Abstract
Programmable analog devices are a powerful new computing substrate that are especially appropriate for performing computationally intensive simulations of neuromorphic and cytomorphic models. Current state of the art techniques for configuring analog devices to simulate dynamical systems do not consider the current and voltage operating ranges of analog device components or the sampling limitations of the digital interface of the device. We present Jaunt, a new solver that scales the values that configure the analog device to ensure the resulting analog computation executes within the operating constraints of the device, preserves the recoverable dynamics of the original simulation, and executes slowly enough to observe these dynamics at the sampled digital outputs. Our results show that, on a set of benchmark biological simulations, 1) unscaled configurations produce incorrect simulations because they violate the operating ranges of the device and 2) Jaunt delivers scaled configurations that respect the operating ranges to produce correct simulations with observable dynamics.
- Biomodel artifact database. https://www.ebi.ac.uk/biomodels-main.Google Scholar
- Sara Achour, Rahul Sarpeshkar, and Martin C Rinard. Configuration synthesis for programmable analog devices with arco. In Proceedings of the 37th ACM SIGPLAN Conference on Programming Language Design and Implementation, pages 177--193. ACM, 2016. Google Scholar
Digital Library
- Kurt Antreich, J Eckmueller, Helmut Graeb, Michael Pronath, E Schenkel, R Schwencker, and S Zizala. Wicked: Analog circuit synthesis incorporating mismatch. In Custom Integrated Circuits Conference, 2000. CICC. Proceedings of the IEEE 2000, pages 511--514. IEEE, 2000.Google Scholar
Cross Ref
- Verena Becker, Marcel Schilling, Julie Bachmann, Ute Baumann, Andreas Raue, Thomas Maiwald, Jens Timmer, and Ursula Klingmüller. Covering a broad dynamic range: information processing at the erythropoietin receptor. Science, 328(5984):1404--1408, 2010.Google Scholar
Cross Ref
- Ben Varkey Benjamin, Peiran Gao, Emmett McQuinn, Shobhit Choudhary, Anand R Chandrasekaran, Jean-Marie Bussat, Rodrigo Alvarez-Icaza, John V Arthur, Paul Merolla, Kwabena Boahen, et al. Neurogrid: A mixed-analog-digital multichip system for large-scale neural simulations. Proceedings of the IEEE, 102(5):699--716, 2014.Google Scholar
Cross Ref
- Stephen Boyd, Seung-Jean Kim, Lieven Vandenberghe, and Arash Hassibi. A tutorial on geometric programming. Optimization and engineering, 8(1):67, 2007.Google Scholar
Cross Ref
- Donald G Buerk. Can we model nitric oxide biotransport? a survey of mathematical models for a simple diatomic molecule with surprisingly complex biological activities. Annual review of biomedical engineering, 3(1):109--143, 2001.Google Scholar
- Edward Burnell and Warren Hoburg. Gpkit software for geometric programming. https://github.com/convexengineering/gpkit, 2017. Version 0.6.0.Google Scholar
- G.E.R. Cowan, R.C. Melville, and Y. Tsividis. A VLSI analog computer/digital computer accelerator. Solid-State Circuits, IEEE Journal of, 41(1):42--53, Jan 2006.Google Scholar
- Ramiz Daniel, Sung Sik Woo, Lorenzo Turicchia, and Rahul Sarpeshkar. Analog transistor models of bacterial genetic circuits. In Biomedical Circuits and Systems Conference (BioCAS), 2011 IEEE, pages 333--336. IEEE, 2011.Google Scholar
Cross Ref
- J.L. Douce and H. Wilson. The automatic synthesis of control systems with constraints. Mathematics and Computers in Simulation, 7(1):18 -- 22, 1965. Google Scholar
Digital Library
- Michael B Elowitz and Stanislas Leibler. A synthetic oscillatory network of transcriptional regulators. Nature, 403(6767):335--338, 2000.Google Scholar
Cross Ref
- Jason Ernst and Manolis Kellis. ChromHMM: automating chromatin-state discovery and characterization. Nature Methods, 9(3):215--6, mar 2012.Google Scholar
Cross Ref
- Hadi Esmaeilzadeh, Adrian Sampson, Luis Ceze, and Doug Burger. Neural acceleration for general-purpose approximate programs. In Proceedings of the 2012 45th Annual IEEE/ACM International Symposium on Microarchitecture, pages 449--460. IEEE Computer Society, 2012. Google Scholar
Digital Library
- Timothy S Gardner, Charles R Cantor, and James J Collins. Construction of a genetic toggle switch in escherichia coli. Nature, 403(6767):339--342, 2000.Google Scholar
Cross Ref
- Ramesh Harjani, L Richard Carley, et al. Oasys: A framework for analog circuit synthesis. Computer-Aided Design of Integrated Circuits and Systems, IEEE Transactions on, 8(12):1247--1266, 1989. Google Scholar
Digital Library
- L. Jaulin, M. Kieffer, O. Didrit, and E. Walter. Applied Interval Analysis: With Examples in Parameter and State Estimation, Robust Control and Robotics. Springer London, 2012.Google Scholar
- L.V. Kolev. Interval Methods for Circuit Analysis. Advanced series on circuits and systems. World Scientific, 1993.Google Scholar
- E Lalonde, A S Ishkanian, J Sykes, M Fraser, H Ross-Adams, N Erho, M J Dunning, S Halim, A D Lamb, N C Moon, G Zafarana, A Y Warren, X Meng, J Thoms, M R Grzadkowski, A Berlin, C L Have, V R Ramnarine, C Q Yao, C A Malloff, L L Lam, H Xie, N J Harding, D Y Mak, K C Chu, L C Chong, D H Sendorek, C P'ng, C C Collins, J A Squire, I Jurisica, C Cooper, R Eeles, M Pintilie, A Dal Pra, E Davicioni, W L Lam, M Milosevic, D E Neal, T van der Kwast, P C Boutros, and R G Bristow. Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study. Lancet Oncol, 15(13):1521--1532, 2014.Google Scholar
Cross Ref
- Frank J Lebeda, Michael Adler, Keith Erickson, and Yaroslav Chushak. Onset dynamics of type a botulinum neurotoxin-induced paralysis. Journal of pharmacokinetics and pharmacodynamics, 35(3):251, 2008.Google Scholar
- MATLAB. R2015b. The MathWorks Inc., Natick, Massachusetts, 2015.Google Scholar
- E.S. Ochotta, R.A. Rutenbar, and L.R. Carley. Synthesis of high-performance analog circuits in ASTRX/OBLX. Computer-Aided Design of Integrated Circuits and Systems, IEEE Transactions on, 15(3):273--294, Mar 1996. Google Scholar
Digital Library
- Yakup Paker and Stephen H. Unger. ADAC -- a programmed direct analog computer. Mathematics and Computers in Simulation, 9(1):16 -- 23, 1967. Google Scholar
Digital Library
- Alberto Paoluzzi, Valerio Pascucci, Michele Vicentino, Claudio Baldazzi, and Simone Portuesi. Geometric Programming, pages 51--93. John Wiley & Sons, Ltd, 2005.Google Scholar
- Denise R. Ferrier PhD. Biochemistry (Lippincott Illustrated Reviews Series). LWW, 2013.Google Scholar
- Sylvain Saighi, Yannick Bornat, Jean Tomas, Gwendal Le Masson, and Sylvie Renaud. A library of analog operators based on the Hodgkin-Huxley formalism for the design of tunable, real-time, silicon neurons. Biomedical Circuits and Systems, IEEE Transactions on, 5(1):3--19, 2011.Google Scholar
- Sams. Arrangement and scaling of equations. Mathematics and Computers in Simulation, 6(3):179 -- 182, 1964. Google Scholar
Digital Library
- Rahul Sarpeshkar. Ultra Low Power Bioelectronics: Fundamentals, Biomedical Applications, and Bio-Inspired Systems. Cambridge University Press, 2010.Google Scholar
Cross Ref
- Christian Schneider and Howard Card. Analog CMOS synaptic learning circuits adapted from invertebrate biology. Circuits and Systems, IEEE Transactions on, 38(12):1430--1438, 1991.Google Scholar
- Richard I Sherwood, Tatsunori Hashimoto, Charles W O'Donnell, Sophia Lewis, Amira a Barkal, John Peter van Hoff, Vivek Karun, Tommi Jaakkola, and David K Gifford. Discovery of directional and nondirectional pioneer transcription factors by modeling DNase profile magnitude and shape. Nature Biotechnology, 32(2):171--8, mar 2014.Google Scholar
Cross Ref
- Renée St Amant, Amir Yazdanbakhsh, Jongse Park, Bradley Thwaites, Hadi Esmaeilzadeh, Arjang Hassibi, Luis Ceze, and Doug Burger. General-purpose code acceleration with limited-precision analog computation. ACM SIGARCH Computer Architecture News, 42(3):505--516, 2014. Google Scholar
Digital Library
- Jonathan J. Y. Teo, Sung Sik Woo, and Rahul Sarpeshkar. Synthetic biology: A unifying view and review using analog circuits. IEEE Trans. Biomed. Circuits and Systems, 9(4):453--474, 2015.Google Scholar
Cross Ref
- Rajko Tomovic. Proceedings of the international association for analog computation method of iteration and analog computation. Mathematics and Computers in Simulation, 1(2):60 -- 63, 1958. Google Scholar
Digital Library
- Herbert Weiner. The illusion of simplicity: the medical model revisited. The American journal of psychiatry, 1978.Google Scholar
- Sung Sik Woo et al. Fast simulation of stochastic biochemical reaction networks on cytomorphic chips. PhD thesis, Massachusetts Institute of Technology, 2016.Google Scholar
- Sung Sik Woo, Jaewook Kim, and Rahul Sarpeshkar. A cytomorphic chip for quantitative modeling of fundamental bio-molecular circuits. IEEE Trans. Biomed. Circuits and Systems, 9(4):527--542, 2015.Google Scholar
Cross Ref
Index Terms
Time Dilation and Contraction for Programmable Analog Devices with Jaunt
Recommendations
Time Dilation and Contraction for Programmable Analog Devices with Jaunt
ASPLOS '18: Proceedings of the Twenty-Third International Conference on Architectural Support for Programming Languages and Operating SystemsProgrammable analog devices are a powerful new computing substrate that are especially appropriate for performing computationally intensive simulations of neuromorphic and cytomorphic models. Current state of the art techniques for configuring analog ...
A Novel Analog to Digital Conversion Concept with Crosstalk Computing
NANOARCH '18: Proceedings of the 14th IEEE/ACM International Symposium on Nanoscale ArchitecturesAnalog to Digital Converters (ADCs) is the core component of computing systems forming a link between the external stimuli and digital microprocessor operations. Current CMOS based fast ADCs are difficult to scale due to the reliance on transistor ...
A circuit implementation of an ultra high speed, low power analog fully programmable MFG
In this article, an analog fully programmable membership function generator MFG is presented. It is capable of generating Gaussian, Triangular and Trapezoidal shapes as well as S or Z shapes. For omitting noise disturbances, differential structures are ...







Comments