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Gasparyan M, Rao S. Parameter Estimation for Kinetic Models of Chemical Reaction Networks from Partial Experimental Data of Species' Concentrations. Bioengineering (Basel) 2023; 10:1056. [PMID: 37760158 PMCID: PMC10526083 DOI: 10.3390/bioengineering10091056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 08/23/2023] [Accepted: 08/31/2023] [Indexed: 09/29/2023] Open
Abstract
The current manuscript addresses the problem of parameter estimation for kinetic models of chemical reaction networks from observed time series partial experimental data of species concentrations. It is demonstrated how the Kron reduction method of kinetic models, in conjunction with the (weighted) least squares optimization technique, can be used as a tool to solve the above-mentioned ill-posed parameter estimation problem. First, a new trajectory-independent measure is introduced to quantify the dynamical difference between the original mathematical model and the corresponding Kron-reduced model. This measure is then crucially used to estimate the parameters contained in the kinetic model so that the corresponding values of the species' concentrations predicted by the model fit the available experimental data. The new parameter estimation method is tested on two real-life examples of chemical reaction networks: nicotinic acetylcholine receptors and Trypanosoma brucei trypanothione synthetase. Both weighted and unweighted least squares techniques, combined with Kron reduction, are used to find the best-fitting parameter values. The method of leave-one-out cross-validation is utilized to determine the preferred technique. For nicotinic receptors, the training errors due to the application of unweighted and weighted least squares are 3.22 and 3.61 respectively, while for Trypanosoma synthetase, the application of unweighted and weighted least squares result in training errors of 0.82 and 0.70 respectively. Furthermore, the problem of identifiability of dynamical systems, i.e., the possibility of uniquely determining the parameters from certain types of output, has also been addressed.
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Affiliation(s)
- Manvel Gasparyan
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea
- Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon 21985, Republic of Korea;
- Department of Data Analysis and Mathematical Modelling, Ghent University, 9000 Ghent, Belgium
| | - Shodhan Rao
- Center for Biosystems and Biotech Data Science, Ghent University Global Campus, Incheon 21985, Republic of Korea;
- Department of Data Analysis and Mathematical Modelling, Ghent University, 9000 Ghent, Belgium
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2
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Sheldon FC, Kolchinsky A, Caravelli F. Computational capacity of LRC, memristive, and hybrid reservoirs. Phys Rev E 2022; 106:045310. [PMID: 36397581 DOI: 10.1103/physreve.106.045310] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Reservoir computing is a machine learning paradigm that uses a high-dimensional dynamical system, or reservoir, to approximate and predict time series data. The scale, speed, and power usage of reservoir computers could be enhanced by constructing reservoirs out of electronic circuits, and several experimental studies have demonstrated promise in this direction. However, designing quality reservoirs requires a precise understanding of how such circuits process and store information. We analyze the feasibility and optimal design of electronic reservoirs that include both linear elements (resistors, inductors, and capacitors) and nonlinear memory elements called memristors. We provide analytic results regarding the feasibility of these reservoirs and give a systematic characterization of their computational properties by examining the types of input-output relationships that they can approximate. This allows us to design reservoirs with optimal properties. By introducing measures of the total linear and nonlinear computational capacities of the reservoir, we are able to design electronic circuits whose total computational capacity scales extensively with the system size. Our electronic reservoirs can match or exceed the performance of conventional "echo state network" reservoirs in a form that may be directly implemented in hardware.
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Affiliation(s)
- Forrest C Sheldon
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
- London Institute for Mathematical Sciences, 21 Albemarle St., London W1S 4BS United Kingdom
| | - Artemy Kolchinsky
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, New Mexico 87501, USA
| | - Francesco Caravelli
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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Caravelli F, Sheldon FC, Traversa FL. Global minimization via classical tunneling assisted by collective force field formation. SCIENCE ADVANCES 2021; 7:eabh1542. [PMID: 34936465 PMCID: PMC8694608 DOI: 10.1126/sciadv.abh1542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 11/05/2021] [Indexed: 06/14/2023]
Abstract
Simple elements interacting in networks can give rise to intricate emergent behaviors. Examples such as synchronization and phase transitions often apply in many contexts, as many different systems may reduce to the same effective model. Here, we demonstrate such a behavior in a model inspired by memristors. When weakly driven, the system is described by movement in an effective potential, but when strongly driven, instabilities cause escapes from local minima, which can be interpreted as an unstable tunneling mechanism. We dub this collective and nonperturbative effect a “Lyapunov force,” which steers the system toward the global minimum of the potential function, even if the full system has a constellation of equilibrium points growing exponentially with the system size. This mechanism is appealing for its physical relevance in nanoscale physics and for its possible applications in optimization, Monte Carlo schemes, and machine learning.
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Affiliation(s)
- Francesco Caravelli
- Theoretical Division (T4), Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Forrest C. Sheldon
- Theoretical Division (T4), Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
- London Institute for Mathematical Sciences, 35a South St., London W1K 2XF, UK
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Jia Q, Mwanandiye ES, Tang WKS. Master-Slave Synchronization of Delayed Neural Networks With Time-Varying Control. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS 2021; 32:2292-2298. [PMID: 32479405 DOI: 10.1109/tnnls.2020.2996224] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
This brief investigates the master-slave synchronization problem of delayed neural networks with general time-varying control. Assuming a linear feedback controller with time-varying control gain, the synchronization problem is recast into the stability problem of a delayed system with a time-varying coefficient. The main theorem is established in terms of the time average of the control gain by using the Lyapunov-Razumikhin theorem. Moreover, the proposed framework encompasses some general intermittent control schemes, such as the switched control gain with external disturbance and intermittent control with pulse-modulated gain function, while some useful corollaries are consequently deduced. Interestingly, our theorem also provides a solution for regaining stability under control failure. The validity of the theorem and corollaries is further demonstrated with numerical examples.
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Wang W, Song W, Yao P, Li Y, Van Nostrand J, Qiu Q, Ielmini D, Yang JJ. Integration and Co-design of Memristive Devices and Algorithms for Artificial Intelligence. iScience 2020; 23:101809. [PMID: 33305176 PMCID: PMC7718163 DOI: 10.1016/j.isci.2020.101809] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Memristive devices share remarkable similarities to biological synapses, dendrites, and neurons at both the physical mechanism level and unit functionality level, making the memristive approach to neuromorphic computing a promising technology for future artificial intelligence. However, these similarities do not directly transfer to the success of efficient computation without device and algorithm co-designs and optimizations. Contemporary deep learning algorithms demand the memristive artificial synapses to ideally possess analog weighting and linear weight-update behavior, requiring substantial device-level and circuit-level optimization. Such co-design and optimization have been the main focus of memristive neuromorphic engineering, which often abandons the “non-ideal” behaviors of memristive devices, although many of them resemble what have been observed in biological components. Novel brain-inspired algorithms are being proposed to utilize such behaviors as unique features to further enhance the efficiency and intelligence of neuromorphic computing, which calls for collaborations among electrical engineers, computing scientists, and neuroscientists.
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Affiliation(s)
- Wei Wang
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano and IU.NET, Piazza L. da Vinci 32, Milano 20133, Italy
| | - Wenhao Song
- Electrical and Computer Engineering Department, University of Southern California, Los Angeles, CA, USA
| | - Peng Yao
- Electrical and Computer Engineering Department, University of Southern California, Los Angeles, CA, USA
| | - Yang Li
- The Andrew and Erna Viterbi Department of Electrical Engineering, Technion-Israel Institute of Technology, Haifa 32000, Israel
| | | | - Qinru Qiu
- Electrical Engineering and Computer Science Department, Syracuse University, NY, USA
| | - Daniele Ielmini
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano and IU.NET, Piazza L. da Vinci 32, Milano 20133, Italy
| | - J Joshua Yang
- Electrical and Computer Engineering Department, University of Southern California, Los Angeles, CA, USA
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Biolek Z, Biolek D, Biolková V, Kolka Z. Higher-Order Hamiltonian for Circuits with ( α, β) Elements. ENTROPY 2020; 22:e22040412. [PMID: 33286186 PMCID: PMC7516879 DOI: 10.3390/e22040412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 03/29/2020] [Accepted: 04/02/2020] [Indexed: 11/25/2022]
Abstract
The paper studies the construction of the Hamiltonian for circuits built from the (α,β) elements of Chua’s periodic table. It starts from the Lagrange function, whose existence is limited to Σ-circuits, i.e., circuits built exclusively from elements located on a common Σ-diagonal of the table. We show that the Hamiltonian can also be constructed via the generalized Tellegen’s theorem. According to the ideas of predictive modeling, the resulting Hamiltonian is made up exclusively of the constitutive relations of the elements in the circuit. Within the frame of Ostrogradsky’s formalism, the simulation scheme of Σ-circuits is designed and examined with the example of a nonlinear Pais–Uhlenbeck oscillator.
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Affiliation(s)
- Zdeněk Biolek
- Department of Microelectronics, Brno University of Technology, 616 00 Brno, Czech Republic; (Z.B.); (D.B.)
- Department of Electrical Engineering, University of Defence, 662 10 Brno, Czech Republic
| | - Dalibor Biolek
- Department of Microelectronics, Brno University of Technology, 616 00 Brno, Czech Republic; (Z.B.); (D.B.)
- Department of Electrical Engineering, University of Defence, 662 10 Brno, Czech Republic
| | - Viera Biolková
- Department of Radio Electronics, Brno University of Technology, 616 00 Brno, Czech Republic;
- Correspondence: ; Tel.: +420-541-146-584
| | - Zdeněk Kolka
- Department of Radio Electronics, Brno University of Technology, 616 00 Brno, Czech Republic;
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Sheldon F, Traversa FL, Di Ventra M. Taming a nonconvex landscape with dynamical long-range order: Memcomputing Ising benchmarks. Phys Rev E 2019; 100:053311. [PMID: 31869932 DOI: 10.1103/physreve.100.053311] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Indexed: 11/07/2022]
Abstract
Recent work on quantum annealing has emphasized the role of collective behavior in solving optimization problems. By enabling transitions of clusters of variables, such solvers are able to navigate their state space and locate solutions more efficiently despite having only local connections between elements. However, collective behavior is not exclusive to quantum annealers, and classical solvers that display collective dynamics should also possess an advantage in navigating a nonconvex landscape. Here we give evidence that a benchmark derived from quantum annealing studies is solvable in polynomial time using digital memcomputing machines, which utilize a collection of dynamical components with memory to represent the structure of the underlying optimization problem. To illustrate the role of memory and clarify the structure of these solvers we propose a simple model of these machines that demonstrates the emergence of long-range order. This model, when applied to finding the ground state of the Ising frustrated-loop benchmarks, undergoes a transient phase of avalanches which can span the entire lattice and demonstrates a connection between long-range behavior and their probability of success. These results establish the advantages of computational approaches based on collective dynamics of continuous dynamical systems.
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Affiliation(s)
- Forrest Sheldon
- Department of Physics, University of California San Diego, La Jolla, California 92093, USA
| | | | - Massimiliano Di Ventra
- Department of Physics, University of California San Diego, La Jolla, California 92093, USA
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Caravelli F. Asymptotic Behavior of Memristive Circuits. ENTROPY 2019; 21:e21080789. [PMID: 33267502 PMCID: PMC7515318 DOI: 10.3390/e21080789] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 08/02/2019] [Accepted: 08/06/2019] [Indexed: 11/16/2022]
Abstract
The interest in memristors has risen due to their possible application both as memory units and as computational devices in combination with CMOS. This is in part due to their nonlinear dynamics, and a strong dependence on the circuit topology. We provide evidence that also purely memristive circuits can be employed for computational purposes. In the present paper we show that a polynomial Lyapunov function in the memory parameters exists for the case of DC controlled memristors. Such a Lyapunov function can be asymptotically approximated with binary variables, and mapped to quadratic combinatorial optimization problems. This also shows a direct parallel between memristive circuits and the Hopfield-Little model. In the case of Erdos-Renyi random circuits, we show numerically that the distribution of the matrix elements of the projectors can be roughly approximated with a Gaussian distribution, and that it scales with the inverse square root of the number of elements. This provides an approximated but direct connection with the physics of disordered system and, in particular, of mean field spin glasses. Using this and the fact that the interaction is controlled by a projector operator on the loop space of the circuit. We estimate the number of stationary points of the approximate Lyapunov function and provide a scaling formula as an upper bound in terms of the circuit topology only.
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Affiliation(s)
- Francesco Caravelli
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
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Zegarac A, Caravelli F. Memristive networks: From graph theory to statistical physics. ACTA ACUST UNITED AC 2019. [DOI: 10.1209/0295-5075/125/10001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Abstract
We present both an overview and a perspective of recent experimental advances and proposed new approaches to performing computation using memristors. A memristor is a 2-terminal passive component with a dynamic resistance depending on an internal parameter. We provide an brief historical introduction, as well as an overview over the physical mechanism that lead to memristive behavior. This review is meant to guide nonpractitioners in the field of memristive circuits and their connection to machine learning and neural computation.
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Mizrahi A, Marsh T, Hoskins B, Stiles MD. Scalable Method to Find the Shortest Path in a Graph with Circuits of Memristors. PHYSICAL REVIEW APPLIED 2018; 10:10.1103/physrevapplied.10.064035. [PMID: 39450158 PMCID: PMC11500059 DOI: 10.1103/physrevapplied.10.064035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2024]
Abstract
Finding the shortest path in a graph has applications in a wide range of optimization problems. However, algorithmic methods scale with the size of the graph in terms of time and energy. We propose a method to solve the shortest-path problem using circuits of nanodevices called memristors and validate it on graphs of different sizes and topologies. It is both valid for an experimentally derived memristor model and robust to device variability. The time and energy of the computation scale with the length of the shortest path rather than with the size of the graph, making this method particularly attractive for solving large graphs with small path lengths.
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Affiliation(s)
- Alice Mizrahi
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
- Maryland NanoCenter, University of Maryland, College Park, Maryland, USA
| | - Thomas Marsh
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - Brian Hoskins
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
| | - M. D. Stiles
- National Institute of Standards and Technology, Gaithersburg, Maryland, USA
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Slipko VA, Pershin YV. Switching synchronization in one-dimensional memristive networks: An exact solution. Phys Rev E 2018; 96:062213. [PMID: 29347366 DOI: 10.1103/physreve.96.062213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Indexed: 11/07/2022]
Abstract
We study a switching synchronization phenomenon taking place in one-dimensional memristive networks when the memristors switch from the high- to low-resistance state. It is assumed that the distributions of threshold voltages and switching rates of memristors are arbitrary. Using the Laplace transform, a set of nonlinear equations describing the memristors dynamics is solved exactly, without any approximations. The time dependencies of memristances are found, and it is shown that the voltage falls across memristors are proportional to their threshold voltages. A compact expression for the network switching time is derived.
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Affiliation(s)
- V A Slipko
- Institute of Physics, Opole University, Opole 45-052, Poland.,Department of Physics and Technology, V. N. Karazin Kharkov National University, Kharkov 61022, Ukraine
| | - Y V Pershin
- Department of Physics and Astronomy, University of South Carolina, Columbia, South Carolina 29208, USA.,Nikolaev Institute of Inorganic Chemistry SB RAS, Novosibirsk 630090, Russia
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Caravelli F. Locality of interactions for planar memristive circuits. Phys Rev E 2017; 96:052206. [PMID: 29347736 DOI: 10.1103/physreve.96.052206] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Indexed: 11/07/2022]
Abstract
The dynamics of purely memristive circuits has been shown to depend on a projection operator which expresses the Kirchhoff constraints, is naturally non-local in nature, and does represent the interaction between memristors. In the present paper we show that for the case of planar circuits, for which a meaningful Hamming distance can be defined, the elements of such projector can be bounded by exponentially decreasing functions of the distance. We provide a geometrical interpretation of the projector elements in terms of determinants of Dirichlet Laplacian of the dual circuit. For the case of linearized dynamics of the circuit for which a solution is known, this can be shown to provide a light cone bound for the interaction between memristors. This result establishes a finite speed of propagation of signals across the network, despite the non-local nature of the system.
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Affiliation(s)
- F Caravelli
- Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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