Publications - Yili Zheng

Book Chapters

  1. Unified Parallel C
    Katherine Yelick and Yili Zheng
    Programming Models for Parallel Computing (Scientific and Engineering Computation), The MIT Press, November 2015, Editor: Pavan Balaji
    Amazon, MIT Press
Journal Papers
  1. Dynamics in cryo EM reconstructions visualized with maximum-likelihood derived variance maps
    Qiu Wang, Tsutomu Matsui, Tatiana Domitrovic, Yili Zheng, Peter C. Doerschuk, John E. Johnson
    Journal of Structural Biology, Volume 181, Issue 3, March 2013, Pages 195-206 
  2. Three-dimensional reconstruction of the statistics of heterogeneous objects from a collection of one projection image of each object  (link)
    Yili Zheng, Qiu Wang, Peter C. Doerschuk 
    Journal of the Optical Society of America A (JOSA A)  Vol. 29, Issue 6, pp. 959-970 (2012) 
  3. Tuning Collective Communication for Partitioned Global Address Space Programming Models (link)
    Rajesh Nishtala, Yili Zheng, Paul H. Hargrove, Katherine A. Yelick
    Journal of Parallel Computing, 37(9): 576-591 (2011) 
  4. Optimizing UPC Programs for Multi-core Systems (link)
    Yili Zheng 
    Journal of Scientific Programming, 18(3-4), 183-191, 2010 
  5. Measuring High-Performance Computing with Real Applications (link)
    Mohamed Sayeed, Hansang Bae, Yili Zheng, Brian Armstrong, Rudolf Eigenmann, Faisal Saied
    Computing in Science & Engineering , vol.10, no.4, pp.60-70, July-Aug. 2008
  6. Kosha: A Peer-to-Peer Enhancement for the Network File System (link)
    Ali R. Butt, Troy A. Johnson, Yili Zheng, Y. Charlie Hu
    Journal of Grid Computing, Special Issue on Peer-to-Peer and Grid Computing, Volume 4 (3), pp. 323-341, September 2006
  7. A statistical approach to computer processing of cryo electron microscope images: virion classification and 3-D reconstruction (link)
    Zhye Yin, Yili Zheng, Peter C. Doerschuk, Padmaja Natarajan, John E. Johnson
    J. Structural Biology, vol. 144, pp. 24-50 (2003)
  8. An ab initio algorithm for low-resolution 3-D reconstruction from cryo electron microscope images (link)
    Zhye Yin, Yili Zheng, Peter C. Doerschuk
    J. Structural Biology, vol. 133, pp. 132-142 (2001)

Conference and Workshop Papers

  1. A Hartree-Fock Application using UPC++ and the New DArray Library
    David Ozog, Amir Kamil, Yili Zheng, Paul Hargrove, Jeff R. Hammond, Allen Malony, Wibe de Jong, Kathy Yelick
    International Parallel and Distributed Processing Symposium (IPDPS), May 2016
  2. Characterizing Heterogeneity Among Virus Particles by Stochastic 3D Signal Reconstruction
    Nan Xu, Yunye Gong, Qiu Wang, Yili Zheng, Peter C. Doerschuk
    Proc. SPIE 9600, Image Reconstruction from Incomplete Data VIII, 96000F, 2015
  3. Implementing High-Performance Geometric Multigrid Solver With Naturally-Grained Messages
    Hongzhang Shan, Samuel Williams, Yili Zheng, Amir Kamil, Katherine Yelick
    9th International Conference on Partitioned Global Address Space Programming Models (PGAS), Oct. 2015
  4. Parallel Hessian Assembly for Seismic Waveform Inversion Using Global Updates
    Scott French, Yili Zheng, Barbara Romanowicz, Katherine Yelick
    International Parallel and Distributed Processing Symposium (IPDPS), May 2015
  5. HabaneroUPC++: a Compiler-free PGAS Library (link)
    Vivek Kumar, Yili Zheng, Vincent Cavé, Zoran Budimlic, Vivek Sarkar
    8th International Conference on Partitioned Global Address Space Programming Models (PGAS), 2014
  6. Evaluation of PGAS Communication Paradigms with Geometric Multigrid (link)
    Hongzhang Shan, Amir Kamil, Samuel Williams, Yili Zheng, Katherine Yelick
    8th International Conference on Partitioned Global Address Space Programming Models (PGAS), 2014
  7. A Local-View Array Library for Partitioned Global Address Space C++ Programs (link)
    Amir Kamil, Yili Zheng, Katherine Yelick
    ACM SIGPLAN International Workshop on Libraries, Languages, and Compilers for Array Programming, June 2014
  8. UPC++: A PGAS Extension for C++ (link)
    Yili Zheng, Amir Kamil, Michael B. Driscoll, Hongzhang Shan, Katherine Yelick
    International Parallel and Distributed Processing Symposium (IPDPS), May 2014
  9. Communication Avoiding and Overlapping for Numerical Linear Algebra
    Evangelos Georganas, Jorge González-Domínguez, Edgar Solomonik, Yili Zheng, Juan Touriño and Katherine Yelick
    Proceedings of the 2012 ACM/IEEE conference on Supercomputing (SC12)
  10. Designing a Unified Programming Model for Heterogeneous Machines (link)
  11. Michael Garland, Manjunath Kudlur, Yili Zheng
    Proceedings of the 2012 ACM/IEEE conference on Supercomputing (SC12)  
  12. PGAS for Distributed Numerical Python Targeting Multi-core Clusters (link)
    Mads Kristensen, Yili Zheng, Brian Vinter
    IEEE International Parallel and Distributed Processing Symposium (IPDPS) 2012
  13. UPC Collectives Library 2.0 (link)
    George Almasi, Paul Hargrove, Gabriel Tanase and Yili Zheng
    Fifth Conference on Partitioned Global Address Space Programming Models (PGAS11), Oct 2011 
  14. Cosmic microwave background map-making at the petascale and beyond (link)
    Rajesh Sudarsan, Julian Borrill, Christopher Cantalupo, Theodore Kisner, Kamesh Madduri, Leonid Oliker, Yili Zheng and Horst Simon
    Proceedings of the international conference on Supercomputing (ICS '11), ACM, New York, NY, USA, 305-316, 2011
  15. Stochastic 3-D signal reconstruction from noisy projection data for heterogeneous instances of objects in electron microscopy imagery (link)
    Yili Zheng, Qiu Wang, Peter C. Doerschuk
    Proceedings of the 2011 IEEE International Symposium on Biomedical Imaging,  pp.918-921, March 2011 
  16. 3-D signal reconstruction from noisy projection data for stochastic objects as a generalization of Gaussian mixture parameter estimation (link)
    Yili Zheng and Peter Doerschuk
    SPIE Optics + Photonics Conference, Proceedings of SPIE Volume 7800, Aug. 2010
  17. Oversubscription on Multicore Processors (link)
    Costin Iancu, Steven Hofmeyr, Filip Blagojevic, Yili Zheng
    IEEE International Parallel and Distributed Processing Symposium (IPDPS) 2010
  18. 3-D Reconstruction from Electron Microscope Images of Heterogeneous Particles (link)
    Peter Doerschuk and Yili Zheng
    Signal Recovery and Synthesis, Optical Society of America, Oct. 2009
  19. Algorithms for sorting and reconstructing heterogeneous nanoscale biological objects from cryo electron microscopy images (link)
    Yili Zheng, Peter C. Doerschuk
    Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Boston, MA, USA, June 28 - July 1, 2009
  20. Special Purpose 3-D Reconstruction and Restoration Algorithms for Electron Microscopy of Nanoscale Objects and an Enabling Software Toolkit (link)
    Cory J. Prust, Kang Wang, Yili Zheng, Peter C. Doerschuk
    Proceedings of the 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, Boston, MA, USA, June 28 - July 1, 2009
  21. A parallel software toolkit for statistical 3-D virus reconstructions from cryo electron microscopy images using computer clusters with multi-core shared-memory nodes (link)
    Yili Zheng, Peter C. Doerschuk 
    IEEE International Parallel and Distributed Processing Symposium (IPDPS) 2008
  22. Image reconstruction in electron microscopy (link)
    Yili Zheng, Seunghee Lee, and Peter C. Doerschuk Proc. SPIE 7076, 70760G (2008). (invited paper)
  23. Shared memory programming for large scale machines (link)
    Christopher Barton, Calin Cascaval, George Almasi, Yili Zheng, Montse Farreras, Siddhartha Chatterje, and Jose Nelson Amaral
    ACM SIGPLAN conference on Programming language design and implementation (PLDI) 2006
  24. A fast algorithm for 3-D reconstruction from unoriented projections and cryo electron microscopy of viruses (link)
    Junghoon Lee, Yili Zheng, Peter C. Doerschuk
    Electronic Imaging 2006
  25. Computing the 3-D structure of viruses from unoriented cryo electron microscope images: a fast algorithm for a statistical approach (link)
    Junghoon Lee, Yili Zheng, Peter C. Doerschuk 
    Engineering in Medicine and Biology Society, 2006. EMBS '06. 28th Annual International Conference of the IEEE Aug. 2006 Page(s):2538 - 2541
  26. HPC Benchmarking and Performance Evaluation With Realistic Applications
    Brian Armstrong, Hansang Bae, Rudolf Eigenmann, Faisal Saied, Mohamed Sayeed, Yili Zheng
    SPEC Benchmark Workshop 2006, January 23, 2006, Austin, Texas
  27. Optimization of MPI Collective Communication on BlueGene/L Systems (link)
    George Almasi, Philip Heidelberger, Charles J. Archer, Xavier Martorell, C. Chris Erway, Jose E. Moreira, B. Steinmacher-Burow, and Yili Zheng
    Proceedings of the 19th Annual International Conference on Supercomputing, ICS 2005, June 20-22, 2005, Cambridge, Massachusetts, USA, pp. 253-262
  28. Maximum likelihood 3D reconstruction of multiple viruses from mixtures of cryo electron microscope images (link) Junghoon Lee, Yili Zheng, Peter C. Doerschuk, Jinghua Tang, and John E. Johnson Proceedings of SPIE 5674, 336 (2005)
  29. Kosha: A Peer-to-Peer Enhancement for the Network File System (link)
    Ali R. Butt, Troy A. Johnson, Yili Zheng, Y. Charlie Hu 
    Proceedings of the 2004 ACM/IEEE conference on Supercomputing (SC04) 
  30. Inverse problems in computational biology
    Zhye Yin, Yili Zheng, Peter C. Doerschuk 
    Proceedings of the Electronic Imaging 2004 Symposium, January 18-22, 2004, San Jose, CA.
  31. Computational 3-D Reconstructions by Optimization for Cryo-Electron Microscopy (link)
    Zhye Yin, Yili Zheng, Peter C. Doerschuk
    Proceedings of the Electronic Imaging 2003 Symposium, January 20-24, 2003, Santa Clara, CA, SPIE Vol. 5016, pp. 71-79
  32. Robustness of 3-D maximum likelihood reconstructions of viruses from cryo electron microscope images (link)
    Zhye Yin, Yili Zheng, Peter C. Doerschuk 
    IEEE International Conference on Acoustics, Speech, and Signal Processing, 2002. Proceedings. (ICASSP '02).  Volume 4, 13-17 May 2002 Page(s):3249 - 3252
  33. A statistical model for cryo electron microscope images and 3-D reconstruction and experimental design [spherical viruses] (link)
    Zhye Yin, Yili Zheng, Peter C. Doerschuk 
    2002 IEEE International Symposium on Biomedical Imaging (ISBI), 2002. Proceedings. 7-10 July 2002 Page(s):673 -  676
  34. 3-D maximum likelihood reconstructions of viruses from cryo electron microscope images and parallel computation (link) 
    Yili Zheng, Zhye Yin, Peter C. Doerschuk 
    2002 International Conference on Image Processing (ICIP). 2002. Proceedings. Volume 2,  22-25 Sept. 2002 Page(s):II-617 - II-620 vol.2
  35. 3-D reconstructions from cryo electron microscope images: an ab initio algorithm (link)
    Zhye Yin, Yili Zheng, Peter C. Doerschuk
    Proceedings of the Optical Society of America Topical Meeting on Signal Recovery and Synthesis, November 2001, pp. 77-79