Papers, Presentations, Theses, Proposals, and Patents

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Here are links to our papers, theses, proposals, and presentations. When several version of a paper were published, for instance one in conference proceedings and another in a journal, these are grouped together and only the most significant version is linked. All materials are subject to copyrights.

Computing with Random Bit Streams

title:	A Scalable Deterministic Approach to Stochastic Computing
authors:	Yadu Kiran and Marc Riedel
appeared in:	Great Lakes Symposium on VLSI (GLSVLSI), 2022

title:	Performing Stochastic Computation Deterministically
authors:	M. Hassan Najafi, Devon Jenson, David Lilja, and Marc Riedel
appeared in:	IEEE Transactions on Very Large Scale Integration (VLSI) Systems, Vol. 27, No. 29, pp. 2925–2938, 2019
presented at:	IEEE International Symposium of Circuits and Systems, 2020
presented at:	IEEE/ACM International Conference on Computer-Aided Design, 2016

title:	Synthesis of Polynomial Functions
authors:	Weikang Qian and Marc Riedel
appeared in:	Chapter 4, Stochastic Computing: Techniques and Applications, Springer, W.J Gross and V. C. Gaudet, Editors, pp. pp. 103–120, 2019

title:	Deterministic Approaches to Bitstream Computing
authors:	Marc Riedel
appeared in:	Chapter 5, Stochastic Computing: Techniques and Applications, Springer, W.J Gross and V. C. Gaudet, Editors, pp. pp. 121–136, 2019

title:	A Survey of Computation-Driven Data Encodings
authors:	Weikang Qian, Runsheng Wang, Yuan Wang, Marc Riedel and Ru Huang
presented at:	IEEE Workshop on Signal Processing Systems, 2019

title:	Deterministic Methods for Stochastic Computing using Low-Discrepancy Sequences
authors:	M. Hassan Najafi, David Lilja, and Marc Riedel
presented at:	IEEE/ACM International Conference on Computer-Aided Design, 2018

title:	Low Cost Sorting Network Circuits using Unary Processing
authors:	M. Hassan Najafi, David Lilja, Marc Riedel, and Kia Bazargan
appeared in:	IEEE Trans. on Very Large Scale Integration Sytems, Vol. 26, No. 8, pp. 1471–1480, 2018
presented at:	IEEE International Conference on Computer Design, 2017

title:	An Overview of Time-Based Computing with Stochastic Constructs
authors:	M. Hassan Najafi, S. Jamali-Zavareh, David Lilja, Marc Riedel, Kia Bazargan and Ramesh Harjani
appeared in:	IEEE Micro, Vol. 37, No. 6, pp. 62--71, 2017

title:	Time-Encoded Values for Highly Efficient Stochastic Circuits
authors:	M. Hassan Najafi, S. Jamali-Zavareh, David Lilja, Marc Riedel, Kia Bazargan and Ramesh Harjani
appeared in:	IEEE Transactions on VLSI, Vol. 25, No. 5, pp. 1644–1657, 2017
presented at:	IEEE International Symposium on Circuits and Systems, 2017

title:	Unary Positional Computing
authors:	McKenzie van der Hagen and Marc Riedel
presented at:	IEEE Global Conference on Signal and Information Processing, 2017

title:	Computing Polynomials with Positive Coefficients using Stochastic Logic by Double NAND Expansion
authors:	Ahmad Salehi, Yin Liu, Marc Riedel, and Keshab Parhi
presented at:	ACM Great Lakes Symposium on VLSI, 2017

title:	Polysynchronous Clocking: Exploiting the Skew Tolerance of Stochastic Circuits
authors:	M. Hassan Najafi, David Lilja, Marc Riedel, and Kia Bazargan
appeared in:	IEEE Transactions on Computers, Vol. 66, No. 10, pp. 1734–1746, 2017 Feature Paper of the Month
presented at:	Work-in-Progress Session, IEEE/ACM Design Automation Conference, 2016
presented at:	IEEE/ACM Asia and South Pacific Design Automation Conference, 2016

title:	A Reconfigurable Architecture with Sequential Logic-based Stochastic Computing
authors:	M. Hassan Najafi, Peng Li, David J. Lilja, Weikang Qian and Marc Riedel
appeared in:	ACM Journal on Emerging Technologies in Computing Systems, Vol. 13, No. 4, pp. 1–28, 2017

title:	Synthesis of Correlated Bit Streams for Stochastic Computing
authors:	Yin Liu, Megha Parhi, Marc Riedel and Keshab Parhi
presented at:	Asilomar Conference on Signals, Systems, and Computers, 2016

title:	Effect of Bit-Level Correlation in Stochastic Computing
authors:	Megha Parhi, Marc Riedel, and Keshab Parhi
presented at:	IEEE International Conference on Digital Signal Processing, Singapore, 2015.

title:	Computation on Stochastic Bit Streams: Digital Image Processing Case Studies
authors:	Peng Li, David Lilja, Weikang Qian, Kia Bazargan and Marc Riedel
appeared in:	IEEE Transactions on VLSI Sytems, Vol. 22, No. 3, pp. 449–462, 2014
appeared in:	Lecture Notes in Computer Science Power and Timing Modeling, Optimization and Simulation Workshop G. Goos, J. Hartmanis, and J. V. Leeuwen Editors, Springer, pp. 235–244, 2012

title:	Logical Computation on Stochastic Bit Streams with Linear Finite State Machines
authors:	Peng Li, David Lilja, Weikang Qian,Kia Bazargan and Marc Riedel
appeared in:	IEEE Transactions on Computers, Vol. 63, No. 6., pp. 1474–1486, 2014
presented at:	IEEE/ACM Asia and South Pacific Design Automation Conference, Sydney, Australia, 2012

title:	IIR Filters Using Stochastic Arithmetic
authors:	Naman Saraf, Kia Bazargan, David Lilja, and Marc Riedel
appeared in:	IEEE/ACM Design, Automation, and Test in Europe, 2014

title:	Stochastic Functions Using Sequential Logic
authors:	Naman Saraf, Kia Bazargan, David Lilja, and Marc Riedel
appeared in:	IEEE International Conference on Computer Design, Asheville, NC, 2013

title:	An Efficient Implementation of Numerical Integration Using Logical Computation on Stochastic Bit Streams
authors:	Weikang Qian, Cheng Wang, Peng Li, David Lilja, Kia Bazargan and Marc Riedel
appeared in:	IEEE/ACM Int'l Conference on Computer-Aided Design, San Jose, CA 2012

title:	The Synthesis of Complex Arithmetic Computation on Stochastic Bit Streams Using Sequential Logic
authors:	Peng Li, David Lilja, Weikang Qian, Kia Bazargan and Marc Riedel
presented at:	IEEE/ACM International Conference on Computer-Aided Design, San Jose, CA 2012
presented at:	IEEE/ACM International Workshop on Logic and Synthesis, Berkeley, CA 2012

title:	Transforming Probabilities with Combinational Logic
authors:	Weikang Qian, Marc Riedel, Hongchao Zhou, and Jehoshua Bruck
appeared in:	IEEE Trans. on Computer-Aided Design of Integrated Circuits and Systems, Vol. 30, No. 9, pp. 1279–1292, 2011
appeared in:	Advanced Techniques in Logic Synthesis, Optimizations and Applications Sunil Khatri and Kanupriya Gulati editors, Springer Publishing, 2011
presented at:	IEEE/ACM International Conference on Computer-Aided Design, San Jose, 2009 (nominated for IEEE/ACM William J. McCalla ICCAD Best Paper Award).
presented at:	IEEE/ACM International Workshop on Logic and Synthesis, Berkeley, CA, 2009

title:	An Architecture for Fault-Tolerant Computation with Stochastic Logic
authors:	Weikang Qian, Xin Li, Marc Riedel, Kia Bazargan, and David Lilja
appeared in:	IEEE Transactions on Computers, Vol. 60, No. 1, pp. 93–105, 2011

title:	The Synthesis of Stochastic Circuits for Nanoscale Computation
authors:	Weikang Qian, John Backes, and Marc Riedel
appeared in:	International Journal of Nanotechnology and Molecular Computation, Vol. 1, No. 4, pp. 39–57, 2010
presented at:	IEEE/ACM International Workshop on Logic and Synthesis, San Diego, CA, 2007

title:	Two-Level Logic Synthesis for Probabilistic Computation
authors:	Weikang Qian and Marc Riedel
presented at:	IEEE/ACM International Workshop on Logic and Synthesis, Irvine, CA, 2010

title:	A Reconfigurable Stochastic Architecture for Highly Reliable Computing
authors:	Xin Li, Weikang Qian, Marc Riedel, Kia Bazargan, and David Lilja
presented at:	Great Lakes Symposium on VLSI, Boston, MA, 2009

title:	Estimation and Optimization of Reliability of Noisy Digital Circuits
authors:	Satish Sivaswamy, Kia Bazargan and Marc Riedel
presented at:	IEEE International Symposium on Quality Electronic Design, San Jose, CA, 2009.

title:	The Synthesis of Stochastic Logic to Perform Multivariate Polynomial Arithmetic
authors:	Weikang Qian and Marc Riedel
presented at:	IEEE/ACM International Workshop on Logic and Synthesis, Lake Tahoe, CA, 2008

title:	The Synthesis of Robust Polynomial Arithmetic with Stochastic Logic
authors:	Weikang Qian and Marc Riedel
presented at:	ACM/EDAC/IEEE Design Automation Conference, Anaheim, CA, 2008

Computing with Molecules

title:	Parallel Pairwise Operations on Data Stored in DNA: Sorting, Shifting, and Searching
authors:	Tonglin Chen, Arnav Solanki and Marc Riedel
presented at:	International Conference on DNA Computing and Molecular Programming, 2021

title:	Cascadable Stochastic Logic for DNA Storage
authors:	Arnav Solanki, Tonglin Chen and Marc Riedel
presented at:	Visual Communications and Image Processing, 2021

title:	Stochastic Computation on DNA strands through Hydroxyl Nicking
authors:	Arnav Solanki, Tonglin Chen and Marc Riedel
presented at:	Foundations of Nanoscience: Self-Assembled Architectures and Devices, 2020

title:	Concentration-Based-Polynomial-Calculations-on-Nicked-DNA
authors:	Tonglin Chen and Marc Riedel
presented at:	IEEE International Conference on Acoustics, Speech, and Signal Processing, 2020

title:	Parallel Binary Sorting and Shifting with DNA
authors:	Tonglin Chen and Marc Riedel
presented at:	International Workshop on Bio-Design Automation, Cambridge, England, 2019.

title:	Computing Mathematical Functions using DNA via Fractional Coding
authors:	Ahmad Salehi, Xingyi Liu, Marc Riedel, and Keshab K. Parhi
appeared in:	Nature Scientific Reports, Vol. 8 No. 8312, 2018

title:	Chemical Reaction Networks for Computing Polynomials
authors:	Ahmad Salehi, Keshab Parhi and Marc Riedel
appeared as:	ACS Synthetic Biology,Vol. 6, No. 1, pp. 76–83, 2017
presented at:	IEEE Globecom Symposium, 2016

title:	Molecular Sensing and Computing Systems
authors:	Ahmad Salehi, Marc Riedel, Keshab Parhi
appeared as:	IEEE Trans. on Molecular, Biological, and Multi-Scale Communications, Vol. 1, No. 3, 2015

title:	Markov Chain Computations using Molecular Reactions
authors:	Ahmad Salehi, Marc Riedel, Keshab Parhi
presented at:	IEEE International Conference on Digital Signal Processing, 2015.

title:	Asynchronous Discrete-Time Signal Processing with Molecular Reactions
authors:	Ahmad Salehi, Marc Riedel, and Keshab Parhi
presented at:	Asilomar Conference on Signals, Systems, and Computers, 2014.

title:	Digital Logic with Molecular Reactions
authors:	Hua Jiang, Marc Riedel, Keshab Parhi
presented at:	IEEE/ACM International Conference on Computer-Aided Design, San Jose, CA, 2013.

title:	Discrete-Time Signal Processing with DNA
authors:	Hua Jiang, Ahmad Salehi, Marc Riedel and Keshab Parhi
appeared in:	ACS Synthetic Biology, Vol. 2 no. 5, pp. 245–254, 2013. Supplementary Information: List of Reactions
appeared in:	IEEE Design & Test of Computers, Vol. 29, No. 3, pp. 21–31, 2012.
presented at:	IEEE/ACM International Conference on Computer-Aided Design, San Jose, CA, 2010.
presented at:	IEEE Workshop on Signal Processing Systems, San Francisco, 2010

title:	Robust Tunable In Vitro Transcriptional Oscillator Networks
authors:	Vishwesh Kulkarni, Thee Chanyaswad, Marc Riedel and Jongmin Kim
presented at:	Allerton Conference, Urbana-Champaign, IL, 2012.

title:	Rate-Independent Constructs for Chemical Computation
authors:	Phil Senum and Marc Riedel
appeared in:	PLoS ONE, Vol. 6, No. 6, 2011. Supplementary Information

title:	Synchronous Sequential Computation with Molecular Reactions
authors:	Hua Jiang, Marc Riedel and Keshab Parhi
presented at:	ACM/EDAC/IEEE Design Automation Conference, San Diego, CA, 2011.

title:	Asynchronous Computation with Molecular Reactions
authors:	Hua Jiang, Marc Riedel and Keshab Parhi
presented at:	Asilomar Conference on Signals, Systems, and Computers, Pacific Grove, CA, 2011.

title:	Binary Counting with Chemical Reactions
authors:	Aleksandra Kharam, Hua Jiang, Marc Riedel and Keshab Parhi
presented at:	Pacific Symposium on Biocomputing, Hawaii, 2011.

title:	Writing and Compiling Code into Biochemistry
authors:	Adam Shea, Brian Fett, Marc Riedel, and Keshab Parhi
presented at:	IEEE/ACM International Conference on Computer-Aided Design, San Jose, CA, 2009; and at Pacific Symposium on Biocomputing, Kona, Hawaii, 2010 (see blog).
presented at:	IEEE/ACM International Workshop on Logic and Synthesis, Berkeley, 2009

title:	Stochastic Transient Analysis of Biochemical Systems
authors:	Bin Cheng and Marc Riedel
presented at:	Pacific Symposium on Biocomputing, Hawaii, 2009.

title:	Module Locking in Biochemical Systems
authors:	Brian Fett and Marc Riedel
presented at:	IEEE/ACM International Conference on Computer-Aided Design, San Jose, CA, 2008; and at Synthetic Biology 4.0, Hong Kong, 2008.

title:	Synthesizing Stochasticity in Biochemical Systems
authors:	Brian Fett, Shuki Bruck, and Marc Riedel
presented at:	ACM/EDAC/IEEE Design Automation Conference, San Diego, 2007; and at Synthetic Biology 3.0, Zürich, 2007.

Computing about Molecules

title:	The Role of Hydrophobicity in Peptide-MHC Binding
authors:	Arnav Solanki, Marc Riedel, James Cornette, Julia Udell, Ishaan Koratkar, and George Vasmatzis
presented at:	3rd International Symposium on Mathematical and Computational Oncology, 2021

View an interactive version of the data for this paper here.

title:	Gene Regulatory Network Modeling Using Literature Curated and High Throughput Data
authors:	Vishwesh Kulkarni, Reza Arastoo, Anupama Bhat, Kalyansundaram Subramanian, Mayuresh Kothare, Marc Riedel and Marc Riedel
appeared in:	Systems and Synthetic Biology, Vol. 6, No. 3–4, pp. 69--77, 2012

title:	Characterizing the Memory of the GAL Regulatory Network in Saccharomyces cerevisiae
authors:	Vishwesh Kulkarni, Venkatesh Kareenhalli, Ganesh Viswananthan, and Marc Riedel
appeared in:	Systems and Synthetic Biology, Vol. 5, No. 3–4, pp. 97--104, 2011

Computing with Nanoscale Lattices

title:	Logic Synthesis for Switching Lattices
authors:	Mustafa Altun and Marc Riedel
appear in:	IEEE Transactions on Computers, Vol. 61, No. 11, pp. 1588–1600, 2012.
presented at:	ACM/EDAC/IEEE Design Automation Conference, Anaheim, CA, 2010.

title:	Synthesizing Logic with Percolation in Nanoscale Lattices
authors:	Mustafa Altun and Marc Riedel
appeared in:	International Journal of Nanotechnology and Molecular Computation, Vol. 3, No. 2, pp. 12–30, 2011.
presented at:	ACM/EDAC/IEEE Design Automation Conference, San Francisco, CA, 2009.

Computing with Feedback

title:	Cyclic Boolean Circuits
authors:	Marc Riedel and Shuki Bruck
appeared in:	Discrete Applied Mathematics, Vol. 160, No. 13–14, pp. 1877–1900, 2012

title:	The Synthesis of Cyclic Dependencies with Boolean Satisfiability
authors:	John Backes and Marc Riedel
appeared in:	ACM Transactions on Design Automation of Electronic Systems Vol. 17, No. 4, pp. 1–24, 2012

title:	The Analysis and Mapping of Cyclic Circuits with Boolean Satisfiability
authors:	John Backes, Brian Fett, and Marc Riedel
appeared as:	Technical Report, UMN
presented at:	IEEE/ACM Int'l Conference on Computer-Aided Design, San Jose, CA, 2008

title:	The Synthesis of Cyclic Dependencies with Craig Interpolation
authors:	John Backes and Marc Riedel
presented at:	IEEE/ACM International Workshop on Logic and Synthesis, Berkeley, CA, 2009

title:	Timing Analysis of Cyclic Combinational Circuits
authors:	Marc Riedel and Shuki Bruck
presented at:	IEEE/ACM International Workshop on Logic and Synthesis, Temecula, CA, 2004

title:	Cyclic Combinational Circuits: Analysis for Synthesis
authors:	Marc Riedel and Shuki Bruck
presented at:	IEEE/ACM Int'l Workshop on Logic and Synthesis, Orange County, CA, 2003

title:	The Synthesis of Cyclic Combinational Circuits
authors:	Marc Riedel and Shuki Bruck
presented at:	ACM/EDAC/IEEE Design Automation Conference, Anahiem, CA, 2003 (winner of DAC Best Paper Award).

Algorithms and Data Structures

title:	Using Cubes of Non-state Variables With Property Directed Reachability
authors:	John Backes and Marc Riedel
presented at:	IEEE/ACM Design Automation & Test in Europe, Grenoble, France, 2013

title:	Resolution Proofs as a Data Structure For Logic Synthesis
authors:	John Backes and Marc Riedel
presented at:	IEEE/ACM International Workshop on Logic Synthesis, La Jolla, CA, 2011

title:	Reduction of Interpolants For Logic Synthesis
authors:	John Backes and Marc Riedel
presented at:	IEEE/ACM International Conference on Computer-Aided Design, San Jose, CA, 2010
presented at:	IEEE/ACM International Workshop on Logic Synthesis, Irvine, CA, 2010

Mathematics

title:	A Study on Monotone Self-Dual Boolean Functions
authors:	Mustafa Altun and Marc Riedel
appeared in:	Acta Mathematicae Applicatae Sinica, Vol. 33, No. 1, pp. 43–52, 2017

title:	Synthesizing Cubes to Satisfy a Given Intersection Pattern
authors:	Weikang Qian, Marc Riedel, and Ivo Rosenberg
appeared in:	Journal of Discrete Applied Mathematics, Vol. 193, pp. 11–38, 2015
presented at:	IEEE/ACM International Workshop on Logic and Synthesis, Irvine, CA, 2010

title:	Networks of Passive Oscillators
authors:	Vishwesh V. Kulkarni, Marc Riedel, and Guy-Bart Stan
presented at:	Allerton Conference, Urbana-Champaign, Illinois, 2011

title:	Uniform Approximation and Bernstein Polynomials with Coefficients in the Unit Interval
authors:	Weikang Qian, Marc Riedel, and Ivo Rosenberg
appeared in:	European Journal of Combinatorics, Vol. 32, No. 3, pp. 448–463, 2011

Theses

title:	Simulating Chemical Reaction Networks for Computing with Naturally-Occurring DNA
author:	Owen Hoffend
degree:	B.S., Computer Engineering, University of Minnesota
year:	2020.

Senior Honors Thesis

title:	Algorithms and Data Structures For Logic Synthesis And Verification Using Boolean Satisfiability (received the University of Minnesota Doctoral Dissertation Fellowship)
author:	John Backes
degree:	Ph.D., Electrical and Computer Engineering, University of Minnesota
year:	2013.

Ph.D. Dissertation

title:	Digital Logic and Signal Processing Computations with Molecular Reactions
author:	Hua Jiang
degree:	Ph.D., Electrical Engineering, University of Minnesota
year:	2012.

Ph.D. Dissertation

title:	Logic Synthesis for Networks of Four-Terminal Switches
author:	Mustafa Altun
degree:	Ph.D., Electrical Engineering, University of Minnesota
year:	2012.

Ph.D. Dissertation

title:	Digital Yet Deliberately Random: Synthesizing Logical Computation on.Stochastic Bit Streams (received the University of Minnesota Doctoral Dissertation Fellowship)
author:	Weikang Qian
degree:	Ph.D., Electrical Engineering, University of Minnesota
year:	2011.

Ph.D. Dissertation

title:	Synthesizing Stochasticity in Biochemical Systems
author:	Brian Fett
degree:	M.S., Biomedical Informatics and Computational Biology, University of Minnesota
year:	2010.

title:	Stochastic Transient Analysis of Biochemical Systems
author:	Bin Cheng
degree:	M.S., Electrical Engineering, University of Minnesota
year:	2010.

title:	Cyclic Combinational Circuits
author:	Marc Riedel
degree:	Ph.D., Electrical Engineering, Caltech, 2004 (winner of Charles H. Wilts Prize for the Best Ph.D. Dissertation in EE at Caltech)
year:	2004.

Ph.D. Dissertation

Funding Proposals

title:	Back to the Future with Printed, Flexible Electronics: Design in a Post-CMOS Era when Transistor Counts Matter Again
Investigators:	Kia Bazargan, Daniel Frisbie, Ramesh Harjani, David Lilja and Marc Riedel.
Agency:	National Science Foundation
Program:	Software and Hardware Foundations
Award:	$800,000
Duration:	2014 – 2017

title:	Advanced Signal Processing with DNA
Investigators:	Keshab Parhi and Marc Riedel
Agency:	National Science Foundation
Program:	Computing and Communications Foundations.
Amount:	$300,000
Duration:	2014 – 2017

title:	Digital Yet Deliberately Random: Synthesizing Logical Computation on Stochastic Bit Streams
Investigators:	Marc Riedel, Kia Bazargan, Ramesh Harjani, and David Lilja.
Agency:	National Science Foundation
Program:	Software and Hardware Foundations
Award:	$300,000
Duration:	2012 – 2014

title:	Digital Signal Processing with Biomolecular Reactions
Investigators:	Keshab Parhi and Marc Riedel
Agency:	National Science Foundation
Program:	Computing and Communications Foundations
Amount:	$400,000
Duration:	2011 – 2014

title:	Synthesizing Signal Processing Functions with Biochemical Reactions
Investigators:	Yiannis Kaznessis, Claudia Dannert Schmidt and Marc Riedel
Agency:	University of Minnesota
Program:	Digital Technology Center Seed Grant.
Amount:	$100,000
Duration:	2011 – 2012

title:	Computing with Things Small, Wet, and Random – Design Automation for Digital Computation with Nanoscale Technologies and Biological Processes
Investigator:	Marc Riedel
Agency:	National Science Foundation
Program:	NSF CAREER Award
Amount:	$500,000
Duration:	2009 – 2014

title:	Synthesizing Signal Processing Functions with Biochemical Reactions
Investigators:	Keshab Parhi and Marc Riedel
Agency:	National Science Foundation
Program:	Computing and Communications Foundations.
Amount:	$200,000
Duration:	2009 – 2011

title:	Tackling the Stochastic Simulation of Biochemical_Networks with Real Computing Power
Investigators:	Marc Riedel and Tim Mullins (IBM)
Agency:	University of Minnesota
Program:	Biomedical Informatics and Computational Biology Traineeships
Amount:	$78,000
Duration:	2007 – 2009

title:	Concurrent Logical and Physical Design of Digital Nanoscale Circuits
Investigator:	Marc Riedel
Agency:	SRC Focus Center Research Program (FCRP)
Program:	Functional Engineered Nano-Architectonics (FENA)
Amount:	$325,000
Duration:	2006 – 2009

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