Bill Thies Ph.D. Candidate Computer Science and Artificial Intelligence Laboratory Massachusetts Institute of Technology The Stata Center, Room 32-G738 32 Vassar Street Cambridge, MA 02139 Phone: (814) 404-8030 Email: thies@mit.edu

News  -  Feb 8:   Innovators In Health featured on MIT homepage and Slashdot  -  Jan 14:   Talk on technology for developing regions at MSR India (abstract, slides)  -  Jan 11:   Twenty health workers trained to use the uBox and uPhone in Bihar, India (details)  -  Dec 5:   Paper on exploiting coarse-grained parallelism presented at MICRO (paper, slides)  -  Dec 1:   Paper on our Audio Wiki to appear at HCI4CID (paper)  -  Nov 10:   Poster on our Audio Wiki to appear at WISARD (abstract)  -  Oct 31:   Paper on schedule/storage optimization appears in TOPLAS (link)  -  Oct 25:   Talk on programmable microfluidics at Berkeley (slides), previously at Stanford (video)  -  Aug 14:   uBox project wins $20K grant from NCIIA (summary)  -  May 24:   Protein folding paper in BMC Bioinformatics (paper)  -  May 8:   Programmable microfluidics article in Natural Computing (Springerlink)  -  Apr 27:   StreamIt featured in the press (Tech Review article)

Curriculum Vitae

Faculty Application

I am a final-year graduate student at MIT CSAIL, working with Professor Saman Amarasinghe and the members of the Commit Group.

My research interests include programming languages, program analysis, and compiler optimizations, especially in the context of multicore architectures and microfluidic chips. I am also interested in creating appropriate information technologies for developing countries.

Current projects include StreamIt, programmable microfluidics, an audio wiki, and TEK. Also check out the ICT4DEV reading group.

Publications (by Subject, by Date)

StreamIt

• A Practical Approach to Exploiting Coarse-Grained Pipeline Parallelism in C Programs.
  William Thies, Vikram Chandrasekhar, and Saman Amarasinghe.
  Proceedings of the 40th IEEE/ACM International Symposium on Microarchitecture (MICRO 2007).
  Chicago, IL, December, 2007. Presentation slides in PDF or PPT.

• Exploiting Coarse-Grained Task, Data, and Pipeline Parallelism in Stream Programs.
  Michael I. Gordon, William Thies, and Saman Amarasinghe.
  Proceedings of the Twelfth International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS 2006).
  San Jose, CA, October, 2006. Presentation slides in PDF or PPT.

• Optimizing Stream Programs Using Linear State Space Analysis.
  Sitij Agrawal, William Thies, and Saman Amarasinghe.
  Proceedings of the 2005 International Conference on Compilers, Architecture, and Synthesis for Embedded Systems (CASES 2005).
  San Francisco, CA, September, 2005. Presentation slides in PDF or PPT.

• A Reconfigurable Architecture for Load-Balanced Rendering.
  Jiawen Chen, Michael I. Gordon, William Thies, Matthias Zwicker, Kari Pulli, and Frédo Durand.
  Proceedings of the SIGGRAPH / Eurographics Workshop on Graphics Hardware.
  Los Angeles, CA, July, 2005. Presentation slides in PDF or PPT.

• Teleport Messaging for Distributed Stream Programs.
  William Thies, Michal Karczmarek, Janis Sermulins, Rodric Rabbah, and Saman Amarasinghe.
  Proceedings of the 2005 Symposium on Principles and Practice of Parallel Programming (PPoPP 2005).
  Chicago, IL, June, 2005. Presentation slides in PDF or PPT.

• Cache Aware Optimization of Stream Programs.
  Janis Sermulins, William Thies, Rodric Rabbah, and Saman Amarasinghe.
  Proceedings of the 2005 Conference on Languages, Compilers, and Tools for Embedded Systems (LCTES 2005).
  Chicago, IL, June, 2005. Presentation slides in PDF or PPT.

• Language and Compiler Design for Streaming Applications.
  Saman Amarasinghe, Michael I. Gordon, Michal Karczmarek, Jasper Lin, David Maze, Rodric M. Rabbah, and William Thies.
  International Journal of Parallel Programming.
  Vol. 33, Nos. 2/3, June 2005.

• Linear Analysis and Optimization of Stream Programs.
  Andrew A. Lamb, William Thies, and Saman Amarasinghe.
  Proceedings of the 2003 Conference on Programming Language Design and Implementation (PLDI 2003).
  San Diego, CA, June, 2003. Presentation slides in PDF or PPT.

• Phased Scheduling of Stream Programs.
  Michal Karczmarek, William Thies, and Saman Amarasinghe.
  Proceedings of the 2003 Conference on Languages, Compilers, and Tools for Embedded Systems (LCTES 2003).
  San Diego, CA, June, 2003. Presentation slides in PDF or PPT.

• A Stream Compiler for Communication-Exposed Architectures.
  Michael I. Gordon, William Thies, Michal Karczmarek, Jasper Lin, Ali S. Meli, Andrew A. Lamb, Chris Leger, Jeremy Wong, Henry Hoffmann, David Maze, and Saman Amarasinghe.
  Proceedings of the Tenth International Conference on Architectural Support for Programming Languages and Operating Systems (ASPLOS 2002).
  San Jose, CA, October, 2002. Presentation slides in PDF or PPT.

• A Common Machine Language for Grid-Based Architectures.
  William Thies, Michal Karczmarek, Michael Gordon, David Maze, Jeremy Wong, Henry Hoffmann, Matthew Brown, and Saman Amarasinghe.
  ACM SIGARCH Computer Architecture News, June, 2002.
  Presentation Slides in PDF or PPT from HPCA 2002 Work-in-Progress Session.

• StreamIt: A Language for Streaming Applications.
  William Thies, Michal Karczmarek, and Saman Amarasinghe.
  Proceedings of the 2002 International Conference on Compiler Construction (CC 2002).
  Grenoble, France, April, 2002. Presentation slides in PDF or PPT.

Programmable Microfluidics

• Abstraction Layers for Scalable Microfluidic Biocomputing.
  William Thies, John Paul Urbanski, Todd Thorsen and Saman Amarasinghe.
  Natural Computing, May, 2007.

• Abstraction Layers for Scalable Microfluidic Biocomputers.
  William Thies, John Paul Urbanski, Todd Thorsen and Saman Amarasinghe.
  Proceedings of the 12th International Meeting on DNA Computing (DNA 2006).
  Seoul, Korea, June, 2006. Presentation slides in PDF or PPT.

• Digital Microfluidics Using Soft Lithography.
  John Paul Urbanski, William Thies, Christopher Rhodes, Saman Amarasinghe and Todd Thorsen.
  Lab on a Chip 2006, 6(1), 96-104.

• Programmable Microfluidics.
  William Thies, J.P. Urbanski, Mats Cooper, David Wentzlaff, Todd Thorsen, and Saman Amarasinghe.
  ASPLOS Wild and Crazy Ideas Session.
  Boston, MA, October, 2004. Presentation slides in PDF or PPT.

Protein Structure Prediction

• Learning Biophysically-Motivated Parameters for Alpha Helix Prediction.
  Blaise Gassend, Charles W. O'Donnell, William Thies, Andrew Lee, Marten van Dijk, and Srinivas Devadas.
  BMC Bioinformatics 2007, 8(Suppl 5):S3.

• Predicting Secondary Structure of All-Helical Proteins Using Hidden Markov Support Vector Machines.
  Blaise Gassend, Charles W. O'Donnell, William Thies, Andrew Lee, Marten van Dijk, and Srinivas Devadas.
  Proceedings of the 2006 Workshop on Pattern Recognition in Bioinformatics (PRIB 2006).
  Hong Kong, August, 2006. Presentation slides in PDF or PPT.

• Learning Biophysically-Motivated Parameters for Alpha Helix Prediction.
  Blaise Gassend, Charles W. O'Donnell, William Thies, Andrew Lee, Marten van Dijk, and Srinivas Devadas.
  Poster Session, 10th International Conference on Research in Computational Molecular Biology (RECOMB 2006 - Poster Session).
  Venice, Italy, April, 2006.

Deadlock Detection

• Static Deadlock Detection for Java Libraries.
  Amy Williams, William Thies, and Michael D. Ernst.
  Proceedings of the 2005 European Conference on Object-Oriented Programming (ECOOP 2005).
  Glasgow, UK, July, 2005. Presentation slides in PDF or PPT.

Audio Wiki

• An Audio Wiki for Publishing User-Generated Content in the Developing World.
  Pratik Kotkar, William Thies, and Saman Amarasinghe.
  HCI for Community and International Development (Workshop at CHI 2008).
  Florence, Italy, April, 2008.

• An Audio Wiki for Building Local Repositories of Knowledge in the Developing World.
  Pratik Kotkar, William Thies, and Saman Amarasinghe.
  Poster Session, Workshop on Wireless Systems: Advanced Research and Development (WISARD).
  Bangalore, India, January, 2008.

TEK

• Searching the World Wide Web in Low-Connectivity Communities.   (html)
  William Thies, Janelle Prevost, Tazeen Mahtab, Genevieve T. Cuevas, Saad Shakhshir, Alexandro Artola, Binh D. Vo, Yuliya Litvak, Sheldon Chan, Sid Henderson, Mark Halsey, Libby Levison, and Saman Amarasinghe.
  Proceedings of the 11th International World Wide Web Conference, Global Community Track.
  Honolulu, Hawaii, May, 2002. Presentation slides in PDF or PPT.

• Providing Web Search Capability for Low-Connectivity Communities.
  Libby Levison, William Thies, and Saman Amarasinghe.
  Proceedings of the 2002 International Symposium on Technology and Society.
  Raleigh, North Carolina, June, 2002.

• The TEK Search Engine.
  Libby Levison, Bill Thies, and Saman Amarasinghe.
  Proceedings of the 2001 Workshop on Development by Design.
  Cambridge, MA, July, 2001.

Schedule/Storage Optimization

• A Step Towards Unifying Schedule and Storage Optimization.
  William Thies, Frédéric Vivien, and Saman Amarasinghe.
  Transactions on Programming Languages and Systems, 29 (6), October 2007.

• A Unified Framework for Schedule and Storage Optimization.
  William Thies.
  M.Eng. Thesis, Massachusetts Institute of Technology, June, 2002.

• A Unified Framework for Schedule and Storage Optimization.
  William Thies, Frédéric Vivien, Jeffrey Sheldon, and Saman Amarasinghe.
  Proceedings of the 2001 Conference on Programming Language Design and Implementation (PLDI 2001).
  Snowbird, UT, June, 2001. Presentation slides in PDF or PPT.

Selected Talks

• Extending the Power of the Internet to the Rural Developing World.   (abstract, video)
  Microsoft Research India, January, 2008.
  Princeton University, March, 2007.
  Also available in PowerPoint format.

• A Practial Approach to Exploiting Coarse-Grained Pipeline Parallelism in C Programs.
  MICRO 2007, Chicago, IL, December, 2007.
  Also available in PowerPoint format.

• Programmable Microfluidics.   (abstract, video)
  UC Berkeley, October, 2007.
  Stanford University, October, 2007.
  Pennsylvania State University, April, 2007.
  Also available in PowerPoint format.

• Predicting Secondary Structure of All-Helical Proteins Using Hidden Markov Support Vector Machines.
  PRIB 2006, Hong Kong, August, 2006.
  Also available in PowerPoint format.

• Abstraction Layers for Scalable Microfluidic Biocomputers.
  DNA 2006, Seoul, Korea, June, 2006.
  Also available in PowerPoint format.

• Optimizing Stream Programs Using Linear State Space Analysis.
  CASES 2005, San Francisco, CA, September, 2005.
  Also available in PowerPoint format.

• Providing Internet Search for Low-Connectivity Communities.   (abstract)
  Google New York, July, 2005.
  Also available in PowerPoint format.

• Teleport Messaging for Distributed Stream Programs.
  PPoPP 2005, Chicago, Illinois, June, 2005.
  Also available in PowerPoint format.

• Programmable Microfluidics.
  ASPLOS Wild and Crazy Ideas Session, Boston, MA, October, 2004.
  Also available in PowerPoint format.

• StreamIt: A Compiler Infrastructure for Stream Programs.
  IBM Programming Languages Day, Yorktown Heights, NY, May, 2004.
  Also available in PowerPoint format.

• Towards Programmable Microfluidics.
  Research Qualifying Examination, MIT EECS, April, 2004.
  Also available in PowerPoint format.

• Architectures, Languages, and Compilers for the Streaming Domain.
  With Saman Amarasinghe.
  PACT 2003 Tutorial, New Orleans, LA, September, 2003.

• StreamIt: High-Level Stream Programming on Raw.
  Raw Introduction Day, Cambridge, MA, March, 2003.
  Also available as a streaming video (low, high).

• StreamIt: A Language for Streaming Applications.
  CC 2002, Grenoble, France, April, 2002.
  Subsequently presented at New England Programming Languages and Systems Symposium (NEPLS), Yale, Connecticut, August, 2002.
  Also available in PowerPoint format.

• A Common Machine Language for Communication-Exposed Architectures.
  HPCA Work-in-Progress Session, Cambridge, Massachussetts, February, 2002.
  Won Prize for Best (Most Entertaining) Presentation!
  Also available in PowerPoint format.

• The TEK System: Browsing the Web in Low-Connectivity Communities.
  HP Labs India, IIT Madras, and University of Moratuwa, January, 2002.
  Also available in PowerPoint format.

• A Unified Framework for Schedule and Storage Optimization.
  PLDI 2001, Snowbird, Utah, June, 2001.
  Also available in PowerPoint format.

Teaching

• 6.046 recitations, Fall 2004.

thies@mit.edu