J Sethian, "Machine learning for micro-tomography", Proceedings of SPIE - The International Society for Optical Engineering, 2017, 10391, doi: 10.1117/12.2274731

B Timmermans, D Stone, M Wehner, H Krishnan, Impact of tropical cyclones on modeled extreme wind-wave climate, Geophysical Research Letters, Pages: 1393--1401 2017, doi: 10.1002/2016GL071681

BJ Daurer, H Krishnan, T Perciano, FRNC Maia, DA Shapiro, JA Sethian, S Marchesini, Nanosurveyor: a framework for real-time data processing., Advanced structural and chemical imaging, Pages: 7 2017, doi: 10.1186/s40679-017-0039-0

M Farmand, R Celestre, P Denes, ALD Kilcoyne, S Marchesini, H Padmore, T Tyliszczak, T Warwick, X Shi, J Lee, YS Yu, J Cabana, J Joseph, H Krishnan, T Perciano, FRNC Maia, DA Shapiro, "Near-edge X-ray refraction fine structure microscopy", Applied Physics Letters, 2017, 110, doi: 10.1063/1.4975377

P Oesterling, C Heine, GH Weber, D Morozov, G Scheuermann, "Computing and visualizing time-varying merge trees for high-dimensional data", Mathematics and Visualization, ( 2017) Pages: 87--101 doi: 10.1007/978-3-319-44684-4_5

GH Weber, MS Bandstra, DH Chivers, HH Elgammal, V Hendrix, J Kua, JS Maltz, K Muriki, Y Ong, K Song, MJ Quinlan, L Ramakrishnan, BJ Quiter, "Web-based visual data exploration for improved radiological source detection", Concurrency Computation, 2017, 29, doi: 10.1002/cpe.4203

M. Wehner, D. Stone, H. Krishnan, K. AchutaRao, F. Castillo, "The deadly combination of heat and humidity in India and Pakistan in summer 201", Bulletin of the American Meteorological Society, 2016, 97:S81-S86, doi: 10.1175/BAMS-D-16-0145.2

Andrew C. Bauer, Kenneth E. Jansen, E. Wes Bethel, Utkarsh Ayachit, Michel Rasquin, Benjamin Matthews, Steve Jordan, "In Situ Analysis and Visualization at Scale with PHASTA and ParaView Catalyst on Mira and Theta", SC16 Scientific Visualization Showcase, 2016,

O. Rübel, M.Dougherty, Prabhat, P. Denes, D. Conant, E. F. Chang, and K. Bouchard, "Methods for Specifying Scientic Data Standards and Modeling Relationships with Applications to Neuroscience," Frontiers in Neuroinformatics", Frontiers in Neuroinformatics, November 4, 2016, 10, doi: 10.3389/fninf.2016.00048

K. E. Bouchard, J, B. Aimone, M. Chun, T. Dean, M. Denker, M. Diesmann, D. D. Donofrio, L. M. Frank, N. Kasthuri, C. Koch, O. Rübel, H. D. Simon, F. T. Sommer, Prabhat, "High-Performance Computing in Neuroscience for Data-Driven Discovery, Integration, and Dissemination", Neuron, November 2, 2016, 92(3):628-631, doi: http://dx.doi.org/10.1016/j.neuron. 2016.10.035

E. Wes Bethel, Martin Greenwald, Kerstin Kleese Dam, Manish Parashar, Stefan M. Wild, H. Steven Wiley, "2016 IEEE 12th International Conference on e-Science", 2016 IEEE 12th International Conference on e-Science, Baltimore, MD, USA, 2016, 213--222,

Hoa Nguyen, D\ aith\ i Stone, E. Wes Bethel, "Statistical Projections for Multi-dimensional Visual Data Exploration", 6th IEEE Symposium on Large Data Analysis and Visualization, 2016,

moderator E. Wes Bethel (organizer, Hank Childs, Ken Moreland, Dave Pugmire, Matt Larsen, Matthieu Dorier, In Situ Efforts and Challenges in Large Data Analysis and Visualization, IEEE Symposium on Large Data Analysis and Visualization (LDAV), 2016,

Brian Friesen, Ann Almgren, Zarija Lukić, Gunther Weber, Dmitriy Morozov, Vincent Beckner, Marcus Day, "In situ and in-transit analysis of cosmological simulations", Computational Astrophysics and Cosmology, 2016, 3 (4):1-18,

Md. Mostofa Ali Patwary, Nadathur Rajagopalan Satish, Narayanan Sundaram, Jialin Liu, Peter Sadowski, Evan Racah, Suren Byna, Craig Tull, Wahid Bhimji, Prabhat, and Pradeep Dubey,, "PANDA: Extreme Scale Parallel K-Nearest Neighbor on Distributed Architectures", 30th IEEE International Parallel & Distributed Processing Symposium (IPDPS) 2016, Chicago, May 23, 2016,

Wahid Bhimji, Debbie Bard, Melissa Romanus, David Paul, Andrey Ovsyannikov, Brian Friesen, Matt Bryson, Joaquin Correa, Glenn K. Lockwood, Vakho Tsulaia, Suren Byna, Steve Farrell, Doga Gursoy, Chris Daley, Vince Beckner, Brian Van Straalen, Nicholas Wright, Katie Antypas, Prabhat,, "Accelerating Science with the NERSC Burst Buffer Early User Program", Cray User Group (CUG) 2016, May 10, 2016,

Harinarayan Krishnan, Burlen Loring, Suren Byna, Michael F. Wehner, Travis A. O'Brien, Prabhat, Chris Paciorek, and Daithi Stone, "Enabling End-to-End Climate Science Workflows in High Performance Computing Environments", The AMS (American Meteorological Society) 96th Annual Meeting, January 6, 2016,

Burlen Loring, Suren Byna, Prabhat, Junmin Gu, Hari Krishnan, Michael Wehner, and Oliver Ruebel, "TECA an Extreme Event Detection and Climate Analysis Package for High Performance Computing", The AMS (American Meteorological Society) 96th Annual Meeting, January 6, 2016,

T Perciano, DM Ushizima, EW Bethel, YD Mizrahi, D Parkinson, JA Sethian, "Reduced-complexity image segmentation under parallel Markov Random Field formulation using graph partitioning", Proceedings - International Conference on Image Processing, ICIP, 2016, 2016-Aug:1259--1263, doi: 10.1109/ICIP.2016.7532560

Utkarsh Ayachit, Andrew Bauer, Earl PN Duque, Greg Eisenhauer, Nicola Ferrier, Junmin Gu, Kenneth E Jansen, Burlen Loring, Zarija Lukic, Suresh Menon, others, "Performance analysis, design considerations, and applications of extreme-scale in situ infrastructures", SC 16: Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis, 2016, 921--932, LBNL 1007264,

O Rübel, B Loring, JL Vay, DP Grote, R Lehe, S Bulanov, H Vincenti, EW Bethel, "WarpIV: In Situ Visualization and Analysis of Ion Accelerator Simulations", IEEE Computer Graphics and Applications, 2016, 36:22--35, doi: 10.1109/MCG.2016.62

DM Ushizima, HA Bale, EW Bethel, P Ercius, BA Helms, H Krishnan, LT Grinberg, M Haranczyk, AA Macdowell, K Odziomek, DY Parkinson, T Perciano, RO Ritchie, C Yang, "IDEAL: Images Across Domains, Experiments, Algorithms and Learning", JOM, 2016, 68:2963--2972, doi: 10.1007/s11837-016-2098-4

SV Venkatakrishnan, KA Mohan, K Beattie, J Correa, E Dart, JR Deslippe, A Hexemer, H Krishnan, AA MacDowell, S Marchesini, SJ Patton, T Perciano, JA Sethian, R Stromsness, BL Tierney, CE Tull, D Ushizima, DY Parkinson, "Making advanced scientific algorithms and big scientific data management more accessible", IS and T International Symposium on Electronic Imaging Science and Technology, 2016, doi: 10.2352/ISSN.2470-1173.2016.19.COIMG-155

DY Parkinson, K Beattie, X Chen, J Correa, E Dart, BJ Daurer, JR Deslippe, A Hexemer, H Krishnan, AA Macdowell, FRNC Maia, S Marchesini, HA Padmore, SJ Patton, T Perciano, JA Sethian, D Shapiro, R Stromsness, N Tamura, BL Tierney, CE Tull, D Ushizima, "Real-time data-intensive computing", AIP Conference Proceedings, 2016, 1741, doi: 10.1063/1.4952921

S Marchesini, H Krishnan, BJ Daurer, DA Shapiro, T Perciano, JA Sethian, FRNC Maia, "SHARP: A distributed GPU-based ptychographic solver", Journal of Applied Crystallography, 2016, 49:1245--1252, doi: 10.1107/S1600576716008074

M Wehner, D Stone, H Krishnan, K Achutarao, F Castillo, 16. The deadly combination of heat and humidity in India and Pakistan in summer 2015, Bulletin of the American Meteorological Society, Pages: S81--S86 2016, doi: 10.1175/BAMS-D-16-0145.1

TA O Brien, WD Collins, K Kashinath, O Rübel, S Byna, J Gu, H Krishnan, PA Ullrich, Resolution dependence of precipitation statistical fidelity in hindcast simulations, Journal of Advances in Modeling Earth Systems, Pages: 976--990 2016, doi: 10.1002/2016MS000671

Deborah A Agarwal, Boris Faybishenko, Vicky L Freedman, Harinarayan Krishnan, Gary Kushner, Carina Lansing, Ellen Porter, Alexandru Romosan, Arie Shoshani, Haruko Wainwright, others, "A science data gateway for environmental management", Concurrency and Computation: Practice and Experience, 2016, 28:1994--2004,

M Alegro, E Amaro, B Loring, H Heinsen, E Alho, L Zollei, D Ushizima, LT Grinberg, "Multimodal Whole Brain Registration: MRI and High Resolution Histology", IEEE Computer Society Conference on Computer Vision and Pattern Recognition Workshops, 2016, 634--642, doi: 10.1109/CVPRW.2016.85

Andrey Ovsyannikov, Melissa Romanus, Brian Van Straalen, Gunther H. Weber, David Trebotich, "Scientific Workflows at DataWarp-Speed: Accelerated Data-Intensive Science using NERSC s Burst Buffer", Proceedings of the 1st Joint International Workshop on Parallel Data Storage & Data Intensive Scalable Computing Systems, IEEE Press, 2016, 1--6, doi: 10.1109/PDSW-DISCS.2016.005

Hamish A. Carr, Gunther H. Weber, Christopher M. Sewell, James P. Ahrens, "Parallel Peak Pruning for Scalable SMP Contour Tree Computation", Proceedings of the 6th IEEE Symposium on Large Data Analysis and Visualization (LDAV), 2016, 75--84, doi: 10.1109/LDAV.2016.7874312

Sugeerth Murugesan, Kristofer Bouchard, Edward Chang, Dougherty, Bernd Hamann, Gunther H. Weber, "Hierarchical Spatio-temporal Visual Analysis of Cluster Evolution in Data", Proceedings of the 7th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics, New York, NY, USA, ACM, 2016, 630--639, doi: 10.1145/2975167.2985688

T Perciano, F Tupin, R Hirata, RM Cesar, "A two-level Markov random field for road network extraction and its application with optical, SAR, and multitemporal data", International Journal of Remote Sensing, 2016, 37:3584--3610, doi: 10.1080/01431161.2016.1201227

Stone, D., H. Shiogama, P. Wolski, O. Angélil, S. Cholias, N. Christidis, A. Dittus, C. Folland, A. King, J. Kinter, H. Krishnan, S.-K. Min, M. Wehner, "The C20C+ Detection and Attribution Project", Fall Meeting of the American Geophysical Union, 2015,

Download File: StoneDAGU2015.pdf (pdf: 4.7 MB)

Hari Krishnan, Suren Byna, Michael Wehner, Junmin Gu, Travis O'Brien, Burlen Loring, Daithi Stone, William Collins, Prabhat, Yunjie Liu, Jeffrey Johnson, and Christopher Paciorek, "Enabling Efficient Climate Science Workflows in High Performance Computing Environments", AGU Fall Meeting, 2015, December 13, 2015,

Soyoung Jeon, Prabhat, Suren Byna, Junmin Gu, William Collins, and Michael Wehner,, "Characterization of extreme precipitation within atmospheric river events over California", Advances in Statistical Climatology, Meteorology and Oceanography (ASCMO), November 21, 2015, 1:45-57, doi: 10.5194/ascmo-1-45-2015

Md. Mostofa Ali Patwary, Suren Byna, Nadathur Rajagopalan Satish, Narayanan Sundaram, Zarija Lukic, Vadim Roytershteyn, Michael J. Anderson, Yushu Yao, Mr Prabhat, and Pradeep Dubey, "BD-CATS: Big Data Clustering at Trillion Particle Scale", Supercomputing 2015 (SC15), Supercomputing 2015 (SC15), November 17, 2015,

Babak Behzad, Suren Byna, Prabhat and Marc Snir, "Pattern-driven Parallel I/O Tuning", 10th Parallel Data Storage Workshop (PDSW) 2015, held in conjunction with SC15, 10th Parallel Data Storage Workshop (PDSW) 2015, to be held in conjunction with SC15, November 16, 2015,

Shane Snyder, Philip Carns, Robert Latham, Misbah Mubarak, Chris Carothers, Babak Behzad, Huong Vu Thanh Luu, Suren Byna, and Prabhat, "Techniques for Modeling Large-scale HPC I/O Workloads", the 6th International Workshop on Performance Modeling, Benchmarking and Simulation of High Performance Computer Systems (PMBS15), in conjunction with SC15, the 6th International Workshop on Performance Modeling, Benchmarking and Simulation of High Performa, November 15, 2015,

Babak Behzad, Suren Byna, Stefan Wild, Prabhat and Marc Snir, "Dynamic Model-driven Parallel I/O Performance Tuning", IEEE Cluster 2015, 2015,

H. Luu, M. Winslett, W. Gropp, R. Ross, P. Carns, K. Harms, Prabhat, S. Byna, Y. Yao,, "A Multi-platform Study of I/O Behavior on Petascale Supercomputers", The 24th ACM International Symposium on High-Performance Parallel and Distributed Computing (HPDC) 2015, 2015,

Wehner, M., Prabhat, K. A. Reed, D. Stone, W. D. Collins, and J. Bacmeister, "Resolution dependence of future tropical cyclone projections of CAM5.1 in the US CLIVAR Hurricane Working Group idealized configurations", Journal of Climate, 2015, 28:3905-3925, doi: 10.1175/JCLI-D-14-00311.1

J. Yang, O. Rübel, M. Mahoney, Prabhat, B.P. Bowen, "Identifying important ions and positions in mass spectrometry imaging data using CUR matrix decompositions", ACS Analytical Chemistry, March 2015, doi: 10.1021/ac5040264

"Machine learning and understanding for intelligent extreme scale scientific computing and discovery", DOE ASCR Machine Learning Workshop Report, January 2015, doi: 10.2172/1471083

J Donatelli, M Haranczyk, A Hexemer, H Krishnan, X Li, L Lin, F Maia, S Marchesini, D Parkinson, T Perciano, D Shapiro, D Ushizima, C Yang, JA Sethian, "CAMERA: The Center for Advanced Mathematics for Energy Research Applications", Synchrotron Radiation News, 2015, 28:4--9, doi: 10.1080/08940886.2015.1013413

Y Li, S Meyer, J Lim, SC Lee, WE Gent, S Marchesini, H Krishnan, T Tyliszczak, D Shapiro, ALD Kilcoyne, WC Chueh, Effects of Particle Size, Electronic Connectivity, and Incoherent Nanoscale Domains on the Sequence of Lithiation in LiFePO<inf>4</inf> Porous Electrodes, Advanced Materials, Pages: 6591--6597 2015, doi: 10.1002/adma.201502276

Yiyang Li, Sophie Meyer, Jongwoo Lim, Sang Chul Lee, William E Gent, Stefano Marchesini, Harinarayan Krishnan, Tolek Tyliszczak, David Shapiro, Arthur L David Kilcoyne, others, Effects of Particle Size, Electronic Connectivity, and Incoherent Nanoscale Domains on the Sequence of Lithiation in LiFePO4 Porous Electrodes, Advanced Materials, Pages: 6591--6597 2015,

Yiyang Li, Sophie Meyer, Jongwoo Lim, Sang Chul Lee, William E Gent, Stefano Marchesini, Harinarayan Krishnan, Tolek Tyliszczak, David Shapiro, Arthur L David Kilcoyne, others, Electrode Lithiation: Effects of Particle Size, Electronic Connectivity, and Incoherent Nanoscale Domains on the Sequence of Lithiation in LiFePO4 Porous Electrodes (Adv. Mater. 42/2015), Advanced Materials, Pages: 6590--6590 2015,

B Loring, H Karimabadi, V Rortershteyn, "A Screen Space GPGPU Surface LIC Algorithm for Distributed Memory Data Parallel Sort Last Rendering Infrastructures", NUMERICAL MODELING OF SPACE PLASMA FLOWS: ASTRONUM-2014, 2015, 498:231--239,

AW Wills, DJ Michalak, P Ercius, ER Rosenberg, T Perciano, D Ushizima, R Runser, BA Helms, "Block Copolymer Packing Limits and Interfacial Reconfigurability in the Assembly of Periodic Mesoporous Organosilicas", Advanced Functional Materials, 2015, 25:4120--4128, doi: 10.1002/adfm.201501059

D Ushizima, T Perciano, D Parkinson, "Fast detection of material deformation through structural dissimilarity", Proceedings - 2015 IEEE International Conference on Big Data, IEEE Big Data 2015, 2015, 2775--2781, doi: 10.1109/BigData.2015.7364080

Soyoung Jeon, Christopher Paciorek, Prabhat, Surendra Byna, William Collins, Michael Wehner, "Uncertainty Quantification for Characterizing Spatial Tail Dependence under Statistical Framework", AGU, Fall Meeting 2014, 2014,

Babak Behzad, Surendra Byna, Stefan M. Wild, Mr. Prabhat, Marc Snir, "Improving Parallel I/O Autotuning with Performance Modeling", ACM Symposium on High-Performance Parallel and Distributed Computing (HPDC 2014), New York, NY, USA, ACM, 2014, 253--256, doi: 10.1145/2600212.2600708

Gunther H. Weber, Hans Johansen, Daniel T. Graves, Terry J. Ligocki, "Simulating Urban Environments for Energy Analysis", Proceedings Visualization in Environmental Sciences (EnvirVis), 2014, LBNL 6652E,

Dáithí Stone, Michael Wehner, Shreyas Cholia, Harinarayan Krishnan, Piotr Wolski, Mark Tadross, Chris Folland, Nikos Christidis, Hideo Shiogama, "The C20C+ Detection and Attribution Project", Integrated Climate Modeling Principal Investigator Meeting 2014, 2014,

D Ushizima, T Perciano, H Krishnan, B Loring, H Bale, D Parkinson, J Sethian, "Structure recognition from high resolution images of ceramic composites", Proceedings - 2014 IEEE International Conference on Big Data, IEEE Big Data 2014, 2014, 683--691, doi: 10.1109/BigData.2014.7004292

H Karimabadi, V Roytershteyn, HX Vu, YA Omelchenko, J Scudder, W Daughton, A Dimmock, K Nykyri, M Wan, D Sibeck, M Tatineni, A Majumdar, B Loring, B Geveci, "The link between shocks, turbulence, and magnetic reconnection in collisionless plasmas", Physics of Plasmas, 2014, 21, doi: 10.1063/1.4882875

W Daughton, TKM Nakamura, H Karimabadi, V Roytershteyn, B Loring, "Computing the reconnection rate in turbulent kinetic layers by using electron mixing to identify topology", Physics of Plasmas, 2014, 21, doi: 10.1063/1.4875730

M Scot Breitenfeld, Kalyana Chadalavada, Robert Sisneros, Surendra Byna, Quincey Koziol, Neil Fortner, Prabhat, Venkat Vishwanath, "Recent Progress in Tuning Performance of Large-scale I/O with Parallel HDF5", The 9th Parallel Data Storage Workshop (PDSW) held in conjunction with SC14, 2014,

Gunther H. Weber, Helwig Hauser, "Interactive Visual Exploration and Analysis", Mathematics and Visualization, (Springer-Verlag: 2014) Pages: 161--174, LBNL 6655E,

Patrick Oesterling, Christian Heine, Gunther H. Weber, Gerik Scheuermann, "A Topology-Based Approach to Visualize the Thematic Composition of Document Collections", Theory and Applications of Natural Language Processing, (Springer International Publishing: 2014) Pages: 63-85 doi: 10.1007/978-3-319-12655-5_4

K Beketayev, D Yeliussizov, D Morozov, GH Weber, B Hamann, "Measuring the distance between merge trees", Mathematics and Visualization, ( 2014) Pages: 151--165 doi: 10.1007/978-3-319-04099-8_10

Dmitriy Morozov, Gunther H Weber, "Distributed Contour Trees", Topological Methods in Data Analysis and Visualization III, (Springer International Publishing: 2014) Pages: 89--102 doi: 10.1007/978-3-319-04099-8\_6

Babak Behzad, Huong Vu Thanh Luu, Joseph Huchette, Surendra Byna, Prabhat, Ruth Aydt, Quincey Koziol, and Marc Snir, "Taming parallel I/O complexity with auto-tuning", In Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC '13), 2013,

David Camp, Hari Krishnan, David Pugmire, Christoph Garth, Ian Johnson, E. Wes Bethel, Kenneth I. Joy, and Hank Childs., "GPU Acceleration of Particle Advection Workloads in a Parallel, Distributed Memory Setting", Proceedings of Eurographics Symposium on Parallel Graphics and Visualization (EGPGV), May 5, 2013,

Hank Childs, Berk Geveci, William J. Schroeder, Jeremy S. Meredith, Kenneth Moreland, Christopher Sewell, Torsten Kuhlen, E.Wes Bethel, "Research Challenges for Visualization Software", IEEE Computer, May 1, 2013, 46:34-43, LBNL 6239E,

Patrick Oesterling, Christian Heine, Gunther H. Weber, Gerik Scheuermann, "Visualizing global structure of nD point clouds as topological 1D height to enable supervised local data analysis", IEEE Transactions on Visualization and Computer Graphics, 2013, 19:514-526, LBNL 5694E,

E Wes Bethel, Prabhat Prabhat, Suren Byna, Oliver R\ ubel, K John Wu, Michael Wehner, "Why high performance visual data analytics is both relevant and difficult", Visualization and Data Analysis 2013, January 2013, 8654:86540B, LBNL LBNL-6063E,

Download File: LBNL-6063E.pdf (pdf: 3.6 MB)

Kesheng Wu, E Bethel, Ming Gu, David Leinweber, Oliver R\ ubel, "A big data approach to analyzing market volatility", Algorithmic Finance, 2013, 2:241--267, LBNL LBNL-6382E,

Understanding the microstructure of the financial market requires the processing of a vast amount of data related to individual trades, and sometimes even multiple levels of quotes. Analyzing such a large volume of data requires tremendous computing power that is not easily available to financial academics and regulators. Fortunately, public funded High Performance Computing (HPC) power is widely available at the National Laboratories in the US. In this paper we demonstrate that the HPC resource and the techniques for data-intensive sciences can be used to greatly accelerate the computation of an early warning indicator called Volume-synchronized Probability of Informed trading (VPIN). The test data used in this study contains five and a half year's worth of trading data for about 100 most liquid futures contracts, includes about 3 billion trades, and takes 140GB as text files. By using (1) a more efficient file format for storing the trading records, (2) more effective data structures and algorithms, and (3) parallelizing the computations, we are able to explore 16,000 different ways of computing VPIN in less than 20 hours on a 32-core IBM DataPlex machine. Our test demonstrates that a modest computer is sufficient to monitor a vast number of trading activities in real-time -- an ability that could be valuable to regulators.

Our test results also confirm that VPIN is a strong predictor of liquidity-induced volatility. With appropriate parameter choices, the false positive rates are about 7% averaged over all the futures contracts in the test data set. More specifically, when VPIN values rise above a threshold (CDF > 0.99), the volatility in the subsequent time windows is higher than the average in 93% of the cases.

Kesheng Wu, Wes Bethel, Ming Gu, David, Oliver R\ ubel, Testing VPIN on Big Data, Available at SSRN 2318259, 2013,

O Rübel, A Greiner, S Cholia, K Louie, EW Bethel, TR Northen, BP Bowen, "OpenMSI: A high-performance web-based platform for mass spectrometry imaging", Analytical Chemistry, 2013, 85:10354--103, doi: 10.1021/ac402540a

E Wes Bethel, Prabhat Prabhat, Suren Byna, R\ ubel, K John Wu, Michael Wehner, Why high performance visual data analytics is both and difficult, IS\&T/SPIE Electronic Imaging, Pages: 86540B-865 2013, doi: 10.1117/12.2010980

DN Williams, T Bremer, C Doutriaux, J Patchett, S Williams, G Shipman, R Miller, DR Pugmire, B Smith, C Steed, EW Bethel, H Childs, H Krishnan, P Prabhat, M Wehner, CT Silva, E Santos, D Koop, T Ellqvist, J Poco, B Geveci, A Chaudhary, A Bauer, A Pletzer, D Kindig, GL Potter, TP Maxwell, Ultrascale visualization of climate data, Computer, Pages: 68--76 2013, doi: 10.1109/MC.2013.119

H Karimabadi, B Loring, P O leary, A Majumdar, M Tatineni, B Geveci, "In-situ visualization for global hybrid simulations", ACM International Conference Proceeding Series, 2013, doi: 10.1145/2484762.2484822

H Karimabadi, V Roytershteyn, M Wan, WH Matthaeus, W Daughton, P Wu, M Shay, B Loring, J Borovsky, E Leonardis, SC Chapman, TKM Nakamura, "Coherent structures, intermittent turbulence, and dissipation in high-temperature plasmas", Physics of Plasmas, 2013, 20, doi: 10.1063/1.4773205

Gunther H. Weber, Hank Childs, Jeremy S. Meredith, "Recent Advances in VisIt: Parallel Crack-free Isosurface Extraction", Numerical Modeling of Space Plasma Flows: Astronum-2012 (Astronomical Society of the Pacific Conference Series), 2013,

Dmitriy Morozov, Gunther Weber, "Distributed Merge Trees", PPoPP 13, New York, NY, USA, ACM, 2013, 93--102, doi: 10.1145/2442516.2442526

T Perciano, MW Urban, NDA Mascarenhas, M Fatemi, AC Frery, GT Silva, "Deconvolution of vibroacoustic images using a simulation model based on a three dimensional point spread function", Ultrasonics, 2013, 53:36--44, doi: 10.1016/j.ultras.2012.03.011

A. C. Frery, T. Perciano, Introduction to Image Processing Using R: Learning by Examples, (2013)

Cyrus Harrison, Paul Navratil, Maysam Mossalem, Ming Jiang, Hank Childs, "Efficient Dynamic Derived Field Generation on Many-Core Architectures Using Python", Workshop on Python for High Performance and Scientific Computing (PyHPC 2012), held in conjunction with the ACM/IEEE Conference on SuperComputing (SC12), November 2012, 11-20,

E. Wes Bethel and Mark Howison, "Multi-core and Many-core Shared-memory Parallel Raycasting Volume Rendering Optimization and Tuning", International Journal of High Performance Computing Applications, 2012, LBNL 5362E,

Hank Childs, Eric Brugger, Brad Whitlock, Jeremy Meredith, Sean Ahern, David Pugmire, Kathleen Biagas, Mark Miller, Cyrus Harrison, Gunther H. Weber, Hari Krishnan, Thomas Fogal, Allen Sanderson, Christoph Garth, E. Wes Bethel, David Camp, Oliver Rubel, Marc Durant, Jean M. Favre, Paul Navratil, "VisIt: An End-User Tool For Visualizing and Analyzing Very Large Data", High Performance Visualization---Enabling Extreme-Scale Scientific Insight, ( October 2012) Pages: 357--372

E. Wes Bethel, David Camp, Hank Childs, Christoph Garth, Mark Howison, Kenneth I. Joy, David Pugmire, "Hybrid Parallelism", High Performance Visualization---Enabling Extreme-Scale Scientific Insight, ( October 2012) Pages: 261--290

Hank Childs, David Pugmire, Sean Ahern, Brad Whitlock, Mark Howison, Prabhat, Gunther Weber, E. Wes Bethel, "Visualization at Extreme Scale Concurrency", High Performance Visualization---Enabling Extreme-Scale Scientific Insight, ( October 2012) Pages: 291--306

Hank Childs, "Parallel Visualization Frameworks", High Performance Visualization---Enabling Extreme-Scale Scientific Insight, ( October 2012) Pages: 9--24

Hank Childs, Kwan-Liu Ma, Hongfeng Yu, Brad Whitlock, Jeremy Meredith, Jean Favre, Scott Klasky, Norbert Podhorszki, Karsten Schwan, Matthew Wolf, Manish Parashar, Fan Zhang, "In Situ Processing", High Performance Visualization---Enabling Extreme-Scale Scientific Insight, ( October 2012) Pages: 171--198

E. Wes Bethel, Hank Childs, Charles Hansen (editors), High Performance Visualization---Enabling Extreme-Scale Scientific Insight, Chapman & Hall, CRC Computational Science, (CRC Press/Francis--Taylor Group: October 2012)

Oliver Rübel, Cameron, G. R. Geddes, Min Chen, Estelle Cormier-Michel, and E. Wes Bethel, "Query-driven Analysis of Plasma-based Particel Acceleration Data", Poster Abstracts of IEEE VisWeek, October 2012,

David Camp, Hank Childs, Christoph Garth, David Pugmire, Kenneth I. Joy, "Parallel Stream Surface Computation for Large Data Sets", Proceedings of IEEE Symposium on Large Data Analysis and Visualization (LDAV), October 2012, 39--47, LBNL 5776E,

Gunther H. Weber, Hank Childs, Jeremy S. Meredith, "Efficient Parallel Extraction of Crack-free Isosurfaces from Adaptive Mesh Refinement (AMR) Data", Proceedings of IEEE Symposium on Large Data Analysis and Visualization (LDAV), October 2012, 31--38, LBNL 5799E,

Paul Navratil, Bill Barth, Hank Childs, "Virtual Rheoscopic Fluids for Dense, Large-Scale Fluid Flow Visualizations", Proceedings of IEEE Symposium on Large Data Analysis and Visualization (LDAV), October 2012, 79--84,

Tamay M. Ozgokmen, Andrew C. Poje, Paul F. Fischer, Hank Childs, Harinarayan Krishnan, Christoph Garth, Angelique C. Haza, Edward Ryan, "On multi-scale dispersion under the influence of surface mixed layer instabilities", Ocean Modelling, October 2012, 56:16-30,

Kelly P. Gaither, Hank Childs, Karl Schulz, Cyrus Harrison, Bill Barth, Diego Donzis, P.K. Yeung, "Using Visualization and Data Analysis to Understand Critical Structures in Massive Time Varying Turbulent Flow Simulations", IEEE Computer Graphics and Applications, July 2012, 32:34-45, LBNL 5911E,

Mehmet Balman, Eric Pouyoul, Yushu Yao, E. Wes Bethel, Burlen Loring, Prabhat, John Shalf, Alex Sim, and Brian L. Tierney, "Experiences with 100G Network Applications", In Proceedings of the Fifth international Workshop on Data-intensive Distributed Computing, in conjunction with ACM High Performance Distributing Computing (HPDC) Conference, 2012, Delft, Netherlands, June 2012, LBNL 5603E, doi: 10.1145/2286996.2287004

Download File: didc-report.pdf (pdf: 11 MB)

100Gbps networking has finally arrived, and many research and educational in- stitutions have begun to deploy 100Gbps routers and services. ESnet and Internet2 worked together to make 100Gbps networks available to researchers at the Super- computing 2011 conference in Seattle Washington. In this paper, we describe two of the first applications to take advantage of this network. We demonstrate a visu- alization application that enables remotely located scientists to gain insights from large datasets. We also demonstrate climate data movement and analysis over the 100Gbps network. We describe a number of application design issues and host tuning strategies necessary for enabling applications to scale to 100Gbps rates.

Hank Childs, Torsten Kuhlen, Fabio Marton (editors), Proceedings of the EuroGraphics Symposium on Parallel Graphics and Visualization (EGPGV), EuroGraphics Association, (EuroGraphics Association: May 2012)

Paul Navratil, Donald Fussell, Calvin Lin, Hank Childs, "Dynamic Scheduling for Large-Scale Distributed-Memory Ray Tracing", Proceedings of EuroGraphics Symposium on Parallel Graphics and Visualization (EGPGV), May 2012, 61-70, LBNL 5930E,

Download File: Navratil-EGPGV-2012.pdf (pdf: 2.1 MB)

E. Wes Bethel, David Camp, Hank Childs, Mark Howison, Hari Krishnan, Burlen Loring, Joerg Meyer, Prabhat, Oliver Ruebel, Daniela Ushizima, Gunther Weber, "Towards Exascale: High Performance Visualization and Analytics – Project Status Report. Technical Report", DOE Exascale Research Conference, April 2012,

Gunther H. Weber, Kenes Beketayev, Peer-Timo Bremer, Bernd Hamann, Maciej Haranczyk, Mario Hlawitschka, Valerio Pascucci, "Comprehensible Presentation of Topological Information", Status report for DOE Exascale Research Conference, April 2012, LBNL 5693E,

Gunther H. Weber, Dmitriy Morozov, Kenes Beketayev, John Bell, Peer-Timo Bremer, Marc Day, Bernd Hamann, Christian Heine, Maciej Haranczyk, Mario Hlawitschka, Valerio Pascucci, Patrick Oesterling, Gerik Scheuermann, "Topology-based Visualization and Analysis of High-dimensional Data and Time-varying Data at the Extreme Scale", DOE Exascale Research Conference, April 2012,

Gunther H. Weber, Peer-Timo Bremer, "In-situ Analysis: Challenges and Opportunities", Position paper for DOE Exascale Research Conference, April 2012, LBNL 5692E,

Jihan Kim, Richard L. Martin, Oliver Rübel, Maciej Haranczyk & Berend Smit, "High-throughput Characterization of Porous Materials Using Graphics Processing Units", Journal of Chemical Theory and Computation, March 16, 2012, 8:1684–1693, LBNL 5409E, doi: 10.1021/ct200787v

We have developed a high-throughput graphics processing unit (GPU) code that can characterize a large database of crystalline porous materials. In our algorithm, the GPU is utilized to accelerate energy grid calculations, where the grid values represent interactions (i.e., Lennard-Jones + Coulomb potentials) between gas molecules (i.e., CH₄ and CO₂) and materials’ framework atoms. Using a parallel flood fill central processing unit (CPU) algorithm, inaccessible regions inside the framework structures are identified and blocked, based on their energy profiles. Finally, we compute the Henry coefficients and heats of adsorption through statistical Widom insertion Monte Carlo moves in the domain restricted to the accessible space. The code offers significant speedup over a single core CPU code and allows us to characterize a set of porous materials at least an order of magnitude larger than those considered in earlier studies. For structures selected from such a prescreening algorithm, full adsorption isotherms can be calculated by conducting multiple Grand Canonical Monte Carlo (GCMC) simulations concurrently within the GPU.

Soile V.E. Keränen, Oliver Rübel, David W. Knowles and Mark D. Biggin, "Computational modeling of cis-regulatory modules from 3D exprression data in Drosophila blastoderm atlas", Drosophila Genetics, March 2012,

Ushizima, D.M., Weber, G., Morozov, D., Bethel, W., Sethian, J.A., "Algorithms for Microstructure Description applied to Microtomography", Carbon Cycle 2.0 Symposium, February 10, 2012,

Richard L. Martin, Prabhat, David D. Donofrio, James A. Sethian & Maciej Haranczyk, "Accelerating Analysis of void spaces in porous materials on multicore and GPU platforms", International Journal of High Performance Computing Applications, February 5, 2012, 26:347-357,

Developing computational tools that enable discovery of new materials for energy-related applications is a challenge. Crystalline porous materials are a promising class of materials that can be used for oil refinement, hydrogen or methane storage as well as carbon dioxide capture. Selecting optimal materials for these important applications requires analysis and screening of millions of potential candidates. Recently, we proposed an automatic approach based on the Fast Marching Method (FMM) for performing analysis of void space inside materials, a critical step preceding expensive molecular dynamics simulations. This breakthrough enables unsupervised, high-throughput characterization of large material databases. The algorithm has three steps: (1) calculation of the cost-grid which represents the structure and encodes the occupiable positions within the void space; (2) using FMM to segment out patches of the void space in the grid of (1), and find how they are connected to form either periodic channels or inaccessible pockets; and (3) generating blocking spheres that encapsulate the discovered inaccessible pockets and are used in proceeding molecular simulations. In this work, we expand upon our original approach through (A) replacement of the FMM-based approach with a more computationally efficient flood fill algorithm; and (B) parallelization of all steps in the algorithm, including a GPU implementation of the most computationally expensive step, the cost-grid generation. We report the acceleration achievable in each step and in the complete application, and discuss the implications for high-throughput material screening.

Surendra Byna, Jerry Chou, Oliver Rubel, Homa Karimabadi, William S Daughter, Vadim Roytershteyn, E Wes Bethel, Mark Howison, Ke-Jou Hsu, Kuan-Wu Lin, others, "Parallel I/O, analysis, and visualization of a trillion particle simulation", SC 12: Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis, January 2012, 1--12,

E. Wes Bethel, "Exploration of Optimization Options for Increasing Performance of a GPU Implementation of a Three-dimensional Bilateral Filter", 2012, LBNL 5406E,

Download File: LBNL-5406E.pdf (pdf: 438 KB)

E. W. Bethel and D. Leinweber and O. Rubel and K. Wu, "Federal Market Information Technology in the Post Flash Crash Era: Roles of Supercomputing", The Journal of Trading, 2012, 7:9-24, LBNL 5263E, doi: 10.3905/jot.2012.7.2.009

Oliver R\ ubel, Surendra Byna, Kesheng Wu, Fuyu Li, Michael Wehner, Wes Bethel, others, "Teca: A parallel toolkit for extreme climate analysis", Procedia Computer Science, Elsevier, January 2012, 9:866--876, LBNL 5352E,

We present TECA, a parallel toolkit for detecting extreme events in large climate datasets. Modern climate datasets expose parallelism across a number of dimensions: spatial locations, timesteps and ensemble members. We design TECA to exploit these modes of parallelism and demonstrate a prototype implementation for detecting and tracking three classes of extreme events: tropical cyclones, extra-tropical cyclones and atmospheric rivers. We process a modern TB-sized CAM5 simulation dataset with TECA, and demonstrate good runtime performance for the three case studies.

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", Mathematics and Visualization, Visualization in Medicine and Life Sciences II, Progress and New Challenges, edited by L. Linsen and B. Hamann and H. Hagen and H.-C. Hege, (Springer Verlag: 2012) Pages: 267-285, LBNL 4891E,

Download File: LBNL-4891E.pdf (pdf: 15 MB)

Mark Howison, E. Wes Bethel, Hank Childs, "Hybrid Parallelism for Volume Rendering on Large, Multi- and Many-core Systems", IEEE Transactions on Visualization and Computer Graphics, January 2012, 18:17-29, LBNL 4370E,

E. W. Bethel, Surendra Byna, Jerry Chou, Cormier-Michel, Cameron G. R. Geddes, Howison, Fuyu Li, Prabhat, Ji Qiang, R\ ubel, Rob D. Ryne, Michael Wehner, Wu, "Big Data Analysis and Visualization: What Do LINACS Tropical Storms Have In Common?", 11th International Computational Accelerator Physics ICAP 2012, Germany, 2012,

EW Bethel, S. Byna, J. Chou, E., CGR Geddes, M. Howison, F. Li J. Q. Prabhat, O. R\ ubel, RD Ryne and, Big Data Analysis and Visualization: What Do LINACS Tropical Storms Have In Common?, 11th International Computational Accelerator Physics ICAP 2012, 2012,

E. Wes Bethel, David Leinweber, Oliver Rübel Kesheng Wu, Federal Market Information Technology in the Crash Era: Roles for Supercomputing, The Journal of Trading, Pages: 9--25 2012, doi: 10.3905/jot.2012.7.2.009

Surendra Byna, Jerry Chou, Oliver R\ ubel, , Homa Karimabadi, William S. Daughton, Roytershteyn, E. Wes Bethel, Mark Howison Ke-Jou Hsu, Kuan-Wu Lin, Arie Shoshani, Uselton, Kesheng Wu, Parallel I/O, Analysis, and Visualization of a Particle Simulation, Proceedings of SuperComputing 2012, 2012,

J Meyer, EW Bethel, JL Horsman, SS Hubbard, H Krishnan, A Romosan, EH Keating, L Monroe, R Strelitz, P Moore, G Taylor, B Torkian, TC Johnson, I Gorton, Visual data analysis as an integral part of environmental management, IEEE Transactions on Visualization and Computer Graphics, Pages: 2088--2094 2012, doi: 10.1109/TVCG.2012.278

H Krishnan, J Meyer, A Romosan, H Childs, EW Bethel, Enabling advanced environmental management via remote and distributed visual data exploration and analysis, Computing and Visualization in Science, Pages: 123--133 2012, doi: 10.1007/s00791-013-0204-5

M Balman, E Pouyoul, Y Yao, EW Bethel, B Loring, Prabhat, J Shalf, A Sim, BL Tierney, "Experiences with 100Gbps network applications", DIDC 12 - 5th International Workshop on Data-Intensive Distributed Computing, 2012, 33--42, doi: 10.1145/2286996.2287004

O. R\ ubel, S. Byna, K. Wu, F. Li, M., W. Bethel, others, "TECA: A Parallel Toolkit for Extreme Climate", Procedia Computer Science, Elsevier, 2012, 9:866--876, doi: 10.1016/j.procs.2012.04.093

D Ushizima, D Morozov, GH Weber, AGC Bianchi, JA Sethian, EW Bethel, "Augmented topological descriptors of pore networks for material science", IEEE Transactions on Visualization and Computer Graphics, 2012, 18:2041--2050, LBNL 5964E, doi: 10.1109/TVCG.2012.200

Download File: LBNL-5964E.pdf (pdf: 5.4 MB)

Allen R Sanderson, Brad Whitlock, H Childs, GH Weber, K Wu, others, "A system for query based analysis and visualization", January 2012, LBNL 5507E,

Download File: LBNL-5507E.pdf (pdf: 562 KB)

TM Özgökmen, AC Poje, PF Fischer, H Childs, H Krishnan, C Garth, AC Haza, E Ryan, On multi-scale dispersion under the influence of surface mixed layer instabilities and deep flows, Ocean Modelling, Pages: 16--30 2012, doi: 10.1016/j.ocemod.2012.07.004

H Krishnan, C Garth, J Gühring, MA Gülsün, A Greiser, KI Joy, Analysis of time-dependent flow-sensitive PC-MRI data, IEEE Transactions on Visualization and Computer Graphics, Pages: 966--977 2012, doi: 10.1109/TVCG.2011.80

M Wan, WH Matthaeus, H Karimabadi, V Roytershteyn, M Shay, P Wu, W Daughton, B Loring, SC Chapman, "Intermittent dissipation at kinetic scales in collisionless plasma turbulence", Physical Review Letters, 2012, 109, doi: 10.1103/PhysRevLett.109.195001

Samuel Gerber, Oliver Rübel, Peer-Timo Bremer, Valerio Pascucci and Ross T. Whitaker, "Morse-Smale Regression", Journal of Computational and Graphical Statistics, January 2012, doi: 10.1080/10618600.2012.657132

Download File: MSR.pdf (pdf: 292 KB)

K Beketayev, GH Weber, D Morozov, A Abzhanov, B Hamann, "Geometry-preserving topological landscapes", Proceedings - WASA 2012: Workshop at SIGGRAPH Asia 2012, 2012, 155--160, doi: 10.1145/2425296.2425324

Dogan Demir, Kenes Beketayev, Gunther H. Weber, Peer-Timo Bremer, Valerio Pascucci, Bernd Hamann, "Topology Exploration with Hierarchical Landscapes", Proceedings of the Workshop at SIGGRAPH Asia 2012, New York, NY, USA, ACM, 2012, 147--154, doi: 10.1145/2425296.2425323

Tina Zhuo, Prabhat, Chris Paciorek and Cari Kaufman, "Distributed Kriging Analysis for Large Spatial Data", Proceedings of IEEE ICDM Workshop on Knowledge Discovery from Climate Data, Vancuover, Canada, December 2011,

Uselton, A., Ushizima, D.M., "I/O Workload Analysis with Server-side Data Collection", Supercomputing (SC), November 13, 2011,

E. Wes Bethel, David Leinweber, Oliver Rübel, Kesheng Wu, "Federal Market Information Technology in the Post Flash Crash Era: Roles of Supercomputing", Workshop on High Performance Computational Finance at SC11, Seattle, WA, USA, November 2011, LBNL 5263E,

David Camp, Christoph Garth, Hank Childs, Dave Pugmire, Kenneth I. Joy, "Streamline Integration Using MPI-Hybrid Parallelism on a Large Multicore Architecture", IEEE Transactions on Visualization and Computer Graphics, November 2011, 17:1702-1713, LBNL 4563E, doi: http://doi.ieeecomputersociety.org/10.1109/TVCG.2010.259

Download File: LBNL-4563E.pdf (pdf: 3.5 MB)

Huang, M.-Y., Mackey, L., Keraenen, S.V.E., Weber, G.H., Jordan, M.I., Knowles, D.W., Biggin, M.D. and Hamann, B., "Visually Relating Gene Expression and in vivo DNA Binding Data", Proceedings of the IEEE International Conference on Bioinformatics and Biomedicine 2011 (IEEE BIBM 2011), Los Alamitos, California, IEEE Computer Society Press, November 2011, 586-589, LBNL 5423E,

Download File: LBNL-5423E.pdf (pdf: 599 KB)

David Camp, Hank Childs, Amit Chourasia, Christoph Garth, Kenneth Joy, "Evaluating the Benefits of An Extended Memory Hierarchy for Parallel Streamline Algorithms", Proceedings IEEE Symposium on Large-Scale Data Analysis and Visualization (LDAV) 2011, Providence, RI, USA, IEEE Press, October 2011, 57-64, LBNL 5503E,

Download File: LBNL-camp.pdf (pdf: 1.1 MB)

R. Ryne, B. Austin, J. Byrd, J. Corlett, E. Esarey, C. G. R. Geddes, W. Leemans, X. Li, Prabhat, J. Qiang, O. Rübel, J.-L. Vay, M. Venturini, K. Wu, B. Carlsten, D. Higdon and N. Yampolsky, "High Performance Computing in Accelerator Science: Past Successes, Future Challenges", Workshop on Data and Communications in Basic Energy Sciences: Creating a Pathway for Scientific Discovery, October 2011,

Ushizima, D.M., Parkinson, D., Nico, P., Ajo-Franklin, J., Macdowell, A., Kocar, B., Bethel E.W, Sethian J.A., "Statistical segmentation and porosity quantification of 3D x-ray microtomography", XXXIV Applications of Digital Image Processing: Proceeding of SPIE 2011, San Diego, CA, USA, August 2011,

Michael Philpott, Prabhat and Yoshiyuki Kawazoe, "Magnetism and Bonding in Graphene Nanodots with H modified Interior, Edge and Apex", J. Chem Physics, August 2011,

Christopher Paciorek, Michael Wehner, and Prabhat, "Computationally-efficient Spatial Analysis of Precipitation Extremes Using Local Likelihood", Statistical and Applied Mathematical Sciences Institute Uncertainty Quantification program, Climate Modeling Opening Workshop, August 2011,

Ushizima, D.M., Weber, G.H., Ajo-Franklin, J., Kim, Y., Macdowell, A., Morozov, D., Nico, P., Parkinson, D., Trebotich, D., Wan, J., and Bethel E.W., "Analysis and visualization for multiscale control of geologic CO2", Journal of Physics: Conference Series, Proceedings of SciDAC 2011, July 2011, LBNL Denver, CO, USA,

Richard L. Martin, Thomas F. Willems, Chris H. Rycroft, Prabhat, Michael Kazi and Maciej Haranczyk, "High-throughput structure analysis and descriptor generation for crystalline porous materials", International Conference on Chemical Structures (Noordwijkerhout, Netherlands), June 5, 2011,

Weber, G.H., Bremer, P.T., Gyulassy A., and Pascucci, "Topology-based Feature Definition and Analysis", Numerical Modeling of Space Plasma Flows, San Diego, CA, USA, Astronomical Society of the Pacific, June 2011, 444:292-297, LBNL 5020E,

Beketayev, K., Weber, G.H., Haranczyk, M., Bremer, P.-T., Hlawitschka, M., and Hamann, B., "Topology-based Visualization of Transformation Pathways in Complex Chemical Systems", Computer Graphics Forum (Special Issue, Proc. Eurographics / IEEE Symposium on Visualization), June 2011, 663-672, LBNL 5242E,

Download File: LBNL-5242E.pdf (pdf: 5.2 MB)

C. Harrison, H. Childs, and K. P. Gaither, "Data-Parallel Mesh Connected Components Labeling and Analysis", Proceedings of EuroGraphics Symposium on Parallel Graphics and Visualization, April 2011, 131-140, LBNL 5944E, doi: 10.2312/EGPGV/EGPGV11/131-140

Download File: Harrison-EGPGV2011.pdf (pdf: 3 MB)

Richard L. Martin, Maciej Haranczyk, Prabhat and James A. Sethian, "PDE-based analysis of void space of porous materials on multicore CPUs", Manycore and Accelerator-based High-performance Scientific Computing 2011 (Berkeley, CA), January 24, 2011,

M Prabhat, S Byna, C Paciorek, G Weber, K Wu, T Yopes, MF Wehner, G Ostrouchov, D Pugmire, R Strelitz, others, "Pattern Detection and Extreme Value Analysis on Large Climate Data", AGUFM, Pages: IN41C--03 January 2011,

Mark Howison, Mike McGreevy, Bruce Palmer, Oliver Ruebel, Kesheng Wu, "ExaHDF5: An I/O Platform for Exascale Data Models, Analysis and Performance", 2011,

Download File: Prabhat.pdf (pdf: 784 KB)

Jerry Chou, Mark Howison, Brian Austin, Kesheng Wu, Ji Qiang, E Wes Bethel, Arie Shoshani, Oliver R\ ubel, Rob D Ryne, "Parallel index and query for large scale data analysis", Proceedings of 2011 international conference for high performance computing, networking, storage and analysis, 2011, 1--11, LBNL 5317E,

Luke J. Gosink, Christoph Garth, John C. Anderson, E. Wes Bethel, and Kenneth I. Joy, "An Application of Multivariate Statistical Analysis for Query-Driven Visualization", IEEE Transactions on Visualization and Computer Graphics, 2011, 11:264-275, LBNL 3536E, doi: 10.1109/TVCG.2010.80

Download File: LBNL-3536E.pdf (pdf: 13 MB)

E. Wes Bethel, John van Rosendale, Dale Southard, Kelly Gaither, Hank Childs, Eric Brugger, Sean Ahern, "Visualization at Supercomputing Centers: The Tale of Little Big Iron and the Three Skinny Guys", IEEE Computer Graphics and Applications, January 2011, 31:90-95, LBNL 4180E,

Download File: skinnyGuys.pdf (pdf: 428 KB)

Maciej Haranczyk, Richard L. Martin, Prabhat, James A. Sethian & E. Wes Bethel, "Computational Approaches for the High-Throughput Analysis of Porous materials for Energy related applications", Scientific Discovery through Advanced Computing 2011, 2011,

J. Chou, K. Wu, O. R\ ubel, M. Howison, Qiang, Prabhat, B. Austin, E. W. Bethel, D. Ryne, A. Shoshani, "Parallel Index and Query for Large Scale Data", SC11, 2011, doi: 10.1145/2063384.2063424

Prabhat, S. Byna, C. Paciorek, G. Weber, Wu, T. Yopes, M. Wehner, W. Collins, G., R. Strelitz, E. W. Bethel, Pattern Detection and Extreme Value Analysis on Large Data, DOE/BER Climate and Earth System Modeling PI Meeting, 2011,

E. W. Bethel, D. Leinweber, O. Rübel, K., Federal Market Information Technology in the Post Crash Era: Roles for Supercomputing, WHPCF, Pages: 23--30 2011, doi: 10.1145/2088256.2088267

Prabhat, Quincey Koziol, Karen Schuchardt, E. Wes Bethel, Jerry Chuo, Mark Howison, Mike, Bruce Palmer, Oliver Ruebel, Kesheng, ExaHDF5: An I/O Platform for Exascale Data Analysis and Performance, SciDAC 2011, 2011,

H. Childs, S. Ahern, J. Meredith, M. Miller, and K. I. Joy, "Comparative Visualization Using Cross-Mesh Field Evaluations and Derived Quantities", Scientific Visualization: Interactions, Features, Metaphors, Dagstuhl, Germany, Dagstuhl Follow-Ups, January 2011, 2:59-72, LBNL 5943E, doi: 10.4230/DFU.Vol2.SciViz.2011.59

Download File: Childs-Dagstuhl2011.pdf (pdf: 8.1 MB)

H Karimabadi, B Loring, HX Vu, Y Omelchenko, M Tatineni, A Majumdar, U Ayachit, B Geveci, "Petascale Global Kinetic Simulations of The Magnetosphere and Visualization Strategies for Analysis of Very Large Multi-Variate Data Sets", NUMERICAL MODELING OF SPACE PLASMA FLOWS - ASTRONUM 2010, 2011, 444:281--+,

Surendra Byna, Michael F Wehner, Kesheng John Wu, "Detecting atmospheric rivers in large climate datasets", Proceedings of the 2nd international workshop on Petascal data analytics: challenges and opportunities, 2011, 7--14,

Extreme precipitation events on the western coast of North America are often traced to an unusual weather phenomenon known as atmospheric rivers. Although these storms may provide a significant fraction of the total water to the highly managed western US hydrological system, the resulting intense weather poses severe risks to the human and natural infrastructure through severe flooding and wind damage. To aid the understanding of this phenomenon, we have developed an efficient detection algorithm suitable for analyzing large amounts of data. In addition to detecting actual events in the recent observed historical record, this detection algorithm can be applied to global climate model output providing a new model validation methodology. Comparing the statistical behavior of simulated atmospheric river events in models to observations will enhance confidence in projections of future extreme storms. Our detection algorithm is based on a thresholding condition on the total column integrated water vapor established by Ralph et al. (2004) followed by a connected component labeling procedure to group the mesh points into connected regions in space. We develop an efficient parallel implementation of the algorithm and demonstrate good weak and strong scaling. We process a 30-year simulation output on 10,000 cores in under 3 seconds.

Jerry Chou, Kesheng Wu, others, "Fastquery: A parallel indexing system for scientific data", 2011 IEEE International Conference on Cluster Computing, 2011, 455--464,

Prabhat, Dmitry Zubarev and W. A. Lester, "Statistical Exploration of Electronic Structure of Molecules from Quantum Monte Carlo Simulations", 2011, LBNL 4564E,

Jerry Chuo, John Wu, Prabhat, "Design of FastQuery: how to generalize Indexing and Querying systems for scientific data", 2011,

Jerry Chuo, John Wu, Prabhat, "FastQuery: a general Index and Query system for scientific data", Scientific and Statistical Database Management Conference 2011, 2011,

MacCarthy, B., Carr, H., Weber, G.H., "Topological Galleries: A High Level User Interface for Topology Controlled Volume Rendering", 2011, LBNL 5019E,

Download File: LBNL-5019E.pdf (pdf: 1.9 MB)

Weber, G.H., Bremer, P.-T. and Pascucci, V., "Topological Cacti: Visualizing Contour-based Statistics", Topological Methods in Data Analysis and Visualization II, (Springer Verlag: 2011) Pages: 63-76, LBNL 5018E,

Deines E., Weber, G.H., Garth, C., Van Straalen, B. Borovikov, S., Martin, D.F., and Joy, K.I., "On the computation of integral curves in adaptive mesh refinement vector fields", Proceedings of Dagstuhl Seminar on Scientific Visualization 2009, Schloss Dagstuhl, 2011, 2:73-91, LBNL 4972E,

Download File: 7.pdf (pdf: 799 KB)

Bremer, P.-T., Weber, G.H., Tierny, J., Pascucci, V., Day, M.S., and Bell, J.B., "Interactive Exploration and Analysis of Large Scale Turbulent Combustion Using Topology-based Data Segmentation", IEEE Transactions on Visualization and Computer Graphics, 2011, 17(9):1307-1324, LBNL 5921E, doi: 10.1109/TVCG.2010.253

G Weber, PT Bremer, M Day, J Bell, V Pascucci, "Feature tracking using Reeb graphs", Mathematics and Visualization, ( 2011) Pages: 241--253, LBNL 4226E, doi: 10.1007/978-3-642-15014-2_20

Download File: LBNL-4226E.pdf (pdf: 3.9 MB)

Min-Yu Huang, Gunther H. Weber, Xiao-Yong Li, Mark D. Biggin, and Bernd Hamann, "Quantitative Visualization of ChIP-chip Data by Using Linked Views", Proceedings IEEE International Conference on Bioinformatics and Biomedicine 2010 (IEEE BIBM 2010) Workshops, Workshop on Integrative Data Analysis in Systems Biology (IDASB), Los Alamitos, California, IEEE Computer Society Press, December 8, 2010, 195-200, LBNL 4491E,

Download File: LBNL-4491E.pdf (pdf: 547 KB)

O. Rübel, Linking Automated Data Analysis and Visualization with Applications in Developmental Biology and High-energy Physics, Schriftenreihe Informatik, (Der Dekan (hrsg), Fachbereich Informatik, Technische Universität Kaiserslautert: December 2010) LBNL 3155E,

Patrick Oesterling, Gerik Scheuermann, Sven Teresniak, Gerhard Heyer, Steffen Koch, Thomas Ertl, Gunther H. Weber, "Two-stage Framework for a Topology-Based Projection and Visualization of Classified Document Collections", Proceedings IEEE Symposium on Visual Analytics Science and Technology (IEEE VAST), Salt Lake City, Utah, USA, October 2010, LBNL 4074E,

Mark Howison, Andreas Adelmann, E. Wes Bethel, Achim Gsell, Benedikt Oswald, Prabhat, "H5hut: A High-Performance I/O Library for Particle-Based Simulations", Proceedings of 2010 Workshop on Interfaces and Abstractions for Scientific Data Storage (IASDS10), Heraklion, Crete, Greece, September 2010, LBNL 4021E,

Download File: LBNL-4021E.pdf (pdf: 716 KB)

Mark Howison, Quincey Koziol, David Knaak, John Mainzer, John Shalf, "Tuning HDF5 for Lustre File Systems", Proceedings of 2010 Workshop on Interfaces and Abstractions for Scientific Data Storage (IASDS10), Heraklion, Crete, Greece, September 2010, LBNL 4803E,

Download File: LBNL-4803E.pdf (pdf: 242 KB)

D. M. Ushizima, F. N. S. Medeiros, J. Cuadros, C. I. O. Martins, "Vessel Network Detection Using Contour Evolution and Color Components", Proceedings of the 32nd Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Buenos Aires, Argentina, PubMed-MedLine, September 2010, 3129-3132,

C. Rycroft, D. M. Ushizima, R. Saye, C. M. Ghajar, J. A. Sethian, "Building a physical cell simulation and comparing with confocal microscopy", Bay Area Physical Sciences - Oncology Center (NCI) Meeting 2010, UCSF Medical Sciences, September 2010,

M. Howison, E. W. Bethel, and H. Childs, "Hybrid Parallelism for Volume Rendering on Large, Multi-core Systems", Journal of Physics: Conference Series, Proceedings of SciDAC 2010, Chattanooga, TN, USA, July 2010, LBNL 4024E,

Download File: LBNL-4024E.pdf (pdf: 4.2 MB)

M. Howison, E. W. Bethel, and H. Childs, "Hybrid Parallelism for Volume Rendering on Large, Multi-core Systems", Proceedings of Astronum 2010, San Diego, CA, USA, June 2010, LBNL 4024E,

T.Fogal, H. Childs, S. Shankar, J. Kruger, R.D. Bergeron, and P. Hatcher, "Large Data Visualization on Distributed Memory Multi-GPU Clusters", High Performance Graphics 2010, June 2010, 57-66, LBNL 4571E,

Download File: HPG2010VR.pdf (pdf: 840 KB)

J. Meredith and H. Childs, "Visualization and Analysis-Oriented Reconstruction of Material Interfaces", Computer Graphics Forum (Proceedings of Eurographics/IEEE-VGTC Symposium on Visualization 2010 (EuroVis 2010)), June 2010, 1241-1250, LBNL 4567E,

Download File: EuroVis2010MIR.pdf (pdf: 2.2 MB)

Mark Howison, E. Wes Bethel, Hank Childs, "MPI-hybrid Parallelism for Volume Rendering on Large, Multi-core Systems", In Proceedings of the Eurographics Symposium on Parallel Graphics and Visualization (EGPGV), Norköping, Sweden, May 2010, LBNL 3297E,

Download File: LBNL-3297E.pdf (pdf: 5 MB)

Martin Isenburg, Peter Lindstrom, and Hank Childs, "Parallel and Streaming Generation of Ghost Data for Structured Grids", IEEE Computer Graphics and Applications, May 2010, 30:32-44, doi: 10.1109/MCG.2010.26

A.Uselton, K.Antypas, D.M.Ushizima, J.Sukharev, "File System Monitoring as a Window Into User I/O Requirements", CUG-2010, May 2010,

Download File: CUG2010.pdf (pdf: 593 KB)

D. M. Ushizima, F. Medeiros, "Retinopathy diagnosis from ocular fundus image analysis, Modeling and Analysis of Biomedical Image", SIAM Conference on Imaging Science (IS10), Chicago, Il, April 2010,

O. Rübel, G. H. Weber, M-Y Huang, E. W. Bethel, M. D. Biggin, C. C. Fowlkes, C. Luengo Hendriks, S. V. E. Keränen, M. Eisen, D. 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, March 2010, 7:64-79, LBNL 382E,

Download File: LBNL-382E-TCBB.pdf (pdf: 11 MB)

D. M. Ushizima and J. Cuadros, "Ocular fundus for retinopathy characterization", Bay Area Vision Meeting, February 5, 2010,

Daniela Ushizima, Cameron Geddes, Estelle Cormier-Michel, E. Wes Bethel, Janet Jacobsen, Prabhat, Oliver Rubel, Gunther Weber, Bernard Hamann, Peter Messmer, Hans Hagen, "Automated detection and analysis of particle beams in laser-plasma accelerator simulations", Machine Learning, edited by Yagang Zhang, (In-Teh: February 2010) Pages: 367-389, LBNL 3845E,

Ichitaro Yamazaki, Zhaojun Bai, Horst D. Simon Lin-Wang Wang, Kesheng Wu, "Adaptive Projection Subspace Dimension for the Lanczos Method", ACM Transactions on Mathematical Software, 2010, 37, doi: 10.1145/1824801.1824805

Oliver R\ ubel, Sean Ahern, E Wes Bethel, Mark D Biggin, Hank Childs, Estelle Cormier-Michel, Angela DePace, Michael B Eisen, Charless C Fowlkes, Cameron GR Geddes, others, "Coupling visualization and data analysis for knowledge discovery from multi-dimensional scientific data", Procedia computer science, Elsevier, January 2010, 1:1757--1764, LBNL 3669E,

Download File: ICCS2010Ruebel.pdf (pdf: 3.7 MB)

Hank Childs, David Pugmire, Sean Ahern, Brad Whitlock, Mark Howison, Prabhat, Gunther Weber, E. Wes Bethel, "Extreme Scaling of Production Visualization Software on Diverse Architectures", IEEE Computer Graphics and Applications, January 2010, 30:22--31, LBNL 3403E, doi: 10.1109/MCG.2010.51

E. Wes Bethel, "Using wesBench to Study the Rendering Performance of Graphics Processing Units", 2010, LBNL 3025E,

Download File: LBNL-3025E.pdf (pdf: 1.2 MB)

Gunther Weber, "Recent advances in visit: Amr streamlines and query-driven visualization", 2010,

Download File: LBNL-3185E.pdf (pdf: 2.1 MB)

Oliver Rübel, Sean Ahern, E. Wes Bethel, D. Biggin, Hank Childs, Estelle, Angela DePace, Michael B. Eisen Charless C. Fowlkes, Cameron G. R. Geddes, Hagen, Bernd Hamann, Min-Yu Huang, Soile E. Keränen, David W. Knowles, Cris L. Hendriks, Jitendra Malik, Jeremy Meredith Peter Messmer, Prabhat, Daniela Ushizima, H. Weber, Kesheng Wu, "Coupling visualization and data analysis for knowledge from multi-dimensional scientific data", Procedia Computer Science, 2010, 1:1751--1758, doi: 10.1016/j.procs.2010.04.197

Andrew Uselton, Howison, J. Wright, Skinner, Keen, Shalf, L. Karavanic, Leonid Oliker, "Parallel I/O performance: From events to ensembles", International Parallel & Distributed Processing Symposium (IPDPS), 2010, 1-11,

Download File: ipdps10ipm.pdf (pdf: 1.7 MB)

H Karimabadi, J Dorelli, HX Vu, B Loring, Y Omelchenko, Is Quadrupole Structure of Out-of-Plane Magnetic Field Evidence for Hall Reconnection?, MODERN CHALLENGES IN NONLINEAR PLASMA PHYSICS: A FESTSCHRIFT HONORING THE CAREER OF DENNIS PAPADOPOULOS, Pages: 137--+ 2010,

E. A. Carvalho, D. M. Ushizima, F. N. S. Medeiros, C. I. O. Martins, R. C. P. Marques, I. N. S. Oliveira, "SAR imagery segmentation by statistical region growing and hierarchical merging", Digital Signal Processing, 2010, 20:1365-1378, doi: 10.1016/j.dsp.2009.10.014

Gladeston C. Leite, Daniela M. Ushizima, Fátima N. S. Medeiros, Gilson G. De Lima, "Wavelet Analysis for Wind Fields Estimation", Sensors, 2010, 10:5994--6016, doi: 10.3390/s100605994

PT Bremer, GH Weber, V Pascucci, M Day, JB Bell, "Analyzing and tracking burning structures in lean premixed hydrogen flames", IEEE Transactions on Visualization and Computer Graphics, 2010, 16:248--260, LBNL 2276E, doi: 10.1109/TVCG.2009.69

Download File: LBNL-2276E.pdf (pdf: 8.5 MB)

E. Wes Bethel, Hank Childs, Ajith Mascarenhas, Valerio Pascucci, and Prabhat, "Scientific Data Management Challenges in High Performance Visual Data Analysis", Scientific Data Management: Challenges, Existing Technology, and Deployment, edited by Arie Shoshani and Doron Rotem, (Chapman & Hall CRC Press: December 2009) LBNL 1449E,

D. Pugmire, H. Childs, C. Garth, S. Ahern, G.H. Weber, "Scalable computation of streamlines on very large datasets", Proc. Supercomputing, Portland, OR, USA, November 2009, LBNL 3264E,

E. W. Bethel, C. Johnson, S. Ahern, J. Bell, P.-T. Bremer, H. Childs, E. Cormier-Michel, M. Day, E. Deines, T. Fogal, C. Garth, C. G. R. Geddes, H. Hagen, B. Hamann, C. Hansen, J. Jacobsen, K. Joy, J. Kruger, J. Meredith, P. Messmer, G. Ostrouchov, V. Pascucci, K. Potter, Prabhat, D. Pugmire, O. Rubel, A. Sanderson, C. Silva, D. Ushizima, G. Weber, B. Whitlock, K. Wu, "Occam's Razor and Petascale Visual Data Analysis", SciDAC 2009, J. of Physics: Conference Series, San Diego, California, July 2009, LBNL 2210E,

Download File: BethelETALSciDAC2009.pdf (pdf: 23 MB)

N. Shah, N., S. E. Dillard, G.H. Weber, B. Hamann, "Volume visualization of multiple alignment of large genomic DNA", Mathematical Foundations of Scientific Visualization, Computer Graphics, and Massive Data Exploration, edited by Torsten Moller and Bernd Hamann and Robert Russell, (Springer-Verlag: July 2009) Pages: 325-342, LBNL 63126,

Download File: LBNL-63126.pdf (pdf: 5 MB)

Luke Gosink, Kesheng Wu, E. Wes Bethel, John D. Owens, Kenneth I. Joy, "Data Parallel Bin-based Indexing for Answering Queries on Multi-core Architecture", Proceedings of the 21st International Conference on Scientific and Statistical Database Management (SSDBM), June 2009, 5566:110-129, LBNL 2211E,

Download File: LBNL-2211E.pdf (pdf: 219 KB)

Mark Howison and Carlo Sequin, "CAD Tools for Creating Space-filling 3D Escher Tiles", Computer-Aided Design and Applications, Reno, NV, USA, June 2009, 6:737-748, LBNL 2467E,

Download File: Howison-LBNL-2467E-2009.pdf (pdf: 1.2 MB)

Shoaib Kamil, Cy Chan, Samuel Williams, Leonid Oliker, John Shalf, Mark Howison, E. Wes Bethel, Prabhat, "A Generalized Framework for Auto-tuning Stencil Computations", BEST PAPER AWARD - Cray User Group Conference (CUG), Atlanta, GA, May 4, 2009, LBNL 2078E,

Download File: cug09-autotune.pdf (pdf: 354 KB)

Best Paper Award

M. Hlawitschka, G.H. Weber, A. Anwander, O.T. Carmichael, B. Hamann and G. Scheuermann, "Interactive Volume Rendering of Diffusion Tensor Data", Visualization and Processing of Tensor Fields: Advances and Perspectives, (Springer-Verlag: April 2009) Pages: 161-176, LBNL 2286E,

Download File: LBNL-2286E.pdf (pdf: 4.9 MB)

S. E. Dillard, V. Natarjan, G. H. Weber, V. Pascucci and B. Hamann, "Topology-guided Tessellation of Quadratic Elements", International Journal of Computational Geometry & Applications (IJCGA), April 2009, 19:195-211, LBNL 63771,

Download File: LBNL-63771.pdf (pdf: 635 KB)

C. Garth, E. Deines, K. Joy, E. W. Bethel, H. Childs, G. Weber, S. Ahern, D. Pugmire, A. Sanderson, C. Johnson, Twists and Turns: Vector Field Visual Data Analysis for Petascale Computational Science, SciDAC Review, Pages: 10-21, 2009,

Download File: vacet.pdf (pdf: 1.5 MB)

Oliver R\ ubel, Cameron GR Geddes, Estelle Cormier-Michel, Kesheng Wu, Gunther H Weber, Daniela M Ushizima, Peter Messmer, Hans Hagen, Bernd Hamann, Wes Bethel, others, "Automatic beam path analysis of laser wakefield particle acceleration data", Computational Science \& Discovery, January 2009, 2:015005, LBNL 2734E,

Download File: LBNL-2734E.pdf (pdf: 15 MB)

K Wu, S Ahern, EW Bethel, J Chen, H Childs, C Geddes, J Gu, H Hagen, B Hamann, J Lauret, others, "FastBit: Interactively Searching Massive Data", Proc. of SciDAC 2009, 2009, LBNL 2164E,

Download File: LBNL-2164E.pdf (pdf: 3.2 MB)

C. G. R. Geddes, E Cormier-Michel, E. H. Esarey, C. B. Schroeder, J.-L. Vay, W. P. Leemans, D. L.. Bruhwiler, J. R. Cary, B. Cowan, M. Durant, P. Hamill, P. Messmer, P. Mullowney, C. Nieter, K. Paul, S. Shasharina, S. Veitzer, G. Weber, O. Rübel, D. Ushizima, Prabhat, E. W.Bethel, K. Wu, Large Fields for Smaller Facility Sources, SciDAC Review, Pages: 13-21, 2009,

Download File: geddes.pdf (pdf: 344 KB)

E. Wes Bethel, "High Performance, Three-Dimensional Bilateral Filtering", 2009, LBNL 1601E,

E Bethel, "Modern Scientific Visualization is More than Just Pretty Pictures", January 2009, LBNL 1450E,

Download File: LBNL-1450E.pdf (pdf: 9.8 MB)

Luke J Gosink, Kesheng Wu, E Wes Bethel, John D Owens, Kenneth I Joy, "Data parallel bin-based indexing for answering queries on multi-core architectures", International Conference on Scientific and Statistical Database Management, 2009, 110--129,

E Wes Bethel, Chris Johnson, Sean Ahern, John Bell, Peer-Timo Bremer, Hank Childs, Estelle Cormier-Michel, Marc Day, Eduard Deines, Tom Fogal, others, "Occam s razor and petascale visual data analysis", Journal of Physics: Conference Series, 2009, 180:012084,

Luke J. Gosink, Kesheng Wu, E. Wes Bethel, D. Owens, Kenneth I. Joy, Data Parallel Bin-Based Indexing for Answering Queries Multi-core Architectures, Lecture Notes in Computer Science, Pages: 110--129 2009, doi: 10.1007/978-3-642-02279-1_9

Oliver R\ ubel, Cameron G R Geddes, Estelle, Kesheng Wu, Prabhat, Gunther H, Daniela M Ushizima, Peter Messmer, Hans, Bernd Hamann, Wes Bethel, "Automatic beam path analysis of laser wakefield acceleration data", Computational Science \& Discovery, 2009, 2:015005,

"Smashing the Trillion Zone Barrier", H. Childs, Scientific Computing, 2009,

H Krishnan, C Garth, KI Joy, Time and streak surfaces for flow visualization in large time-varying data sets, IEEE Transactions on Visualization and Computer Graphics, Pages: 1267--1274 2009, doi: 10.1109/TVCG.2009.190

G. H. Weber, O. Rübel, M.-Y. Huang, A. H. 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 Transactions on Computational Biology and Bioinformatics, 2009, 6:296-309, LBNL 63776, doi: 10.1109/TCBB.2007.70249

Download File: LBNL-63776.pdf (pdf: 11 MB)

C. I. O. Martins, D. M. Ushizima, F. N. S. Medeiros, F. N. Bezerra, R. C. P. Marques, N. D. A. Mascarenhas, "Iterative Self-dual Reconstruction on Radar Image Recovery", Proc. of IEEE Workshop on Applications of Computer Vision, Snowbird, Utah, 2009, 37-42, LBNL 3846E,

Regis C. P. Marques, Fatima N. S. Medeiros, Daniela M. Ushizima, "Target Dectection on SAR Images Using Level Set Methods", IEEE Transactions on Systems, Man and Cybernetics, 2009, 39:214-222, LBNL 958E, doi: 10.1109/TSMCC.2008.2006685

PT Bremer, GH Weber, J Tierny, V Pascucci, MS Day, JB Bell, "A topological framework for the interactive exploration of large scale turbulent combustion", e-Science 2009 - 5th IEEE International Conference on e-Science, January 2009, 247--254, LBNL 3183E, doi: 10.1109/e-Science.2009.42

Download File: LBNL-3183E.pdf (pdf: 4.5 MB)

O. Rübel, Prabhat, K. Wu, H. Childs, J. Meredith, C.G.R. Geddes, E. Cormier-Michel, S. Ahern, G.H. Weber, P. Messmer, H. Hagen, B. Hamann and E.W. Bethel, "High Performance Multivariate Visual Data Exploration for Extemely Large Data", Supercomputing (SC), Austin, Texas, USA, November 2008, LBNL 716E,

Download File: LBNL-716E.pdf (pdf: 8.7 MB)

O. Rübel, Prabhat, K. Wu, H. Childs, J. Meredith, C.G.R. Geddes, E. Cormier-Michel, S. Ahern, G.H. Weber, P. Messmer, H. Hagen, B. Hamann and E.W. Bethel, "Application of High-performance Visual Analysis Methods to Laser Wakefield Particle Acceleration Data", IEEE Visualization 2008, October 2008,

Download File: LBNL-952E.pdf (pdf: 1.3 MB)

B. Paul, S. Ahern, E. W. Bethel, E. Brugger, R. Cook, J. Daniel, K. Lewis, J. Owen, and D. Southard, "Chromium Renderserver: Scalable and Open Remote Rendering Infrastructure", IEEE Transactions on Visualization and Computer Graphics, May 2008, 14:627-639, LBNL 63693,

Download File: LBNL-63693-CRRS.pdf (pdf: 2.7 MB)

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, J. Malik, "A Quantitative Spatio-temporal Atlas of Gene Expression in the Drosophila Blastoderm", Cell, April 18, 2008, 133:364-374,

G.H. Weber, V. Beckner, H. Childs, T. Ligocki, M. Miller, B. van Straalen, E.W. Bethel, "Visualization of Scalar Adaptive Mesh Refinement Data", Numerical Modeling of Space Plasma Flows: Astronum-2007 (Astronomical Society of the Pacific Conference Series), April 2008, 385:309-320, LBNL 220E,

Download File: LBNL-220E.pdf (pdf: 1.5 MB)

J. Chen, I. Yoon and E. W. Bethel, "Interactive, Internet Delivery of Visualization via Structured, Prerendered Multiresolution Imagery.", IEEE Transactions on Visualization and Computer Graphics, March 2008, 14:302-312, LBNL 62252,

Download File: LBNL-62252-chen-tvcg.pdf (pdf: 2.1 MB)

Daniela Ushizima, Oliver Rübel, Prabhat, Gunther Weber, E. Wes Bethel, Cecilia Aragon, Cameron Geddes, Estelle Cormier-Michel, Bernd Hamann, Peter Messmer, Hans Hagen, "Automated Analysis for Detecting Beams in Laser Wakefield Simulations", 2008 Seventh International Conference on Machine Learning and Applications, Proceedings of IEEE ICMLA'08, 2008, 382-387, LBNL 960E,

Download File: LBNL-960E.pdf (pdf: 528 KB)

Luke J. Gosink, John C. Anderson, E. Wes Bethel, Kenneth I. Joy, "Query-Driven Visualization of Time-Varying Adaptive Mesh Refinement Data", IEEE Transactions on Visualization and Computer Graphics, 2008, 14:1715-1722, LBNL 803E,

Download File: LBNL-803E.pdf (pdf: 4.3 MB)

Luke J Gosink, "Bin-hash indexing: A parallel method for fast query processing", 2008, LBNL 729E,

Download File: LBNL-729E.pdf (pdf: 511 KB)

E. Wes Bethel, Chris Johnson, Charles Hansen, Claudio Silva, Steven Parker, Allen Sanderson, Lee Myers, Martin Cole, Xavier Tricoche, Sean Ahern, George Ostrouchov, Dave Pugmire, Jamison Daniel, Jeremy Meredith, Valerio Pascucci, Hank Childs, Peer-Timo Bremer, Ajith Mascarenhas, Ken Joy, Bernd Hamann, Christoph Garth, Cecilia Aragon, Gunther Weber, and Prabhat, Seeing the Unseeable, SciDAC Review, Pages: 24-33, 2008,

Download File: vacet2.pdf (pdf: 1.1 MB)

O. Rübel, G. H. Weber, M-Y Huang, E. W. Bethel, S. V. E. Keränen, C. C. Fowlkes, C. L. Luengo Hendriks, A. H. DePace, L. Simirenko, M. B. Eisen, M. D. Biggin, H. Hagen, J. Malik, D. W. Knowles and B. Hamann, "PointCloudXplore 2: Visual Exploration of 3D Gene Expression", Visualization of Large and Unstructured Data Sets, edited by C. Garth, H. Hagen, M. Hering-Bertram, (Gesellschaft fuer Informatik (GI): 2008) LBNL 249E,

Download File: LBNL-249E.pdf (pdf: 2.9 MB)

William T.C. Kramer, John M. Shalf, E. Wes Bethel, D. Agarwal, Michael Banda, John Hules, Juan C. Meza, Leonid Oliker, Horst Simon, David Skinner, Francesca Verdier, Howard Walter, Michael Wehner, and Katherine Yelick, "HPC in 2016: A View Point from NERSC", Proceedings of the Cray User Group Conference, Helsinki, Finland, 2008,

Luke J. Gosink, Kesheng Wu, E. Wes Bethel, D. Owens, Kenneth I. Joy, Bin-Hash Indexing: A Parallel Method For Fast Processing, 2008,

E. Wes Bethel, Oliver Rübel, Prabhat, Wu, Gunther H. Weber, Valerio Pascucci Hank Childs, Ajith Mascarenhas, Jeremy, Sean Ahern, "Modern Scientific Visualization is More than Just Pictures", Numerical Modeling of Space Plasma Flows: (Astronomical Society of the Pacific Series), St. Thomas, USVI, 2008, 301--317,

Oliver R\ ubel, Prabhat, Kesheng Wu, Hank, Jeremy Meredith, Cameron G. R. Geddes, Cormier-Michel, Sean Ahern, Gunther H., Peter Messmer, Hans Hagen, Bernd Hamann E. Wes Bethel, Application of High-performance Visual Analysis to Laser Wakefield Particle Acceleration Data, IEEE Visualization 2008, 2008,

Oliver R\ ubel, Prabhat, Kesheng Wu, Hank, Jeremy Meredith, Cameron G. R. Geddes, Cormier-Michel, Sean Ahern, Gunther H., Peter Messmer, Hans Hagen, Bernd Hamann E. Wes Bethel, High Performance Multivariate Visual Data Exploration Extemely Large Data, SuperComputing 2008 (SC08), Pages: 51 2008,

C Garth, H Krishnan, X Tricoche, T Bobach, KI Joy, Generation of accurate integral surfaces in time-dependent vector fields, IEEE Transactions on Visualization and Computer Graphics, Pages: 1404--1411 2008, doi: 10.1109/TVCG.2008.133

M.-Y. Huang, O. Rübel, G.H. Weber, C.L. Luengo Hendriks, M.D. Biggin, H. Hagen, B. Hamann, "Segmenting Gene Expression Patterns of Early-stage Drosophila Embryos.", Mathematical Methods for Visualization in Medicine and Life Sciences, edited by L. Linsen, H. Hagen, B. Hamann, (Springer-Verlag: January 2008) Pages: 313--327, LBNL 62450,

Download File: LBNL-62450.pdf (pdf: 3.7 MB)

C.I.O. Martins, R.M.S. Veras, G.L.B. Ramalho, F.N.S. Medeiros, D. M. Ushizima, "Automatic Microaneurysm Detection and Characterization Through Digital Color Fundus Images", Brazilian Artificial Intelligence Community Conference, Tenth Brazilian Symposium on Neural Networks, Proceedings of IEEE SBRN'2008, 2008,

AR Fuller, H Krishnan, K Mahrous, B Hamann, KI Joy, Real-time procedural volumetric fire, Proceedings - I3D 2007, ACM SIGGRAPH Symposium on Interactive 3D Graphics and Games, Pages: 175--180 2007, doi: 10.1145/1230100.1230131

Shengyin Gu, Iain Anderson, Victor Kunin, Michael Cipriano, Minovitsky, Gunther H. Weber, Nina Amenta, Bernd Hamann Inna Dubchak, "TreeQ-VISTA: An Interactive Tree Visualization Tool with Functional Query Capabilities", Bioinformatics, 2007, 23:764--766, doi: 10.1093/bioinformatics/btl643

Gunther H. Weber, Scott E. Dillard, Hamish Carr, Pascucci, Bernd Hamann, "Topology-Controlled Volume Rendering", IEEE Transactions on Visualization and Computer Graphics, 2007, 13:330--341, doi: 10.1109/TVCG.2007.47

Oliver G. Staadt, Vijay Natarjan, Gunther H. Weber, F. Wiley, B. Hamann, "Interactive Processing and Visualization of Image Data for Biomedical and Science Applications", BMC Cell Biology, 2007, 8:S10, doi: 10.1186/1471-2121-8-S1-S10

Gunther H. Weber, Peer-Timo Bremer, Valerio Pascucci, "Topological Landscapes: A Terrain Metaphor for Scientific Data", IEEE Transactions on Visualization and Computer Graphics Issue: Proceedings of IEEE Visualization 2007), 2007, 13:1416--1423, doi: 10.1109/TVCG.2007.70601

K. Wu, K. Stockinger, A. Shoshani, Wes, "FastBit--Helps Finding the Proverbial Needle in a", 2006, LBNL LBNL-PUB/963,

Luke Gosink, John Shalf, Kurt Stockinger, Wu, Wes Bethel, "HDF5-FastQuery: Accelerating Complex Queries on Datasets using Fast Bitmap Indices", SSDBM 2006, Vienna, Austria, July 2006, IEEE Computer Society Press., 2006, 149--158,

Luke Gosink, John Shalf, Kurt Stockinger, Kesheng Wu, Wes Bethel, HDF5-FastQuery: Accelerating complex queries on HDF datasets using fast bitmap indices, 18th International Conference on Scientific and Statistical Database Management (SSDBM 06), Pages: 149--158 2006,

E. Wes Bethel, Scott Campbell, Eli Dart, Kurt Stockinger, Kesheng Wu, Accelerating Network Traffic Analysis Using Visualization, Symposium on Visual Analytics Science and Technology Baltimore, Maryland, USA, October 31 - November 2006, Pages: 115--122 2006,

E. Wes Bethel, Scott Campbell, Eli Dart, John Shalf, Kurt Stockinger, Kesheng Wu, High Performance Visualization using Query-Driven and Analytics, 2006,

Kurt Stockinger, E. Wes Bethel, Scott Campbell, Eli Dart, Kesheng Wu, Detecting distributed scans using high-performance visualization, SC 06, Pages: 82 2006,

Cris L. Luengo Hendriks, Soile V. E. Keränen, C. Fowlkes, Lisa Simirenko, Gunther H. Weber, H. DePace, Clara Henriquez, David W. Kaszuba, Hamann, Michael B. Eisen, Jitendra Malik, Damir Sudar, D. Biggin, David W. Knowles, "Three-dimensional Morphology and Gene Expression in the Drosophila Blastoderm at Cellular Resolution I: Data Acquisition Pipeline", Genome Biology, 2006, 7:R123, doi: 10.1186/gb-2006-7-12-r123

E. Wes Bethel, Scott Campbell, Eli Dart, Lee, Steven A. Smith, Kurt Stockinger, Tierney, Kesheng Wu, "Interactive Analysis of Large Network Data Collections Query-Driven Visualization", 2005,

Kurt Stockinger, John Shalf, Kesheng Wu, E Wes Bethel, "Query-driven visualization of large data sets", VIS 05. IEEE Visualization, 2005., 2005, 167--174,

Kurt Stockinger, John Shalf, Wes Bethel, Kesheng Wu, DEX: Increasing the Capability of Scientific Data Analysis by Using Efficient Bitmap Indices to Accelerate Scientific Visualization, SSDBM, Pages: 35-44 2005,

Horst D. Simon, William T.C. Kramer, David H. Bailey, Michael J. Banda, E. Wes Bethel, Jonathan T. Carter, James M. Craw, William J. Fortney, John A. Hules, Nancy L. Meyer, Juan C. Meza, Esmond G. Ng, Lynn E. Rippe, William C. Saphir, Francesca Verdier, Howard A. Walter, Katherine A. Yelick, "Science-Driven Computing: NERSC's Plan for 2006-2010", 2005,

Kurt Stockinger, Kesheng Wu, Scott Campbell, Lau, Mike Fisk, Eugene Gavrilov, Alex, Christopher E. Davis, Rick Olinger, Rob, Jim Prewett, Paul Weber, Thomas P., E. Wes Bethel, Steve Smith, Network Traffic Analysis With Query Driven, SC 2005, 2005,

Gunther H. Weber, Martin Öhler, Oliver Kreylos, John Shalf, Wes Bethel, Bernd Hamann, Gerik Scheuermann, "Parallel Cell Projection Rendering of Adaptive Mesh Refinement Data", IEEE Symposium on Parallel and Large-Data Visualization and Graphics, 2003, 51-60,

E. Wes Bethel, Greg Abram, John Shalf, Randall Frank, Jim Ahrens, Steve Parker, N. Samatova, Mark Miller, Interoperability of Visualization Software and Data Models is NOT an Achievable Goal, IEEE Visualization, Pages: 607-610 2003,

T. J. Jankun-Kelly, Kreylos, Ma, Hamann, I. Joy, John Shalf, E. Wes Bethel, Deploying Web-Based Visual Exploration Tools on the Grid, IEEE Computer Graphics and Applications, Pages: 40-50 2003,

E. Wes Bethel, John Shalf, Grid-Distributed Visualizations Using Connectionless Protocols, IEEE Computer Graphics and Applications, Pages: 51-59 2003,

John Shalf, E. Wes Bethel, The Grid and Future Visualization System Architectures, IEEE Computer Graphics and Applications, Pages: 6-9 2003,

Gunther H. Weber, Oliver Kreylos, Terry J. Ligocki, Jonh Shalf, Hans Hagen, Bernd Hamann, Ken I. Joy, Kwan-Liu Ma, "High-quality Volume Rendering of Adaptive Mesh Refinement Data", VMV, 2001, 121-128,