2019

An Overlay Architecture for Pattern Matching
publication: Proc. 30th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2019).
authors: Rasha Karakchi, Charles A. Daniels, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


OpenVX Graph Optimization for Visual Processor Units
publication: Proc. 30th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2019).
authors: Madushan Abeysinghe, Jesse Villarreal, Lucas Weaver, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


2018

Fast Coordination of Power Electronic Converters for Energy Routing in Shipboard Power Systems
publication: Proc. 2018 International Ship Control Systems Symposium (iSCSS 2018).
authors: H. L. Ginn III, J. D. Bakos, A. Benigni
document: [ PDF DocumentView the PDF ]


2017

A Dynamically Reconfigurable Automata Processor Overlay
publication: Proc. International Conference on Reconfigurable Computing and FPGAs 2017 (ReConFig 2017).
authors: Rasha Karakchi, Lothrop O. Richards, and Jason D. Bakos
document: [ PDF DocumentView the PDF ]


Control System Communication Architecture for Power Electronic Building Blocks
publication: Proc. IEEE Electric Ship Technologies Symposium 2017 (ESTS 2017).
authors: Ivan Panchenko, Jason D. Bakos, Herbert L. Ginn
document: [ PDF DocumentView the PDF ]


System-Level, FPGA-Based, Real-Time Simulation of Ship Power Systems
publication: IEEE Trans. on Energy Conversion Systems, Vol. 32, No. 2.
authors: Matthew Milton, Andrea Benigni, Jason Bakos
document: [ PDF DocumentView the PDF ]


2016

High-Level Synthesis of a Genomic Database Search Engine
publication: Proc. 2016 International Conference on Reconfigurable Computing and FPGAs (ReConFig 2016).
authors: Rasha Karakchi, Jordan Bradshaw, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


Two-Hit Filter Synthesis for Genomic Database Search
publication: Proc. 24th IEEE International Symposium on Field-Programmable Custom Computing Machines.
authors: Jordan Bradshaw, Rasha Karakchi, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


2015

Embedded Systems: ARM Programming and Optimization
publication: Elsevier, 2015 (textbook).
authors: Jason D. Bakos


Memory Interface Design for 3D Stencil Kernels on a Massively Parallel Memory System
publication: ACM Transactions on Reconfigurable Technology and Systems (TRETS), Vol. 8, Issue 4, 2015.
authors: Zheming Jin, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


2014

Lucas-Kanade Optical Flow Estimation on the TI C66x Digital Signal Processor
publication: Proc. 18th Annual IEEE High Performance Extreme Computing Conference (HPEC 2014), Sept. 2014.
authors: Fan Zhang, Yang Gao, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


Sparse Matrix-Vector Multiply on the Keystone II Digital Signal Processor
publication: Proc. 18th Annual IEEE High Performance Extreme Computing Conference (HPEC 2014), Sept. 2014.
authors: Yang Gao, Fan Zhang, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


Large-scale Pairwise Sequence Alignments on a Large-scale GPU Cluster
publication: IEEE Design and Test, January/February 2014.
authors: Ibrahim Savran, Yang Gao, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


2013

Accuracy, Cost, and Performance Tradeoffs for Floating-Point Accumulation
publication: Proc. 2013 International Conference on Reconfigurable Computing and FPGAs (ReConFig 2013).
authors: Krishna Nagar, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


Sparse Matrix-Vector Multiply on the Texas Instruments C6678 Digital Signal Processor
publication: Proc. The 24th IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP 2013), Washington D.C., June 5-7, 2013.
authors: Yang Gao, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


Memory Access Scheduling on the Convey HC-1
publication: Proc. The 21st IEEE International Symposium on Field-Programmable Custom Computing Machines (FCCM'13), Seattle, Washington, April 28-30, 2013.
authors: Zheming Jin, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


Accelerating Frequent Itemset Mining on Graphics Processing Units
publication: Journal of Supercomputing, February 2013, DOI 10.1007/s11227-013-0887-x.
authors: Fan Zhang, Yan Zhang, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


A Heuristic Scheduler for Port-Constrained Floating-Point Pipelines
publication: International Journal of Reconfigurable Computing, Vol. 2013, Article ID 849545, 9 pages, 2013. doi:10.1155/2013/849545.
authors: Zheming Jin, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


Extending the BEAGLE Library to a Multi-FPGA Platform
publication: BMC Bioinformatics, BMC Bioinformatics 2013, 14:25.
authors: Zheming Jin, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


An FPGA-Based Accelerator for Frequent Itemset Mining
publication: ACM Trans. Reconfigurable Technology and Systems (TRETS), Vol. 6, Issue 1, May 2013.
authors: Yan Zhang, Fan Zhang, Zheming Jin, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


2012

GPU Acceleration of Pyrosequencing Noise Removal
publication: Proc. 2012 Symposium on Application Accelerators in High Performance Computing (SAAHPC 2012), Argonne National Laboratory, July 10-11, 2012.
authors: Yang Gao, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


A Cluster-on-a-Chip Architecture for High-Throughout Phylogeny Search
publication: IEEE Trans. on Parallel and Distributed Systems, Vol. 23, No. 4, April 2012.
authors: Tiffany M. Mintz, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


2011

Frequent Itemset Mining on Large-Scale Shared Memory Machines
publication: Proc. IEEE International Conference on Cluster Computing (CLUSTER 2011), Sept. 26-30, 2011.
authors: Yan Zhang, Fan Zhang, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


GPApriori: GPU-Accelerated Frequent Itemset Mining
publication: Proc. IEEE International Conference on Cluster Computing (CLUSTER 2011), Sept. 26-30, 2011.
authors: Fan Zhang, Yan Zhang, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


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


2010

High-Performance Heterogeneous Computing with the Convey HC-1
publication: Computing in Science and Engineering, Vol. 12, No. 6, November/December 2010.
authors: Jason D. Bakos
document: [ PDF DocumentView the PDF ]


Integrated Circuit Implementation for a GaN HFET Driver Circuit
publication: IEEE Transactions on Industry Applications, Vol. 46, No. 5, Sept/Oct. 2010.
authors: Bo Wang, Marco Riva, Jason D. Bakos, Antonello Monti
document: [ PDF DocumentView the PDF ]


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


FPGA acceleration of the phylogenetic likelihood function for Bayesian MCMC inference methods
publication: BMC Bioinformatics 2010, 11:184.
authors: Stephanie Zierke, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


2009

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


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


An Integrated Reduction Technique for a Double Precision Accumulator
publication: 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.
authors: Krishna K. Nagar, Jason D. Bakos
document: [ PDF DocumentView the PDF ]


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


2008

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


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


2007

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


FPGA Acceleration of Gene Rearrangement Analysis
publication: Proc. 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM'07), April 23-25, 2007.
authors: Jason D. Bakos
document: [ PDF DocumentView the PDF ]


Lightweight Error Correction Coding for System-Level Interconnects
publication: IEEE Transactions on Computers, Vol. 56, No. 3, March 2007.
authors: Jason D. Bakos, Donald M. Chiarulli, Steven P. Levitan
document: [ PDF DocumentView the PDF ]


2006

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


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


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


2005

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


Area, power, and pin efficient bus structures using multi-bit-differential signaling
publication: 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.
authors: Donald M. Chiarulli, Jason D. Bakos, Joel R. Martin, Steven P. Levitan
document: [ PDF DocumentView the PDF ]


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


2004

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


Photonic Packaging for Mixed-Technology Sensor Systems
publication: 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.
authors: Donald Chiarulli, Jason Bakos, Leo Selavo, Steven Levitan, John Hansson, Michael Weisser
document: [ PDF DocumentView the PDF ]


Modeling and Simulation of Fiber Image Guide Multi-Chip Modules for MOEMS Applications
publication: 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.
authors: 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
document: [ PDF DocumentView the PDF ]


2003

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


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


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


2002

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