Publications
============

Recent
------

#. Indiana University (Fox, Qiu, Crandall, von Laszewski), Rutgers
   (Jha), Virginia Tech (Marathe), Kansas (Paden), Stony Brook (Wang),
   Arizona State (Beckstein), Utah (Cheatham), "Datanet: CIF21 DIBBs:
   Middleware and High Performance Analytics Libraries for Scalable Data
   Science" presentation at "Advancing the state-of-the-art in
   high-performance computing, communications and data analytics"
   workshop at Pittsburgh PA May 17-18 2016.

   -  Full version: http://dsc.soic.indiana.edu/presentations/DibbsSPIDAL-May17-2016\_v4.pptx
   -  Smaller version:  http://dsc.soic.indiana.edu/presentations/DibbsSPIDAL-May17-2016\_v4S.pptx

Rutgers University
------------------

#. Hadoop on HPC: Integrating Hadoop and Pilot-based Dynamic Resource
   Management Andre Luckow, Ioannis Paraskevakos, George
   Chantzialexiou, Shantenu Jha Workshop on High-Performance Big Data
   Computing, 2016 [`link <http://arxiv.org/abs/1602.00345>`_] [`bib
   <https://www.github.com/saga-project/radical.wp/raw/master/publications/bib/hadoop-on-hpc.bib>`_]
   : hadoop-on-hpc `http://arxiv.org/abs/1602.00345
   <http://arxiv.org/abs/1602.00345>`_

#. Pilot-Abstraction: A Valid Abstraction for Data-Intensive Application
   on HPC, Hadoop and Cloud Infrastructures?, Andre Luckow,
   Pradeep Mantha, Shantenu Jha pdf version
   `here <http://arxiv.org/pdf/1501.05041v1.pdf>`__
#. A Tale of Two Data-Intensive Paradigms: Applications, Abstractions,
   and Architectures, Shantenu Jha, Judy Qiu, Andre Luckow,
   Pradeep Mantha, Geoffrey C. Fox 2014 IEEE International Congress on
   Big Data (BigData Congress), 2014 pdf version
   `here <http://arxiv.org/abs/1403.1528>`__

Stony Brook University and Emory University
-------------------------------------------

#. Ablimit Aji and Fusheng Wang (2016). `Challenges and Approaches in
   Spatial Big Data Management 
   <http://www.crcnetbase.com/doi/abs/10.1201/b19694-3>`_. Big Data:
   Storage, Sharing, and Security (3S) Fei Hu.  Auerbach Publications.

#. Cong Xie, Wen Zhong， Jun Kong , Wei Xu, Klaus Mueller, and Fusheng
   Wang (2016). IEVQ: An Iterative Example-based Visual Query for
   Pathology Database.  Proceedings of the Second International
   Workshop on Data Management and Analytics for Medicine and
   Healthcare.

#. Hoang Vo, Jun Kong, Dejun Teng, Yanhui Liang, Ablimit Aji, George
   Teodoro and Fusheng Wang (2016). A MapReduce Based High Performance
   Whole Slide Image Analysis Framework in the Cloud.  Proceedings of
   the Second International Workshop on Data Management and Analytics
   for Medicine and Healthcare.

#. Jun Kong, Pengyue Zhang, Yanhui Liang, George Teodorou,
   Daniel J. Brat and Fusheng Wang (2016). `Robust Cell Segmentation
   for Histological Images of Glioblastoma
   <http://ieeexplore.ieee.org/Xplore/defdeny.jsp?url=http%3A%2F%2Fieeexplore.ieee.org%2Fstamp%2Fstamp.jsp%3Ftp%3D%26arnumber%3D7493444&denyReason=-134&arnumber=7493444&productsMatched=null&userType=inst>`_.
   International Symposium on Biomedical Imaging (ISBI 2016).

#. Xin Chen and Fusheng Wang (). Integrative Spatial Data Analytics
   for Public Health Studies of New York State.  Proceedings of AMIA
   2016 Annual Symposium.

#. Yanhui Liang, Jun Kong, Yangyang Zhu and Fusheng Wang
   (2016). Three-Dimensional Data Analytics for Pathology Imaging.
   First International Workshop on Data Management and Analytics for
   Medicine and Healthcare (DMAH 2015).

#. Liver Whole Slide Image Analysis for 3D Vessel
   Reconstruction. Y. Liang, F. Wang, D. Treanor, D. Magee, G. Teodoro, Y. Zhu,
   J. Kong International Symposium on Biomedical Imaging: From Nano to
   Macro (ISBI’2015), Accepted, Brooklyn, NY, USA, April 16-19, 2015.
#. Automated Cell Recognition with 3D Fluorescence Microscopy
   Images. J. Kong, F. Wang, G. Teodoro, Y. Liang, Y. Zhu, C.
   Tucker-Burden, D.J. Brat International Symposium on Biomedical
   Imaging: From Nano to Macro (ISBI’2015), Accepted, Brooklyn, NY,
   USA, April 16-19, 2015.
#. A Framework for 3D Vessel Analysis using Whole Slide Images of Liver
   Tissue Sections, Y. Liang, F. Wang, D. Treanor, D. Magee, N.
   Roberts, G. Teodoro, Y. Zhu, J. Kong International Journal of
   Computational Biology and Drug Design. In Press
#. High Performance Spatial Queries for Spatial Big Data: from Medical
   Imaging to GIS, F. Wang, A. Aji and H. Vo In Press. ACM
   SIGSPATIAL Special Issue, 2015
#. Effective Temporal Modeling for Scalable Spatio-Temporal
   Queries. H. Vo and F. Wang To Appear in Proc. of the International
   Workshop on Spatiotemporal Computing (IWSC'2015). Fairfax,
   Virginia, July 13-15th, 2015
#. High Performance Integrated Spatial Big Data Analytics, X.
   Chen, H. Vo, A. Aji and F. Wang In Proc. of the Third ACM SIGSPATIAL
   International Workshop on Analytics for Big Geospatial Data
   (BigSpatial-2014), Nov 4, 2014, Dallas, TX, USA
#. Haggis: Turbo Charge A MapReduce based Spatial Data Warehousing
   System with GPU Engine, Ablimit Aji, George Teodoro and
   Fusheng Wang In Proc. of the Third ACM SIGSPATIAL International
   Workshop on Analytics for Big Geospatial Data (BigSpatial-2014), Nov
   4, 2014, Dallas, TX, USA
#. SATO: A Spatial Data Partitioning Framework for Scalable Query
   Processing, A. Aji, G. Teodoro and F. Wang In Proc. of the
   22nd ACM SIGSPATIAL International Conference on Advances in
   Geographic Information Systems (ACM SIGSPATIAL 2014), November 4-7,
   2014, Dallas, TX, USA

Indiana University
------------------
#.  Supun Kamburugamuve, Pulasthi Wickramasinghe, Saliya Ekanayake,
    Chathuri Wimalasena, Milinda Pathirage, Geoffrey Fox,
    "TSmap3D: Browser Visualization of High Dimensional Time Series Data",
    Technical report May 10 2016
    pdf version
    `here <http://dsc.soic.indiana.edu/publications/tsmap3d.pdf>`__
#.  Saliya Ekanayake, Supun Kamburugamuve and Geoffrey Fox,
    “SPIDAL: High Performance Data Analytics with Java and MPI on Large Multicore HPC Clusters”,
    Technical Report January 5 2016, Proceedings of 24th
    High Performance Computing Symposium (HPC 2016),
    April 3-6, 2016, Pasadena, CA, USA as part of the SCS Spring Simulation Multi-Conference (SpringSim'16)
    pdf version
    `here <http://dsc.soic.indiana.edu/publications/hpc2016-spidal-high-performance-submit-18-public.pdf>`__
#.  Geoffrey Fox, Judy Qiu, Shantenu Jha, Saliya Ekanayake, and Supun Kamburugamuve,
    “Big Data, Simulations and HPC Convergence”
    Technical Report January 30 2016. DOI: 10.13140/RG.2.1.1858.8566
    pdf version
    `here <http://dsc.soic.indiana.edu/publications/HPCBigDataConvergence.pdf>`__
#.  Supun Kamburugamuve, Saliya Ekanayake, Milinda Pathirage, Geoffrey Fox,
    “Towards High Performance Processing of Streaming Data in Large Data Centers”
    Technical Report January 26 2016, to be published in proceedings of
    HPBDC 2016 IEEE International Workshop on High-Performance Big Data
    Computing in conjunction with The 30th IEEE International Parallel and
    Distributed Processing Symposium (IPDPS 2016),Chicago Hyatt Regency,
    Chicago, Illinois USA, Friday, May 27th, 2016
    pdf version
    `here <http://dsc.soic.indiana.edu/publications/high_performance_processing_stream.pdf>`__
#.  Bingjing Zhang, Peng Bo, Judy Qiu, "Model Data-Centric Computation
    Abstractions in Machine Learning Applications", to appear in
    3rd Workshop on Algorithms and Systems for MapReduce and Beyond (BeyondMR2016),
    held in conjunction with SIGMOD/PODS2016, July 1, 2016
    pdf version
    `here <http://ipcc.soic.iu.edu/Computation%20Abstractions.pdf>`__
#.  Bingjing Zhang, Bo Peng, Judy Qiu,
    “High Performance LDA through Collective Model Communication Optimization”,
    Proceedings of International Conference on Computational Science (ICCS2016) conference,
    June 6-8, 2016, San Diego, California.
    pdf version
    `here <http://ipcc.soic.iu.edu/Harp-LDA.pdf>`__
#.  Binging Zhang,” A Collective Communication Layer for the Software Stack of Big Data Analytics”,
    Doctoral Symposium. Proceedings of IEEE International Conference on
    Cloud Engineering (IC2E2016) Conference, April 4-8, 2016, Berlin, Germany.
    `here <http://ipcc.soic.iu.edu/A%20Collective%20Communication%20Layer.pdf>`__
#.  Towards HPC-ABDS: An Initial High-Performance Big Data Stack, in
    Building Robust Big Data Ecosystem, Judy Qiu, Shantenu Jha,
    Andre Luckow and Geoffrey C. Fox, ISO/IEC JTC 1 Study Group on Big
    Data. March 18-21, 2014. San Diego Supercomputer Center, San Diego
    pdf version
    `here <http://dsc.soic.indiana.edu/publications/nist-hpc-abds.pdf>`__
#.  High Performance High Functionality Big Data Software Stack In Big
    Data and Extreme-scale Computing (BDEC), Geoffrey Fox, Judy
    Qiu, and Shantenu Jha Fukuoka, Japan, 2014 pdf version
    `here <http://www.exascale.org/bdec/sites/www.exascale.org.bdec/files/whitepapers/fox.pdf>`__
#.  A Tale of Two Data-Intensive Approaches: Applications, Architectures
    and Infrastructure, Shantenu Jha, Judy Qiu, Andre Luckow,
    Pradeep Mantha, and Geoffrey C. Fox In 3rd International IEEE
    Congress on Big Data Application and Experience Track. June 27- July
    2, 2014. Anchorage, Alaska pdf version
    `here <http://arxiv.org/abs/1403.1528>`__
#.  HPC-ABDS Kaleidoscope of over 300 Apache Big Data Stack and HPC
    Technologies Accessed April 8, 2014 Available
    `here <http://hpc-abds.org/kaleidoscope/>`__
#.  Towards an Understanding of Facets and Exemplars of Big Data
    Applications, Geoffrey C. Fox, Shantenu Jha, Judy Qiu, and
    Andre Luckow In 20 Years of Beowulf: Workshop to Honor Thomas
    Sterling's 65th Birthday, October 14, 2014. Annapolis, MD pdf
    version
    `here <http://dsc.soic.indiana.edu/publications/OgrePaperv9.pdf>`__
#.  Big Data Use Cases and Requirements, Geoffrey Fox and Wo
    Chang In 1st Big Data Interoperability Framework Workshop: Building
    Robust Big Data Ecosystem ISO/IEC JTC 1 Study Group on Big Data
    March 18 - 21, 2014. San Diego Supercomputer Center, San Diego, CA
    pdf version
    `here <http://dsc.soic.indiana.edu/publications/NISTUseCase.pdf>`__
#.  NIST Big Data Use Case & Requirements 2013 [accessed March 1, 2015]
    Available `here <http://bigdatawg.nist.gov/V1_output_docs.php>`__
#.  Ogres: A Systematic Approach to Big Data Benchmarks,
    Geoffrey C. Fox, Shantenu Jha, Judy Qiu, and Andre Luckow In Big
    Data and Extreme-scale Computing (BDEC) January 29-30, 2015.
    Barcelona pdf version
    `here <http://www.exascale.org/bdec/sites/www.exascale.org.bdec/files/whitepapers/OgreFacets.pdf>`__
#.  Towards a Comprehensive Set of Big Data Benchmarks, Geoffrey
    C. Fox, Shantenu Jha, Judy Qiu, Saliya Ekanayake, and Andre Luckow
    February 15, 2015 pdf version
    `here <http://dsc.soic.indiana.edu/publications/OgreFacetsv9.pdf>`__
#. ESTIMATING BEDROCK AND SURFACE LAYER BOUNDARIES AND CONFIDENCE
   INTERVALS IN ICE SHEET RADAR IMAGERY USING MCMC, Stefan
   Lee, Jerome Mitchell, David J. Crandall, and Geoffrey C. Fox The
   International Conference on Image Processing (ICIP), Paris, France.
   October 27-29, 2014 pdf version `here
   <http://dsc.soic.indiana.edu/publications/ICIPpaper.pdf>`__
#. Harp: Collective Communication on Hadoop, Bingjing Zhang,
   Yang Ruan, and Judy Qi In IEEE International Conference on Cloud
   Engineering (IC2E), March 9-12, 2015. Tempe, AZ pdf version `here
   <http://dsc.soic.indiana.edu/publications/HarpQiuZhang.pdf>`__
#. HPC-ABDS: High Performance Computing Enhanced Apache Big Data
   Stack. Geoffrey Fox, Judy Qiu, Shantenu Jha, Supun Kamburugamuve
   and Andre Luckow Invited talk at 2nd International Workshop on
   Scalable Computing For Real-Time Big Data Applications (SCRAMBL'15)
   at CCGrid2015, the 15th IEEE/ACM International Symposium on
   Cluster, Cloud and Grid Computing, held in Shenzhen, Guangdong,
   China pdf version `here
   <http://dsc.soic.indiana.edu/publications/HPC-ABDSDescribedv2.pdf>`__
#. Parallel Clustering of High-Dimensional Social Media Data
   Streams. Xiaoming Gao, Emilio Ferrara, Judy Qiu Presented at
   CCGrid2015, the 15th IEEE/ACM International Symposium on Cluster,
   Cloud and Grid Computing, held in Shenzhen, Guangdong, China pdf
   version `here
   <http://dsc.soic.indiana.edu/publications/Parallel%20Clustering%20of%20High-Dimensional%20Social%20Media%20Data%20Streams_v11.pdf>`__

University of Kansas
--------------------

#. John Paden, Theresa Stumpf, Wideband DOA Estimation for Ice Sheet
   Bed Mapping, Paper#: 101, 2016 IEEE International Symposium on
   Phased Array Systems & Technology, 18-21 October 2016
   Massachusetts, USA.

#. Radiostratigraphy and age structure of the Greenland Ice
   Sheet. MacGregor, J.A.  M.A. Fahnestock, G.A. Catania, J.D. Paden,
   S. Gogineni, S.C. Rybarski, S.K. Young, A.N. Mabrey, B.M. Wagman and
   M. Morlighem Journal of Geophysical Research Earth Surface, Jan 2015,
   2014JF003215. pdf version
   `here <http://onlinelibrary.wiley.com/doi/10.1002/2014JF003215/full>`__
#. Bed Topography of Jakobshavn and Byrd Glaciers In Big Data and
   Extreme-scale Computing (BDEC), S. Gogineni, J.-B. Yan, J.
   Paden, C. Leuschen, J. Li, F. Rodriguez-Morales, D. Braaten, K.
   Purdon, Z. Wang, W. Liu, and J. Gauch Journal of Glaciology, vol. 60,
   no. 223, pp. 813-833, Nov 2014. pdf version
   `here <http://www.ingentaconnect.com/content/igsoc/jog/2014/00000060/00000223/art00001>`__
#. Radar Mapping of Isunguata Sermia Glacier, Greenland, In Big Data and
   Extreme-scale Computing (BDEC), Ken Jezek, Xiaoqing Wu, John
   Paden, Carl Leuschen IGS Journal of Glaciology, vol. 59, no. 218,
   1135-1146, 2013.
#. Layer-finding in Radar Echograms using Probabilistic Graphical Models
   2012 International Conference on Pattern Recognition, David
   J. Crandall, Geoffrey C. Fox, John D. Paden Journal of Glaciology,
   vol. 60, no. 223, pp. 813-833, Nov 2014. pdf version
   `here <http://vision.soic.indiana.edu/wp/wp-content/uploads/icpr12-ice1.pdf>`__
#. High-Altitude Radar Measurements of Ice Thickness over the Antarctic
   and Greenland Ice Sheets as a part of Operation Ice Bridge,
   Jilu Li, John Paden, Carl Leuschen, Fernando Rodriguez-Morales,
   Richard Hale, Emily Arnold, Reid Crowe, Daniel Gomez-Garcia, and
   Sivaprasad Gogineni, IEEE Transactions on Geoscience and Remote
   Sensing, 2012, vol.50, no. 12, doi: 10.1109/TGRS.2012.2203822. pdf
   version
   `here <http://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=6248690>`__
#. Ice-sheet bed 3-D tomography, John Paden, Torry Akins, David
   Dunson, Christopher Allen, Sivaprasad Gogineni Journal of Glaciology,
   56 (195), 3-11. pdf version
   `here <http://www.researchgate.net/publication/233559746_Ice-sheet_bed_3-D_tomography>`__
#. Comparison of tomographic methods for ice bottom mapping,,
   John D. Paden, Sahana Raghunandan, Shannon Blunt, Carl Leuschen
   International Glaciological Society Radioglaciology 2013 Meeting,
   Sept 9-13, entry 67A084. Information available
   `here <http://www.igsoc.org/symposia/2013/kansas/proceedings/proceedings.html>`__
#. 3D Imaging of Ice Sheets, John Paden, Christopher Allen,
   Prasad Gogineni IEEE Geoscience and Remote Sensing Symposium, 2010
   (IGARSS ’10), Honolulu, Hawaii, 25-30 July, 2010. pdf version 
   `here <http://geodesy.unr.edu/hanspeterplag/library/IGARSS2010/pdfs/4526.pdf>`__

Arizona State University
------------------------

#. MDAnalysis: A toolkit for the analysis of molecular dynamics
   simulations.  N. Michaud-Agrawal, E. J. Denning, T. B. Woolf,
   and O. Beckstein. J Comp Chem, 32:2319–2327, 2011. doi:
   10.1002/jcc.21787. More information
   `here <http://www.mdanalysis.org>`__

Virginia Polytechnic Institute and State University
---------------------------------------------------

#. Alam M, Khan M, Vullikanti A, Marathe M (2016) An Efficient and
   Scalable Algorithmic Method for Generating Large–Scale Random
   Graphs. In Proceedings of the The International Conference for High
   Performance Computing, Networking, Storage and Analysis. Salt Lake
   City, UT, November 13-18, 2016

#. Arifuzzaman S, Khan M, Marathe M (2015) `A Space-efficient Parallel
   Algorithm for Counting Exact Triangles in Massive Networks
   <https://ndssl.vbi.vt.edu/cms/ViewItem.php?id=70042831-53a3-9994-ed6c-3bff503f23b2>`_. In
   Proceedings of the 17th IEEE International Conference on High
   Performance Computing and Communications.  New York City, NY,
   August 24-26

#. Parallel Algorithms for Generating Random Networks with Given Degree
   Sequences.  Maksudul Alam and Maleq Khan. 12th IFIP
   International Conference on Network and Parallel Computing (NPC), New
   York City, Sep. 2015. pdf version
   `here <http://arxiv.org/abs/1406.1215>`__.

#. A Space-efficient Parallel Algorithm for Counting Exact Triangles in
   Massive Networks.  Shaikh Arifuzzaman, Maleq Khan and Madhav
   Marathe. 17th IEEE International Conference on High Performance
   Computing and Communications (HPCC), New York City, Aug. 2015. pdf
   version
   `here <http://staff.vbi.vt.edu/maleq/papers/sptriangle.pdf>`__.

#. Fast Parallel Conversion of Edge List to Adjacency List for
   Large-Scale Graphs.  Shaikh Arifuzzaman and Maleq Khan. 23rd
   High Performance Computing Symposium (HPC), Alexandria, VA, USA,
   April 2015. pdf version
   `here <http://staff.vbi.vt.edu/maleq/papers/conversion.pdf>`__.

#. Distributed Memory Parallel Algorithms for Massive Graphs.  
   Maksudul Alam, Shaikh Arifuzzaman, Hasanuzzaman Bhuiyan, Maleq Khan,
   V.S. Anil Kumar, and Madhav Marathe. Parallel Graph Algorithms, CRC
   Press / Taylor & Francis, 2015 Ed. David Bader.