Refereed Publications

2011

Yan Zhang, Fan Zhang, Jason D. Bakos, "Frequent Itemset Mining on Large-Scale Shared Memory Machines," Proc. IEEE International Conference on Cluster Computing (CLUSTER11), Sept. 26-30, 2011.
Download : [pdf]

Fan Zhang, Yan Zhang, Jason D. Bakos, "GPApriori: GPU-Accelerated Frequent Itemset Mining," Proc. IEEE International Conference on Cluster Computing (CLUSTER11), Sept. 26-30, 2011.
Download : [pdf]

Tiffany M. Mintz, Jason D. Bakos, "A Cluster-on-a-Chip Architecture for High-Throughout Phylogeny Search," IEEE Trans. on Parallel and Distributed Systems, to appear.
Download : [pdf]

Krishna K. Nagar, Jason D. Bakos, "A Sparse Matrix Personality for the Convey HC-1," Proc. 19th Annual IEEE International Symposium on Field Programmable Custom Computing Machines (FCCM'11), May 1-3, 2011.
Download : [pdf]

2010

Jason D. Bakos, "High-Performance Heterogeneous Computing with the Convey HC-1," Computing in Science and Engineering, Vol. 12, No. 6, November/December 2010.
Download : [pdf]

Bo Wang, Marco Riva, Jason D. Bakos, Antonello Monti, "Integrated Circuit Implementation for a GaN HFET Driver Circuit," IEEE Transactions on Industry Applications, Vol. 46, No. 5, Sept/Oct. 2010.
Download : [pdf]

Ibrahim Savran, Jason D. Bakos, "GPU Acceleration of Near-Minimal Logic Minimization," Proc. 2010 Symposium on Application Accelerators in High Performance Computing (SAAHPC'10), July 13-15, 2010.
Download : [pdf]

Stephanie Zierke, Jason D. Bakos, "FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods," BMC Bioinformatics 2010, 11:184.
Download : [pdf]

2009

Krishna. K. Nagar, Jason D. Bakos, "A High-Performance Double Precision Accumulator," Proc. IEEE International Conference on Field-Programmable Technology (IC-FPT'09), Dec. 9-11, 2009.
Download : [pdf]

Yan Zhang, Yasser Shalabi, Rishabh Jain, Krishna K. Nagar, Jason D. Bakos, "FPGA vs. GPU for Sparse Matrix Vector Multiply," Proc. IEEE International Conference on Field-Programmable Technology (IC-FPT'09), Dec. 9-11, 2009.
Download : [pdf]

Krishna K. Nagar, Jason D. Bakos, "An Integrated Reduction Technique for a Double Precision Accumulator," Proc. Third International Workshop on High-Performance Reconfigurable Computing Technology and Applications (HPRCTA'09), held in conjunction with Supercomputing 2009 (SC'09), Nov. 15, 2009.
Download : [pdf]

Jason D. Bakos, Krishna K. Nagar, "Exploiting Matrix Symmetry to Improve FPGA-Accelerated Conjugate Gradient," Proc. 17th Annual IEEE International Symposium on Field Programmable Custom Computing Machines (FCCM'09), April 5-8, 2009.
Download : [pdf]

2008

Jason D. Bakos, Panormitis E. Elenis, "A Special-Purpose Architecture for Solving the Breakpoint Median Problem," Proc. IEEE Transactions on Very Large Scale Integration (VLSI) Systems, Vol. 16, No. 12, Dec. 2008.
Download : [pdf]

B. Wang, M. Riva, J. Bakos, A. Monti, "Integrated Circuit Implementation for a GaN HFETs Driver Circuit," Proc. IEEE Applied Power Electronics Conference and Exposition (APEC'08), Austin, TX, Feb. 24-28, 2008.
Download : [pdf]

2007

Jason D. Bakos, Panormitis E. Elenis, Jijun Tang, "FPGA Acceleration of Phylogeny Reconstruction for Whole Genome Data," Proc. 7th IEEE International Symposium on Bioinformatics & Bioengineering (BIBE'07), Boston, MA, 14-17 Oct. 2007.
Download : [pdf]

Jason D. Bakos, “FPGA Acceleration of Gene Rearrangement Analysis,” Proc. 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM'07), April 23-25, 2007.
Download : [pdf]

Jason D. Bakos, Donald M. Chiarulli, Steven P. Levitan, “Lightweight Error Correction Coding for System-Level Interconnects,” IEEE Transactions on Computers, Vol. 56, No. 3, March 2007.
Download : [pdf]

2006

Jason D. Bakos, Charles L. Cathey, E. Allen Michalski, "Predictive Load Balancing for Interconnected FPGAs," Proc. 16th International Conference on Field Programmable Logic and Applications (FPL'06), Madrid, Spain, August 28-30, 2006.
Download : [pdf]

Charles L. Cathey, Jason D. Bakos, Duncan A. Buell, "A Reconfigurable Distributed Computing Fabric Exploiting Multilevel Parallelism," Proc. 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM'06), April 24-26, 2006.
Download : [pdf]

Donald M. Chiarulli, Sam Dickerson, Jason D. Bakos, Joel R. Martin, Steven P. Levitan, "Efficient Optical Communications Using Multibit Differential Signaling," Proc. SPIE Symposium on Optoelectronics, Photonics West: Photonics Packaging and Integration VIII, Paper No. 6126-16, San Jose, CA, 21-26 January 2006.
Download : [pdf]

2005

Donald M. Chiarulli, Jason D. Bakos, Joel R. Martin, Steven P. Levitan, "Area, Power, and Pin Efficient Bus Transceiver Using Multi-Bit-Differential Signaling," Proc. IEEE International Symposium on Circuits and Systems (ISCAS'05), pp. 1662 - 1665 Vol. 2, Kobe, Japan, May 23-26, 2005.
Download : [pdf]

Donald M. Chiarulli, Jason D. Bakos, Joel R. Martin, Steven P. Levitan, "Area, power, and pin efficient bus structures using multi-bit-differential signaling," Proc. SPIE Symposium on Microtechnologies for the New Millennium 2005, pp. 5837-04, VLSI Circuits and Systems II, 5837-4, Sevilla, Spain, May 9-11, 2005.
Download : [pdf]

Steven P. Levitan, Donald M. Chiarulli, Sam Dickerson, Jason Bakos, Joel Martin, "Power Efficient Communication Using Multi-Bit-Differential Signaling," Proc. IEEE/LEOS 16th Annual Workshop on Interconnections within High-Speed Digital Systems, Santa Fe, NM, May 8-11, 2005.

2004

Donald M. Chiarulli, Steven P. Levitan, Jason Bakos, Charles Kuznia, "Active Substrates for Optoelectronic Interconnect," Proc. IEEE International Symposium on Circuits and Systems (ISCAS'04), Volume 5, pp. V-592 - V-595, Vancouver, Canada, May 23-26, 2004.
Download : [pdf]

Donald Chiarulli, Jason Bakos, Leo Selavo, Steven Levitan, John Hansson, Michael Weisser, "Photonic Packaging for Mixed-Technology Sensor Systems," Topical Meeting on Optics in Computing, European Optical Society (OC'04), Integrated Photonics Research and Optics in Computing (IPR-OiC’2004), pp. 113-114, Engelberg, Switzerland, April 21-23, 2004.
Download : [pdf]

Steven P. Levitan, Timothy P. Kurzweg, Jose A. Martinez, Mark Kahrs, Jason Bakos, Craig Windish, Jason Boles, John Hansson, Michael Weisser, Charles Kuznia, Donald M. Chiarulli, "Modeling and Simulation of Fiber Image Guide Multi-Chip Modules for MOEMS Applications," Proc. SPIE Photonics West: Micromachining and Microfabrication/MOEMS and Miniaturized Systems IV, Vol. 5346-18, pp. 141-150, San Jose, CA, 25-30 January 2004.
Download : [pdf]

2003

Jason Bakos, Donald Chiarulli, and Steven Levitan, "Optoelectronic Multi-Chip Module Demonstrator System," in Optics in Computing, OSA Technical Digest, (Optical Society of America, Washington DC, 2003) pp 117-119.
Download : [pdf]

D. Chiarulli, S. Levitan, J. Bakos, "Optoelectronic Multi-Chip Modules," Proc. 10th Annual Conference of Mixed Design of Integrated Circuits and Systems (MIXDES'03), Lodz, Poland, June 26-28, 2003.
Download : [pdf]

Leo Selavo, Jason Bakos, Donald M. Chiarulli, Steven P. Levitan, "Encoding Benefits for Fast Optical Transceivers," Proc. 14th IEEE-LEOS Annual Workshop on Interconnections within High-Speed Digital Systems, Santa Fe, New Mexico, 4 – 7 May 2003.

2002

J. D. Bakos, D. M. Chiarulli, and S. P. Levitan, "Optoelectronic Multi-Chip-Module Implementation of a 64 Channel Crossbar Switch," Proc. International Conference of Optics in Computing (OC'02) pp. 161-163, Taipei, Taiwan, April 8 - 11, 2002.
Download : [pdf]

---