PUBLISHED WORKS
2019
An Overlay Architecture for Pattern Matching
Rasha Karakchi, Charles A. Daniels, Jason D. Bakos | Proc. 30th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2019).
OpenVX Graph Optimization for Visual Processor Units
Madushan Abeysinghe, Jesse Villarreal, Lucas Weaver, Jason D. Bakos | Proc. 30th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2019).
2018
Fast Coordination of Power Electronic Converters for Energy Routing in Shipboard Power Systems
H. L. Ginn III, J. D. Bakos, A. Benigni | Proc. 2018 International Ship Control Systems Symposium (iSCSS 2018).
2017
A Dynamically Reconfigurable Automata Processor Overlay
Rasha Karakchi, Lothrop O. Richards, and Jason D. Bakos | Proc. International Conference on Reconfigurable Computing and FPGAs 2017 (ReConFig 2017).
Control System Communication Architecture for Power Electronic Building Blocks
Ivan Panchenko, Jason D. Bakos, Herbert L. Ginn | Proc. IEEE Electric Ship Technologies Symposium 2017 (ESTS 2017).
System-Level, FPGA-Based, Real-Time Simulation of Ship Power Systems
Matthew Milton, Andrea Benigni, Jason Bakos | IEEE Trans. on Energy Conversion Systems, Vol. 32, No. 2.
2016
High-Level Synthesis of a Genomic Database Search Engine
Rasha Karakchi, Jordan Bradshaw, Jason D. Bakos | Proc. 2016 International Conference on Reconfigurable Computing and FPGAs (ReConFig 2016).
Two-Hit Filter Synthesis for Genomic Database Search
Jordan Bradshaw, Rasha Karakchi, Jason D. Bakos | Proc. 24th IEEE International Symposium on Field-Programmable Custom Computing Machines.
2015
Embedded Systems: ARM Programming and Optimization
Jason D. Bakos | Elsevier, 2015 (textbook).
Memory Interface Design for 3D Stencil Kernels on a Massively Parallel Memory System
Zheming Jin, Jason D. Bakos | ACM Transactions on Reconfigurable Technology and Systems (TRETS), Vol. 8, Issue 4, 2015.
2014
Lucas-Kanade Optical Flow Estimation on the TI C66x Digital Signal Processor
Fan Zhang, Yang Gao, Jason D. Bakos | Proc. 18th Annual IEEE High Performance Extreme Computing Conference (HPEC 2014), Sept. 2014.
Sparse Matrix-Vector Multiply on the Keystone II Digital Signal Processor
Yang Gao, Fan Zhang, Jason D. Bakos | Proc. 18th Annual IEEE High Performance Extreme Computing Conference (HPEC 2014), Sept. 2014.
Large-scale Pairwise Sequence Alignments on a Large-scale GPU Cluster
Ibrahim Savran, Yang Gao, Jason D. Bakos | IEEE Design and Test, January/February 2014
2013
Accuracy, Cost, and Performance Tradeoffs for Floating-Point Accumulation
Krishna Nagar, Jason D. Bakos | Proc. 2013 International Conference on Reconfigurable Computing and FPGAs (ReConFig 2013).
Sparse Matrix-Vector Multiply on the Texas Instruments C6678 Digital Signal Processor
Yang Gao, Jason D. Bakos | Proc. The 24th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2013), Washington D.C., June 5-7, 2013.
Memory Access Scheduling on the Convey HC-1
Zheming Jin, Jason D. Bakos | Proc. The 21st IEEE International Symposium on Field-Programmable Custom Computing Machines (FCCM’13), Seattle, Washington, April 28-30, 2013.
Accelerating Frequent Itemset Mining on Graphics Processing Units
Fan Zhang, Yan Zhang, Jason D. Bakos | Journal of Supercomputing, February 2013, DOI 10.1007/s11227-013-0887-x.
A Heuristic Scheduler for Port-Constrained Floating-Point Pipelines
Zheming Jin, Jason D. Bakos | International Journal of Reconfigurable Computing, Vol. 2013, Article ID 849545, 9 pages, 2013. doi:10.1155/2013/849545.
Extending the BEAGLE Library to a Multi-FPGA Platform
Zheming Jin, Jason D. Bakos | BMC Bioinformatics, BMC Bioinformatics 2013, 14:25.
BMC Bioinformatics, BMC Bioinformatics 2013, 14:25
Yan Zhang, Fan Zhang, Zheming Jin, Jason D. Bakos | ACM Trans. Reconfigurable Technology and Systems (TRETS), Vol. 6, Issue 1, May 2013.
2012
GPU Acceleration of Pyrosequencing Noise Removal
Yang Gao, Jason D. Bakos | Proc. 2012 Symposium on Application Accelerators in High Performance Computing (SAAHPC 2012), Argonne National Laboratory, July 10-11, 2012.
A Cluster-on-a-Chip Architecture for High-Throughout Phylogeny Search
Tiffany M. Mintz, Jason D. Bakos | IEEE Trans. on Parallel and Distributed Systems, Vol. 23, No. 4, April 2012.
2011
Frequent Itemset Mining on Large-Scale Shared Memory Machines
Yan Zhang, Fan Zhang, Jason D. Bakos | Proc. IEEE International Conference on Cluster Computing (CLUSTER 2011), Sept. 26-30, 2011.
GPApriori: GPU-Accelerated Frequent Itemset Mining
Fan Zhang, Yan Zhang, Jason D. Bakos | Proc. IEEE International Conference on Cluster Computing (CLUSTER 2011), Sept. 26-30, 2011.
A Sparse Matrix Personality for the Convey HC-1
Krishna K. Nagar, Jason D. Bakos | Proc. 19th Annual IEEE International Symposium on Field Programmable Custom Computing Machines (FCCM’11), May 1-3, 2011.
2010
High-Performance Heterogeneous Computing with the Convey HC-1
Jason D. Bakos | Computing in Science and Engineering, Vol. 12, No. 6, November/December 2010.
Integrated Circuit Implementation for a GaN HFET Driver Circuit
Bo Wang, Marco Riva, Jason D. Bakos, Antonello Monti | IEEE Transactions on Industry Applications, Vol. 46, No. 5, Sept/Oct. 2010.
GPU Acceleration of Near-Minimal Logic Minimization
Ibrahim Savran, Jason D. Bakos | Proc. 2010 Symposium on Application Accelerators in High Performance Computing (SAAHPC’10), July 13-15, 2010.
FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods
Stephanie Zierke, Jason D. Bakos | BMC Bioinformatics 2010, 11:184.
2009
A High-Performance Double Precision Accumulator
Krishna. K. Nagar, Jason D. Bakos | Proc. IEEE International Conference on Field-Programmable Technology (IC-FPT’09), Dec. 9-11, 2009.
FPGA vs. GPU for Sparse Matrix Vector Multiply
Yan Zhang, Yasser Shalabi, Rishabh Jain, Krishna K. Nagar, Jason D. Bakos | Proc. IEEE International Conference on Field-Programmable Technology (IC-FPT’09), Dec. 9-11, 2009.
An Integrated Reduction Technique for a Double Precision Accumulator
Krishna K. Nagar, Jason D. Bakos | 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.
Exploiting Matrix Symmetry to Improve FPGA-Accelerated Conjugate Gradient
Jason D. Bakos, Krishna K. Nagar | Proc. 17th Annual IEEE International Symposium on Field Programmable Custom Computing Machines (FCCM’09), April 5-8, 2009.
2008
A Special-Purpose Architecture for Solving the Breakpoint Median Problem
Jason D. Bakos, Panormitis E. Elenis | Proc. IEEE Transactions on Very Large Scale Integration (VLSI) Systems, Vol. 16, No. 12, Dec. 2008.
Integrated Circuit Implementation for a GaN HFETs Driver Circuit
B. Wang, M. Riva, J. Bakos, A. Monti | Proc. IEEE Applied Power Electronics Conference and Exposition (APEC’08), Austin, TX, Feb. 24-28, 2008.
2007
FPGA Acceleration of Phylogeny Reconstruction for Whole Genome Data
Jason D. Bakos, Panormitis E. Elenis, Jijun Tang | Proc. 7th IEEE International Symposium on Bioinformatics & Bioengineering (BIBE’07), Boston, MA, 14-17 Oct. 2007.
FPGA Acceleration of Gene Rearrangement Analysis
Jason D. Bakos | Proc. 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM’07), April 23-25, 2007.
Lightweight Error Correction Coding for System-Level Interconnects
Jason D. Bakos, Donald M. Chiarulli, Steven P. Levitan | IEEE Transactions on Computers, Vol. 56, No. 3, March 2007.
2006
Predictive Load Balancing for Interconnected FPGAs
Jason D. Bakos, Charles L. Cathey, E. Allen Michalski | Proc. 16th International Conference on Field Programmable Logic and Applications (FPL’06), Madrid, Spain, August 28-30, 2006.
A Reconfigurable Distributed Computing Fabric Exploiting Multilevel Parallelism
Charles L. Cathey, Jason D. Bakos, Duncan A. Buell | Proc. 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM’06), April 24-26, 2006.
Efficient Optical Communications Using Multibit Differential Signaling
Donald M. Chiarulli, Sam Dickerson, Jason D. Bakos, Joel R. Martin, Steven P. Levitan | Proc. SPIE Symposium on Optoelectronics, Photonics West: Photonics Packaging and Integration VIII, Paper No. 6126-16, San Jose, CA, 21-26 January 2006.
2005
Area, Power, and Pin Efficient Bus Transceiver Using Multi-Bit-Differential Signaling
Donald M. Chiarulli, Jason D. Bakos, Joel R. Martin, Steven P. Levitan | Proc. IEEE International Symposium on Circuits and Systems (ISCAS’05), pp. 1662 – 1665 Vol. 2, Kobe, Japan, May 23-26, 2005.
Area, power, and pin efficient bus structures using multi-bit-differential signaling
Donald M. Chiarulli, Jason D. Bakos, Joel R. Martin, Steven P. Levitan | 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.
Power Efficient Communication Using Multi-Bit-Differential Signaling
Steven P. Levitan, Donald M. Chiarulli, Sam Dickerson, Jason Bakos, Joel Martin | Proc. IEEE/LEOS 16th Annual Workshop on Interconnections within High-Speed Digital Systems, Santa Fe, NM, May 8-11, 2005.
2004
Active Substrates for Optoelectronic Interconnect
Donald M. Chiarulli, Steven P. Levitan, Jason Bakos, Charles Kuznia | Proc. IEEE International Symposium on Circuits and Systems (ISCAS’04), Volume 5, pp. V-592 – V-595, Vancouver, Canada, May 23-26, 2004.
Photonic Packaging for Mixed-Technology Sensor Systems
Donald Chiarulli, Jason Bakos, Leo Selavo, Steven Levitan, John Hansson, Michael Weisser | 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.
Modeling and Simulation of Fiber Image Guide Multi-Chip Modules for MOEMS Applications
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 | 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.
2003
Optoelectronic Multi-Chip Module Demonstrator System
Jason Bakos, Donald Chiarulli, and Steven Levitan | Optics in Computing, OSA Technical Digest, (Optical Society of America, Washington DC, 2003) pp 117-119.
Optoelectronic Multi-Chip Modules
D. Chiarulli, S. Levitan, J. Bakos | Proc. 10th Annual Conference of Mixed Design of Integrated Circuits and Systems (MIXDES’03), Lodz, Poland, June 26-28, 2003.
Encoding Benefits for Fast Optical Transceivers
Leo Selavo, Jason Bakos, Donald M. Chiarulli, Steven P. Levitan | Proc. 14th IEEE-LEOS Annual Workshop on Interconnections within High-Speed Digital Systems, Santa Fe, New Mexico, 4 – 7 May 2003.
2002
Optoelectronic Multi-Chip-Module Implementation of a 64 Channel Crossbar Switch
J. D. Bakos, D. M. Chiarulli, and S. P. Levitan | Proc. International Conference of Optics in Computing (OC’02) pp. 161-163, Taipei, Taiwan, April 8 – 11, 2002.