Publications

Journals, Book Chapters, and Thesis

• Seung-Hee Bae, Daniel Halperin, Jevin West, Martin Rosvall, and Bill Howe,
  "Scalable and Efficient Flow-Based Community Detection for Large-Scale Graph Analysis,"
  ACM Transactions on Knowledge Discovery in Data (TKDD), 2016 [accepted]
• Seung-Hee bae,
  "Scalable High Performance Multidimensional Scaling,"
  Ph.D. Dissertation, Indiana University, 2012.
• Adam Hughes, Yang Ruan, Saliya Ekanayake, Seung-Hee Bae, Qunfeng Dong, Mina Rho, Judy Qiu, and Geoffrey Fox,
  "Interpolative Multidimensional Scaling Techniques for the Identification of Clusters in Very Large Sequence Sets,"
  Special Issue of BMC Bioinformatics, vol. 13, no. Suppl 2, p. S9, 2012
• Judy Qiu and Seung-Hee Bae,
  "Performance of Windows Multicore Systems on Threading and MPI,"
  Concurrency and Computation: Practice and Experience,Vol 24(1): 14-28, 2012
• Jong Youl Choi, Seung-Hee Bae, Judy Qiu, Bin Chen, and David Wild,
  "Browsing Large Scale Cheminformatics Data with Dimension Reduction,"
  Concurrency and Computation: Practice and Experience,Vol 23(17): 2315-2325, 2011
• Thilina Gunarathne, Tak-Lon Wu, Jong Youl Choi, Seung-Hee Bae, and Judy Qiu,
  "Cloud Computing Paradigms for Pleasingly Parallel Biomedical Applications,"
  Concurrency and Computation: Practice and Experience,Vol 23(17): 2338-2354, 2011
• Judy Qiu, Jaliya Ekanayake, Thilina Gunarathne, Jong Youl Choi, Seung-Hee Bae, Hui Li, Bingjing Zhang, Tak-Lon Wu, Yang Ruan, Saliya Ekanayake, Adam Hughes, and Geoffrey Fox,
  "Hybrid cloud and cluster computing paradigms for life science applications,"
  BMC Bioinformatics, vol. 11, no. Suppl 12, p. S3, 2010.
• Judy Qiu, Jaliya Ekanayake, Thilina Gunarathne, Jong Youl Choi, Seung-Hee Bae, Yang Ruan, Saliya Ekanayake, Stephen Wu, Scott Beason, Geoffrey Fox, Mina Rho, and Haixu Tang,
  "Data Intensive Computing for Bioinformatics,"
  in Data Intensive Distributed Computing,IGI Publishers, 2010.
• Geoffrey Fox, Seung-Hee Bae, Jaliya Ekanayake, Xiaohong Qiu, and Huapeng Yuan,
  "Parallel Data Mining from Multicore to Cloudy Grids,"
  in High Speed and Large Scale Scientific Computing, IOS Press, Amsterdam, ISBN:978-1-60750-073-5, 2009
  (extended from Proceedings of HPC 2008 High Performance Computing and Grids workshop, Cetraro, Italy, Jul. 2008)
• Seung-Hee Bae, Haixu Tang, Jing Wu, Jun Xie, and Sun Kim,
  "dPattern: Transcription Factor Binding Site (TFBS) Discovery in Human Genome using a Discriminative Pattern Analysis,"
  Bioinformatics, 2007, Vol23(19):2619-2621.      [dPattern web server]
• Seung-Hee Bae,
  "An Adaptive Method for the Mutation Rates of Hybrid Genetic Algorithms,"
  M.S. Thesis, Seoul National University, 2004.

Conference & Workshop

• Seung-Hee Bae and Bill Howe,
  "GossipMap: A Distributed Community Detection Algorithm for Billion-Edge Directed Graphs,"
  in Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC '15), Austin, Texas, Nov. 2015.
• Seung-Hee Bae, Daniel Halperin, Jevin West, Martin Rosvall, and Bill Howe,
  "Scalable Flow-Based Community Detection for Large-Scale Network Analysis,"
  in Proceedings of IEEE International Conference on Data Mining Workshops (ICDMW 2013), Dallas, Texas, Dec. 2013. [pdf]
• Yang Ruan, Saliya Ekanayake, Mina Rho, Haixu Tang, Seung-Hee Bae, Judy Qiu, and Geoffrey Fox,
  "DACIDR: Deterministic Annealed Clustering with Interpolative Dimension Reduction using a Large Collection of 16S rRNA Sequences,"
  in Proceedings of ACM Conference on Bioinformatics, Computational Biology and Biomedicine (ACM BCB), Orlando, Florida, Oct. 2012.
• Seung-Hee Bae, Judy Qiu, and Geoffrey Fox,
  " Adaptive Interpolation of Multidimensional Scaling,"
  in Proceedings of International Conference on Computational Science (ICCS 2012), Omaha, Nebraska, Jun. 2012
• Seung-Hee Bae, Judy Qiu, and Geoffrey C. Fox,
  "Multidimensional Scaling by Deterministic Annealing with Iterative Majorization algorithm,"
  in Proceedings of 6th IEEE e-Science Conference, Brisbane, Austrailia, Dec. 2010.
• Seung-Hee Bae, Jong Youl Choi, Judy Qiu, and Geoffrey Fox,
  "Dimension Reduction and Visualization of Large High-dimensional Data via Interpolation,"
  in Proceedings of The ACM International Symposium on High Performance Distributed Computing (HPDC 2010), Chicago, Illinois, Jun. 2010.
• Jong Youl Choi, Seung-Hee Bae, Judy Qiu, Geoffrey Fox, Bin Chen, and David Wild,
  "Browsing Large Scale Cheminformatics Data with Dimension Reduction,"
  in Proceedings of Emerging Computational Methods for the Life Sciences Workshop of ACM HPDC 2010, Chicago, Illinois, Jun. 2010.
• Jaliya Ekanayake, Hui Li, Bingjing Zhang, Thilina Gunarathne, Seung-Hee Bae, Judy Qiu, and Geoffrey Fox,
  "Twister: A Runtime for Iterative MapReduce,"
  in Proceedings of the First International Workshop on MapReduce and its Applications of ACM HPDC 2010, Chicago, Illinois, Jun. 2010.
• Jong Youl Choi, Seung-Hee Bae, Xiaohong Qiu, and Geoffrey Fox,
  "High Performance Dimension Reduction and Visualization for Large High-dimensional Data Analysis,"
  in Proceedings of the The 10th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2010), Melbourne, Australia, May 2010.
• Judy Qiu, Scott Beason, Seung-Hee Bae, Saliya Ekanayake, and Geoffrey Fox,
  "Performance of Windows Multicore Systems on Threading and MPI,"
  in Proceeding of Frontiers of GPU, Multi- and Many-Core Systems Workshop of 10th IEEE/ACM CCGrid 2010, Melbourne, Australia, May 2010.
• Xiaohong Qiu, Jaliya Ekanayake, Thilina Gunarathne, Seung-Hee Bae, Jong Youl Choi, Scott Beason, and Geoffrey Fox,
  "Using MapReduce Technologies in Bioinformatics and Medical Informatics,"
  in Proceedings of Using Clouds for Parallel Computations in Systems Biology workshop at SC09, Portland, Oregon, Nov. 2009.
• Seung-Hee Bae,
  "Parallel Multidimensional Scaling Performance on Multicore Systems,"
  in Proceedings of Advanced in High-Performance E-Science Middleware and Applications Workshop at eScience 2008, Indianapolis, IN, USA, Dec. 2008.
• Xiaohong Qiu, Geoffrey Fox, Huapeng Yuan, Seung-Hee Bae, George Chrysanthakopoulos, and Henrik Frystyk Nielsen,
  "Parallel Data Mining on Multicore Clusters,"
  in Proceedings of 7th International Conference on Grid and Cooperative Computing (GCC2008), Shenzhen, China, Oct. 2008.
• Geoffrey Fox, Seung-Hee Bae, Jaliya Ekanayake, Xiaohong Qiu, and Huapeng Yuan,
  "Parallel Data Mining from Multicore to Cloudy Grids,"
  in Proceedings of HPC 2008 High Performance Computing and Grids workshop, Cetraro, Italy, Jul. 2008
• Xiaohong Qiu, Geoffrey Fox, Huapeng Yuan, Seung-Hee Bae, George Chrysanthakopoulos, and Henrik Frystyk Nielsen,
  "Performance of Multicore Systems on Parallel Dataminig Services,"
  in Proceedings of International Conference on Computational Science (ICCS 2008), Krakow, Poland, Jun. 23-25, 2008
• Xiaohong Qiu, Geoffrey Fox, Huapeng Yuan, Seung-Hee Bae, George Chrysanthakopoulos, and Henrik Frystyk Nielsen,
  "Parallel Clustering and Dimensional Scaling on Multicore Systems,"
  in Proceedings of The 2008 High Performance Computing & Simulation Conference (HPCS 2008), Nicosia, Cyprus, Jun. 3-6, 2008
• Geoffrey Fox, Seung-Hee Bae, Rajarshi Guha, Marlon E. Pierce, Xiaohong Qiu, David J. Wild , and Huapeng Yuan,
  "High Performance Robust Datamining for Cheminformatics"
  PAPER ID: 1168842 at Division of Chemical Information session on, Cheminformatics: From Teaching to Research at Spring 2008 American Chemical Society National Meeting & Exposition, April 6-10, 2008 New Orleans, LA, USA
• Xiaohong Qiu, Geoffrey Fox, Huapeng Yuan, Seung-Hee Bae, George Chrysanthakopoulos, and Henrik Nielsen,
  "High Performance Data Mining"
  at Shanghai Many-Core Workshop, Mar. 27-28, 2008, Shanghai, China
• Xiaohong Qiu, Geoffrey Fox, Huapeng Yuan, Seung-Hee Bae, George Chrysanthakopoulos, and Henrik Frystyk Nielsen,
  "High Performance Multi-Paradigm Messaging Runtime Integrating Grids and Multicore Systems,"
  in Proceedings of The 3rd IEEE International Conference on e-Science and Grid Computing (eScience 2007), Bangalore India, Dec. 10-13 2007
• Geoffrey Fox, Huapeng Yuan, Seung-Hee Bae, Xiaohong Qiu, George Chrysanthakopoulos, and Henrik Frystyk Nielsen,
  "Web 2.0 Grids and Cyberinfrastructure,"
  Web 2.0 Workshop at The 21st Open Grid Forum - OGF21 Seattle, Washington October 15-19, 2007
• Seung-Hee Bae and Byung-Ro Moon,
  "Mutation Rates in the Context of Hybrid Genetic Algorithms,"
  Genetic and Evolutionary Computational Conference, LNCS 3103, pp. 381-382, 2004.
• Hwa-Jung Lee, Seung-Hee Bae, and Youngsup Kim,
  "Research for National Space Data Application based on XML,"
  The Korean Association of Geographic Information Studies [KAGIS] Annual Spring Conference, May, 2001.

Poster & Demo

• Seung-Hee Bae, Judy Qiu, and Geoffrey Fox,
  "Scalable Dimension Reduction for Large Abstract Data Visualization,"
  Poster at IEEE Cluster 2011 Austin, Texas, Sept. 2011
• Judy Qiu, Adam Lee Hughes, Saliya Ekanayake, Thilina Gunarathne, Stephen Tak-lon Wu, Hui Li, Jong Youl Choi, Seung-Hee Bae, and Yang Ruan,
  "Parallel Applications And Tools For Cloud Computing Environments,"
  Demonstration at CloudCom 2010 Conference Nov. 30-Dec. 3, 2010, Indianapolis, IN, USA.
• Judy Qiu, Jong Youl Choi, Seung-Hee Bae, Thilina Gunarathne, Geoffrey Fox, Bin Cao, and David Wild,
  "Browsing Large Scale Cheminformatics Data with Dimension Reduction,"
  Demonstration at 10th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid 2010), May 17-20, 2010, Melbourne, Australia
• Xiaohong Qiu, Scott Beason, Seung-Hee Bae, Jaliya Ekanayake, Jong Youl Choi, Ruan Yang, presented by Geoffrey Fox,
  "Parallel Data Analysis from Multicore to Cloudy Grids,"
  at Microsoft External Research Symposium, Mar. 31, 2009, Seattle,WA, USA.
• Geoffrey Fox, Xiaohong Qiu, Huapeng Yuan, Seung-Hee Bae, George Chrysanthakopoulos, Henrik Frystyk Nielsen, Rajarshi Guha, David Wild, Haixu Tang, and Neil Devadasan,
  "Service Aggregated Linked Sequential Activities: High Performance Data Mining On Multi-core Systems"
  at Microsoft All Hands Meeting, Mar. 5-8, 2008, Seattle, WA, USA
• Geoffrey Fox, Seung-Hee Bae, Rajarshi Guha, Marlon E. Pierce, Xiaohong Qiu, David J. Wild , Huapeng Yuan, Neil M Devadasan, George Chrysanthakopoulos, and Henrik Frystyk Nielsen,
  "Parallel Clustering in a Cheminformatics Grid,"
  The 2007 Microsoft eScience Workshop at RENCI (UNC, Chapel Hill, North Carolina), Oct. 2007
• Xiaohong Qiu, Geoffrey Fox, Huapeng Yuan, Seung-Hee Bae, George Chrysanthakopoulos, and Henrik Frystyk Nielsen,
  " Performance of a Multi-Paradigm Messaging Runtime on Multicore Systems,"
  Grid 2007 Conference, Austin Texas, Sep. 2007
• Seung-Hee Bae, Haixu Tang, Jing Wu, Jun Xie, and Sun Kim,
  "A Mixture Model Approach to Identification of Interferon-Stimulated Response Element,"
  Third Annual Indiana Bioinformatics Conference, May, 2006.

Technical Papers

• Seung-Hee Bae, Judy Qiu, and Geoffrey Fox,
  "Visualization of Large High-Dimensional Data via Interpolation Approach of Multidimensional Scaling,"
  Technical Report, Jul. 2012
• Seung-Hee Bae, Judy Qiu, and Geoffrey Fox,
  "High Performance Multidimensional Scaling for Large High-Dimensional Data Visualization,"
  Technical report, Apr. 2012
• Jaliya Ekanayake, Thilina Gunarathne, Judy Qiu, Geoffrey Fox, Scott Beason, Jong Youl Choi, Yang Ruan, Seung-Hee Bae, and Hui Li,
  "Applicability of DryadLINQ to Scientific Applications,"
  Technical Report, Jan. 2010.

Presentations

• "GossipMap: A Distributed Community Detection Algorithm for Billion-Edge Directed Graphs,"
  in Proceedings of the International Conference on High Performance Computing, Networking, Storage and Analysis (SC '15), Austin, Texas, Nov. 2015.
• "Scalable Flow-Based Community Detection for Large-Scale Network Analysis,"
  in Proceedings of IEEE International Conference on Data Mining Workshops (ICDMW 2013), Dallas, Texas, Dec. 2013.
• "Adaptive Interpolation of Multidimensional Scaling,"
  in Proceedings of International Conference on Computational Science (ICCS 2012), Omaha, Nebraska, Jun. 2012
• "Multidimensional Scaling by Deterministic Annealing with Iterative Majorization algorithm,"
  in Proceedings of 6th IEEE e-Science Conference, Brisbane, Austrailia, Dec. 2010.
• "Dimension Reduction and Visualization of Large High-dimensional Data via Interpolation,"
  in Proceedings of The ACM International Symposium on High Performance Distributed Computing (HPDC 2010), Chicago, Illinois, Jun. 2010.
• "Parallel Multidimensional Scaling Performance on Multicore Systems,"
  in Proceedings of Advanced in High-Performance E-Science Middleware and Applications Workshop at eScience 2008, Indianapolis, IN, USA, Dec. 11, 2008.