Papers, Theses, and Presentations

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: 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

Paper

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	Paper
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	Paper

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

Paper

Slides

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

Paper

Slides

title: A Reconfigurable Architecture with Sequential Logic-based Stochastic Computing authors: M. Hassan Najafi, Peng Li, David J. Lilja, Weikang Qian and Marc Riedel to appear in: ACM Journal on Emerging Technologies in Computing Systems, 2017

Paper

title: A Deterministic Approach to Stochastic Computing authors: Devon Jenson and Marc Riedel presented at: IEEE/ACM International Conference on Computer-Aided Design, 2016

Paper

Slides

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

Paper

Slides

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.

Paper

Slides

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

Paper

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

Paper

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

Paper

Slides

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

Paper

Slides

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

Paper

Slides

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

Paper

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

Paper

Slides

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

Paper

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

Paper

Slides

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

Paper

Slides

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

Paper

Slides

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.

Paper

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

Paper

Poster

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

Paper

Slides

Computing with Molecules

title: Stochastic Computation on DNA strands through Hydroxyl Nicking authors: Arnav Solanki, Tonglin Chen and Marc Riedel presented at: [hhttps://www2.cs.duke.edu/FNANO/ Foundations of Nanoscience: Self-Assembled Architectures and Device (FNANO20)], Snowbird, Utah, 2020 (Virtual Meeting)

[File:FNANO20_Random_Cutting.pdf Paper]

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title: Parallel Binary Sorting and Shifting with DNA authors: Tonglin Chen and Marc Riedel presented at: 11th International Workshop on Bio-Design Automation, Cambridge, England, 2019.

Paper

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

Paper

Supplement

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

Paper

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

Paper

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

Paper

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.

Paper

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.

Paper

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

Paper

Slides

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.

Paper

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

Paper

Slides

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.

Paper

Slides

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.

Paper

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

Paper

Slides

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

Paper

Slides

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

Paper

Slides

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.

Paper

Slides

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.

Paper

Slides

Computing about Molecules

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

Paper

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

Paper

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.

Paper

Slides

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.

Paper

Slides

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

Paper

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

Paper

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

Paper

Slides

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

Paper

Slides

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

Paper

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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

Paper

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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).

Paper

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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

Paper

Poster

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

Paper

Slides

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

Paper

Slides

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

Paper

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

Paper

Slides

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

Paper

Slides

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

Paper

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Theses

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

Slides

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

Slides

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

Slides

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

Slides

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

M.S. Thesis

Slides

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

M.S. Thesis

Slides

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

Slides

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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

Proposal

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

Proposal

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

Proposal

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

Proposal

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

Proposal

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

Proposal

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

Proposal

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

Proposal

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

Proposal

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