Publications by Type

Publications by Date - Representative Papers

Books Edited
  1. Computational Biology and Bioinformatics
    C.-W. Tseng (ed.)
    Advances in Computers, Volume 68, Elsevier, 2006.

  2. Languages and Compilers for Parallel Computing, 15th Workshop, LCPC 2002, College Park, MD USA, July 2002, Revised Papers
    B. Pugh and C.-W. Tseng (eds.)
    Lecture Notes in Computer Science, Volume 2481, Springer-Verlag, 2005.

Journal Articles
  1. An Unsupervised, Model-Free, Machine-Learning Combiner for Peptide Identification from Tandem Mass Spectra
    N. Edwards, X. Wu, and C.-W. Tseng
    Clinical Proteomics, 5(1):23-36, March 2009.

  2. A Message Passing Benchmark For Unbalanced Applications
    J. Dinan, S. Olivier, G. Sabin, J. Prins, P. Sadayappan, C.-W. Tseng
    Simulation Modelling Practice and Theory, 16(9):1177-1189, 2008.

  3. HMMatch: Peptide Identification by Spectral Matching of Tandem Mass Spectra Using Hidden Markov Models
    X. Wu, C.-W. Tseng, and N. Edwards
    Journal of Computational Biology, 14(8):1025-1043, 2007.

  4. Exploiting Locality for Irregular Scientific Codes
    H. Han and C.-W. Tseng
    IEEE Transactions on Parallel and Distributed Systems, 17(7):606-618, July 2006.

  5. The Efficacy of Software Prefetching and Locality Optimizations on Future Memory Systems
    A.-H. Badawy, A. Aggarwal, D. Yeung, and C.-W. Tseng.
    Journal of Instruction-Level Parallelism, Vol. 6, October 2004.

  6. Towards a First Vertical Prototyping of an Extremely Fine-grained Parallel Programming Approach
    D. Naishlos, J. Nuzman, C.-W. Tseng, and U. Vishkin
    Theory of Computing Systems, 36:521-552, August 2003
    (Invited Paper from SPAA'01)

  7. Efficient Compiler and Run-Time Support for Parallel Irregular Reductions
    H. Han and C.-W. Tseng
    Parallel Computing, 26(13-14):1861-1887, 2000.
    (Special Issue on Parallel Computing for Irregular Applications)

  8. Eliminating Barrier Synchronization for Compiler-Parallelized Codes on Software DSMs
    H. Han, C.-W. Tseng, and P. Keleher.
    International Journal of Parallel Programming, 26(5):591-612, October 1998.
    (Invited paper from LCPC'97)

  9. Performance of the Prototype Fortran D Compiler
    C.-W. Tseng.
    Software: Practice and Experience, 7(27):763-796, July 1997.

  10. Characterizing the Memory Behavior of Compiler-Parallelized Applications
    E. Torrie, M. Martonosi, C.-W. Tseng, and M. Hall.
    IEEE Transactions on Parallel and Distributed Systems, 7(12):1225-1238, December 1996.

  11. Interprocedural Compilation of Fortran D
    M. Hall, S. Hiranandani, K. Kennedy, and C.-W. Tseng.
    Journal of Parallel and Distributed Computing, 38(2):114-129, November 1996.

  12. Memory Referencing Behavior in Compiler-Parallelized Applications
    E. Torrie, M. Martonosi, M. Hall, and C.-W. Tseng.
    International Journal of Parallel Programming, 24(4), August 1996.
    (Invited paper from PACT'96)

  13. Improving Data Locality with Loop Transformations
    K. McKinley, S. Carr, and C.-W. Tseng.
    ACM Transactions on Programming Languages and Systems, 18(4):424-453, July 1996.

  14. Requirements for Data-Parallel Programming Environments
    V. Adve, A. Carle, E. Granston, S. Hiranandani, K. Kennedy, C. Koelbel, J. Mellor-Crummey, C.-W. Tseng, and S. Warren.
    IEEE Transactions on Parallel and Distributed Technology, 2(3):48-58, Fall 1994.

  15. Integrated Support for Task and Data Parallelism
    K. M. Chandy, I. Foster, K. Kennedy, C. Koelbel, and C.-W. Tseng.
    International Journal of Supercomputer Applications, 8(2):80-98, Summer 1994.

  16. Evaluating Compiler Optimizations for Fortran D
    S. Hiranandani, K. Kennedy, and C.-W. Tseng.
    Journal of Parallel and Distributed Computing, 21(1):27-45, April 1994.

  17. Unified Compilation of Fortran 77D and 90D
    A. Choudhary, G. Fox, S. Hiranandani, K. Kennedy, C. Koelbel, S. Ranka, and C.-W. Tseng.
    Letters on Programming Languages and Systems, 2(1-4):95-114, March-December 1993.

  18. Analysis and Transformation in an Interactive Parallel Programming Tool
    K. Kennedy, K. McKinley, and C.-W. Tseng.
    Concurrency: Practice and Experience, 5(7):575-602, October 1993.

  19. The Power Test for Data Dependence
    M. J. Wolfe and C.-W. Tseng.
    IEEE Transactions on Parallel and Distributed Systems, 3(5):591-601, September 1992.

  20. Compiling Fortran D for MIMD Distributed-Memory Machines
    S. Hiranandani, K. Kennedy, and C.-W. Tseng.
    Communications of the ACM, 35(8):66-80, August 1992.
    (Invited paper from Supercomputing'91)

  21. Interactive Parallel Programming Using the ParaScope Editor
    K. Kennedy, K. McKinley, and C.-W. Tseng.
    IEEE Transactions on Parallel and Distributed Systems, 2(3):329-341, July 1991.

Book Chapters
  1. Peptide Identification via Tandem Mass Spectroscopy
    X. Wu, N. Edwards, and C.-W. Tseng
    in Computational Biology and Bioinformatics, Advances in Computers, Volume 68 (C.-W. Tseng, ed.), Elsevier, 2006.

  2. Searching Sequence Databases Using High Performance BLASTs
    X. Wu, and C.-W. Tseng
    in Parallel Computing for Bioinformatics and Computational Biology (A. Zomaya, ed.), John Wiley & Sons, 2005.

  3. A Comparison of Locality Transformations for Irregular Codes
    H. Han and C.-W. Tseng
    5th International Workshop on Languages, Compilers, and Run-time Systems for Scalable Computers (LCR'2000), (S. Dwarkadas, ed.), Lecture Notes in Computer Science, Springer-Verlag, 2000.

  4. Compiler and Run-time Support for Improving Locality in Scientific Codes (Extended Abstract)
    H. Han, G. Rivera, and C.-W. Tseng
    Languages and Compilers for Parallel Computing, 12th International Workshop, (J. Ferrante et al., eds.), Lecture Notes in Computer Science, Springer-Verlag, 1999.

  5. Improving Compiler and Run-Time Support for Irregular Reductions Using Local Writes
    H. Han and C.-W. Tseng
    Languages and Compilers for Parallel Computing, 11th International Workshop, (S. Chatterjee et al., eds.), Lecture Notes in Computer Science, Springer-Verlag, 1998.

  6. Reducing Synchronization Overhead for Compiler-Parallelized Codes on Software DSMs (Extended Abstract)
    H. Han, C.-W. Tseng, and P. Keleher
    Languages and Compilers for Parallel Computing, 10th International Workshop, (Z. Li et al., eds.), Lecture Notes in Computer Science, Springer-Verlag, 1997.

  7. An Overview of the Fortran D Programming System
    S. Hiranandani, K. Kennedy, C. Koelbel, U. Kremer, and C.-W. Tseng.
    Languages and Compilers for Parallel Computing, 4th International Workshop, (U. Banerjee et al., eds.), Lecture Notes in Computer Science, Springer-Verlag, 1992.

  8. Compiler Support for Machine-Independent Parallel Programming in Fortran D
    S. Hiranandani, K. Kennedy, and C.-W. Tseng.
    Languages, Compilers, and Run-Time Environments for Distributed Memory Machines, (J. Saltz and P. Mehrotra, eds.), North-Holland, Amsterdam, The Netherlands, 1992.

Refereed Conference Papers
  1. BioBench: A Benchmark Suite of Bioinformatics Applications,
    K. Albayraktaroglu, A. Jaleel, X. Wu, B. Jacob, M. Franklin, C.-W. Tseng, and D. Yeung
    IEEE International Symposium on Performance Analysis of Systems and Software (ISPASS), Austin, TX, March 2005.

  2. Towards a First Vertical Prototyping of an Extremely Fine-grained Parallel Programming Approach
    D. Naishlos, J. Nuzman, C.-W. Tseng, and U. Vishkin
    13th ACM Symposium on Parallel Algorithms and Architectures (SPAA'01), Crete, Greece, July 2001.

  3. Evaluating the Impact of Memory System Performance on Software Prefetching and Locality Optimizations
    A.-H. Badawy, A. Aggarwal, D. Yeung, and C.-W. Tseng.
    2001 International Conference on Supercomputing (ICS'01), Sorrento, Italy, June 2001.

  4. A Comparison of Parallelization Techniques for Irregular Reductions
    H. Han and C.-W. Tseng
    15th International Conference on Parallel and Distributed Computing (IPDPS'01), San Francisco, CA, April 2001.
    (Extended Paper)

  5. Tiling Optimizations for 3D Scientific Computations
    G. Rivera and C.-W. Tseng.
    SC'00, Dallas, TX, November 2000.

  6. Locality Optimizations for Multi-Level Caches
    G. Rivera and C.-W. Tseng.
    SC'99, Portland, OR, November 1999.

  7. A Comparison of Compiler Tiling Algorithms
    G. Rivera and C.-W. Tseng.
    8th International Conference on Compiler Construction (CC'99), Amsterdam, The Netherlands, March 1999.

  8. Improving Compiler and Run-Time Support for Adaptive Irregular Codes
    H. Han and C.-W. Tseng.
    International Conference on Parallel Architectures and Compilation Techniques (PACT'98), Paris, France, October 1998.

  9. Eliminating Conflict Misses for High Performance Architectures
    G. Rivera and C.-W. Tseng.
    1998 International Conference on Supercomputing (ICS'98), Melbourne, Australia, July 1998.

  10. Data Transformations for Eliminating Conflict Misses
    G. Rivera and C.-W. Tseng.
    1998 ACM SIGPLAN Conference on Programming Language Design and Implementation (PLDI'98), Montreal, Canada, June 1998.

  11. Compile-time Synchronization Optimizations for Software DSMs
    H. Han and C.-W. Tseng.
    12th International Parallel Processing Symposium (IPPS'98), Orlando, FL, April 1998.
    (Extended paper)

  12. Enhancing Software DSM for Compiler-Parallelized Applications
    P. Keleher and C.-W. Tseng.
    11th International Parallel Processing Symposium (IPPS'97), Geneva, Switzerland, April 1997.
    (Extended paper)

  13. Compiler Optimizations for Eliminating Barrier Synchronization
    C.-W. Tseng.
    5th ACM Symposium on Principles and Practice of Parallel Programming (PPOPP'95), Santa Barbara, CA, July 1995.

  14. Unified Compilation Techniques for Shared and Distributed Address Space Machines
    C.-W. Tseng, J. Anderson, S. Amarasinghe, and M. Lam,
    1995 International Conference on Supercomputing (ICS'95), Barcelona, Spain, July 1995.

  15. Evaluating the Impact of Advanced Memory Systems on Compiler-Parallelized Codes
    E. Torrie, C.-W. Tseng, M. Martonosi, and M. Hall.
    International Conference on Parallel Architectures and Compilation Techniques (PACT'95), Limassol, Cyprus, June 1995.

  16. An Overview of the SUIF Compiler for Scalable Parallel Machines
    S. Amarasinghe, J. Anderson, M. Lam, and C.-W. Tseng.
    7th SIAM Conference on Parallel Processing for Scientific Computing, San Francisco, CA, February 1995.

  17. The D Editor: A New Interactive Parallel Programming Tool
    S. Hiranandani, K. Kennedy, C.-W. Tseng, and S. Warren.
    Supercomputing '94 (SC'94), Washington, DC, November 1994.

  18. Compiler Optimizations for Improving Data Locality
    S. Carr, K. McKinley, and C.-W. Tseng.
    6th International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS-VI), San Jose, CA, October 1994.

  19. Preliminary Experiences with the Fortran D Compiler
    S. Hiranandani, K. Kennedy, and C.-W. Tseng.
    Supercomputing '93 (SC'93), Portland, OR, November 1993.

  20. Interprocedural Compilation of Fortran D for MIMD Distributed-Memory Machines
    M. Hall, S. Hiranandani, K. Kennedy, and C.-W. Tseng.
    Supercomputing '92 (SC'92), Minneapolis, MN, November 1992.

  21. Compiling Fortran 77D and 90D for MIMD Distributed-Memory Machines
    A. Choudhary, G. Fox, S. Hiranandani, K. Kennedy, C. Koelbel, S. Ranka, and C.-W. Tseng.
    4th Symposium on Frontiers of Massively Parallel Computation (Frontiers'92), McLean, VA, October 1992.

  22. Evaluation of Compiler Optimizations for Fortran D on MIMD Distributed-Memory Machines
    S. Hiranandani, K. Kennedy, and C.-W. Tseng.
    1992 International Conference on Supercomputing (ICS'92), Washington DC, July 1992.

  23. Compiler Optimizations for Fortran D on MIMD Distributed-Memory Machines
    S. Hiranandani, K. Kennedy, and C.-W. Tseng.
    Supercomputing '91 (SC'91), Albuquerque, NM, November 1991.

  24. Analysis and Transformation in the ParaScope Editor
    K. Kennedy, K. McKinley, and C.-W. Tseng.
    1991 International Conference on Supercomputing (ICS'91), Cologne, Germany, June 1991.

  25. Practical Dependence Testing
    G. Goff, K. Kennedy, and C.-W. Tseng.
    ACM SIGPLAN '91 Conference on Programming Language Design and Implementation (PLDI'91), Toronto, Canada, June 1991.

Refereed Workshop Papers
  1. Dynamic Load Balancing of Unbalanced Computations Using Message Passing
    J. Dinan, S. Olivier, J. Huan, J. Liu, J. Prins, P. Sadayappan and C.-W. Tseng
    6th International Workshop on Performance Modeling, Evaluation, and Optimization of Parallel and Distributed Systems (PMEO-PDS 2007), Long Beach, CA, March 2007

  2. UTS: An Unbalanced Tree Search Benchmark,
    S. Olivier, J. Huan, J. Liu, J. Prins, J. Dinan, P. Sadayappan and C.-W. Tseng
    Workshop on Languages and Compilers for High-Performance Computing (LCPC'06), New Orleans, LA, November 2006.

  3. ESTmapper: Efficiently Aligning DNA Sequences to Genomes
    X. Wu, W.-J. Lee, and C.-W. Tseng
    4th IEEE International Workshop on High Performance Computational Biology (HiCOMB'05), Denver, CO, April 2005.

  4. Evaluating the Impact of Programming Language Features on the Performance of Parallel Applications on Cluster Architectures
    K. Berlin, J. Huan, M. Jacob, G. Kochhar, J. Prins, B. Pugh, P. Sadayappan, J. Spacco, and C.-W. Tseng
    Workshop on Languages and Compilers for High-Performance Computing (LCPC'03), College Station, TX, October 2003.

  5. Evaluating the XMT Parallel Programming Model
    D. Naishlos, J. Nuzman, C.-W. Tseng, and U. Viskin
    6th International Workshop on High-Level Parallel Programming Models and Supportive Environments (HIPS'01), San Francisco, CA, April 2001.

  6. Evaluating Multi-threading in the Prototype XMT Environment
    D. Naishlos, J. Nuzman, C.-W. Tseng, and U. Viskin
    4th ACM Workshop on Multi-threaded Execution, Architecture, and Compilation (MTEAC-4), Monterey, CA, December 2000.
    (Best paper award)

  7. Improving Locality For Adaptive Irregular Scientific Codes
    H. Han and C.-W. Tseng
    Workshop on Languages and Compilers for High-Performance Computing (LCPC'00), White Plains, NY, August 2000.

  8. Software Support for Improving Locality in Scientific Codes
    H. Han, G. Rivera, and C.-W. Tseng
    8th Workshop on Compilers for Parallel Computers (CPC'2000), Aussois, France, January 2000.

  9. Eliminating Conflict Misses for Tiled Codes (Abstract)
    G. Rivera and C.-W. Tseng
    Dagstuhl Seminar on Tiling for Optimal Resource Utilization, Wadern, Germany, August 1998.

  10. Improving Compiler and Run-time Support for Irregular Reductions
    H. Han and C.-W. Tseng
    Workshop on Languages and Compilers for Parallel Computing (LCPC'98), Chapel Hill, NC, August 1998.

  11. Compiler Optimizations for High Performance Architectures
    H. Han, G. Rivera, and C.-W. Tseng.
    Second SUIF Compiler Workshop, Stanford University, Stanford, CA, August 1997.

  12. Reducing Synchronization Overhead for Compiler-Parallelized Codes on Software DSMs
    H. Han, C.-W. Tseng, and P. Keleher.
    Workshop on Languages and Compilers for Parallel Computing (LCPC'97), Minneapolis, MN, August 1997.

  13. Improving the Compiler/Software DSM Interface: Preliminary Experiences
    P. Keleher and C.-W. Tseng.
    First SUIF Compiler Workshop, Stanford University, Stanford, CA, January 1996.

  14. Communication Analysis for Shared and Distributed Memory Machines
    C.-W. Tseng.
    Workshop on Compiler Optimizations on Distributed Memory Systems, 7th IEEE Symposium on Parallel and Distributed Processing, San Antonio, TX, October 1995.

  15. Design and Implementation of the D Editor
    S. Hiranandani, K. Kennedy, C.-W. Tseng, and S. Warren.
    Second Workshop on Environments and Tools for Parallel Scientific Computing, SIAM, Townsend, TN, May 1994

Other Papers
  1. Locality Optimizations For Adaptive Irregular Scientific Codes
    H. Han and C.-W. Tseng
    Technical Report, Dept. of Computer Science, University of Maryland, November 2000.

  2. Software Support For Improving Locality in Advanced Scientific Codes
    C.-W. Tseng.
    Technical Report CS-TR-4168, Dept. of Computer Science, University of Maryland, June 2000.

  3. Improving Locality For Adaptive Irregular Scientific Codes
    H. Han and C.-W. Tseng.
    Technical Report CS-TR-4039, Dept. of Computer Science, University of Maryland, September 1999.

  4. Data Layout Optimizations for High-Performance Architectures
    C.-W. Tseng.
    Technical Report CS-TR-3818, Dept. of Computer Science, University of Maryland, February 1997.

  5. Efficient Machine-Independent Programming of High-Performance Multiprocessors
    C.-W. Tseng.
    Technical Report CS-TR-3545, Dept. of Computer Science, University of Maryland, October 1995.

  6. SUIF: An Infrastructure for Research on Parallelizing and Optimizing Compilers
    R. Wilson, R. French, C. Wilson, S. Amarasinghe, J. Anderson, S. Tjiang, S.-W. Liao, C.-W. Tseng, M. Hall, M. Lam, and J. Hennessy.
    ACM SIGPLAN Notices, 29(12):31-37, December 1994.

  7. SUIF: A Parallelizing and Optimizing Research Compiler
    R. Wilson, R. French, C. Wilson, S. Amarasinghe, J. Anderson, S. Tjiang, S.-W. Liao, C.-W. Tseng, M. Hall, M. Lam, and J. Hennessy.
    Technical Report CSL-TR-94-620, Computer Systems Laboratory, Stanford University, May 1994.

  8. An Optimizing Fortran D Compiler for MIMD Distributed-Memory Machines
    Chau-Wen Tseng.
    Ph.D. Thesis, Rice COMP TR93-199, Dept. of Computer Science, Rice University, January 1993.

  9. Fortran D Language Specification
    G. Fox, S. Hiranandani, K. Kennedy, C. Koelbel, U. Kremer, C.-W. Tseng, and M. Wu.
    Rice COMP TR90-141, Dept. of Computer Science, Rice University, December 1990.

Poster & Oral Presentations
  1. Improving the Reliability of Peptide Identifications using Machine Learning
    X. Wu, C.-W. Tseng, and N. Edwards
    Oral Presentation at 4th Annual Conference of the US Human Proteome Organisation (US HUPO 2008), Bethesda, MD, March 2008.

  2. Peptide Identification by Spectral Matching of Tandem Mass Spectra using Hidden Markov Models
    X. Wu, C.-W. Tseng, and N. Edwards
    Poster at 4th Annual Conference of the US Human Proteome Organisation (US HUPO 2008), Bethesda, MD, March 2008.

  3. Peptide Identification by Spectral Matching of Tandem Mass Spectra using Hidden Markov Models
    X. Wu, N. Edwards, and C.-W. Tseng
    Poster at 2006 RECOMB Satellite Conferences on Systems Biology and Computational Proteomics, San Diego, CA, December 2006.

  4. Experimental Comparison of Peptide Identification Algorithms,
    X. Wu, N. Edwards, and C.-W. Tseng
    Poster at 9th Annual Conference on Computational Genomics, Baltimore, MD, October 2006.

  5. Novel Peptide Identification Using ESTs and Genomic Sequence
    N. Edwards, X. Wu, and C.-W. Tseng
    Poster at 2nd Annual Conference of the US Human Proteome Organisation (US HUPO 2006), Boston, MA, March 2006.

  6. ESTmapper: Efficiently Clustering EST Sequences Using Genome Maps
    X. Wu, W.-J. Lee, D. Gupta, and C.-W. Tseng
    Poster at 8th International Conference on Research in Computational Molecular Biology (RECOMB 2004), San Diego, CA, March 2004.

  7. Searching Bioinformatic Sequence Databases using UM-BLAST---A Wrapper for High-Performance BLASTs
    X. Wu and C.-W. Tseng
    Poster at 8th International Conference on Research in Computational Molecular Biology (RECOMB 2004), San Diego, CA, March 2004.

Tutorials
  1. Software Support for Improving Locality in Scientific Applications
    C.-W. Tseng, Compiler Techniques for High-Performance Computing (CTHPC'03), Taipei, Taiwan, March 2003.

  2. Compiler Techniques for High-Performance Architectures
    C.-W. Tseng, Academica Sinica, Taipei, Taiwan, January 1998.

  3. Compilation and Runtime Support for Massively Parallel Processors
    J. Saltz and C.-W. Tseng,
    Supercomputing '93, Portland, OR, November 1993.
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