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Masashi Aono

Tokyo Institute of Technology, Earth-Life Science Institute, Faculty Member

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Research Interests
- Life/Mind/Intelligence/Computation/Information...What are we trying to say?
- Mathematical Modeling of Complex Systems
- Experimental Development of Bio-Computers
- Amoeba-based Computing

Education & Appointments
- 1995-1999: BA. Faculty of Environment and Information Studies, Keio University, Japan.
- 1999-2004: MA & PhD. Dept. of Information Media Science, Kobe University, Japan.
- 2004-2007: Frontier Research System, RIKEN, Japan.
- 2007: present position.
Address: 2-12-1-E3-10 Ookayama, Meguro-ku, Tokyo,
152-8550, JAPAN

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Papers by Masashi Aono

Remarkable problem-solving ability of unicellular amoeboid organism and its mechanism

Royal Society Open Science, 2018

Choosing a better move correctly and quickly is a fundamental skill of living organisms that corr... more Choosing a better move correctly and quickly is a fundamental skill of living organisms that corresponds to solving a computationally demanding problem. A unicellular plasmodium of Physarum polycephalum searches for a solution to the travelling salesman problem (TSP) by changing its shape to minimize the risk of being exposed to aversive light stimuli. In our previous studies, we reported the results on the eight-city TSP solution. In this study, we show that the time taken by plasmodium to find a reasonably high-quality TSP solution grows linearly as the problem size increases from four to eight. Interestingly, the quality of the solution does not degrade despite the explosive expansion of the search space. Formulating a computational model, we show that the linear-time solution can be achieved if the intrinsic dynamics could allocate intracellular resources to grow the plasmodium terminals with a constant rate, even while responding to the stimuli. These results may lead to the de...

A Strategy for Origins of Life Research

by Olaf Witkowski, Christopher Butch, Martin Biehl, Takashi Ikegami, Kensei Kobayashi, Eric Smith, Ueno Yuichiro, Masashi Aono, Ana Barahona, and Norman Packard

Astrobiology, 2015

Contents 1. Introduction 1.1. A workshop and this document 1.2. Framing origins of life science 1... more Contents 1. Introduction 1.1. A workshop and this document 1.2. Framing origins of life science 1.2.1. What do we mean by the origins of life (OoL)? 1.2.2. Defining life 1.2.3. How should we characterize approaches to OoL science? 1.2.4. One path to life or many? 2. A Strategy for Origins of Life Research 2.1. Outcomes-key questions and investigations 2.1.1. Domain 1: Theory 2.1.2. Domain 2: Practice 2.1.3. Domain 3: Process 2.1.4. Domain 4: Future studies 2.2. EON Roadmap 2.3. Relationship to NASA Astrobiology Roadmap and Strategy documents and the European AstRoMap Appendix I Appendix II Supplementary Materials References.

Amoeba-inspired Spatiotemporal Dynamics for Physically Implemented Satisfiability Problem Solvers

by Masashi Aono and Song-Ju Kim

Natural computing is a new discipline that aims to develop nature-inspired computers by using phy... more Natural computing is a new discipline that aims to develop nature-inspired computers by using physical dynamics and fluctuations of interacting devices. Inspired by the amoeba, which exhibits spatiotemporal oscillatory dynamics and sophisticated computing capabilities , we extracted the essential spatiotemporal dynamics by which the amoeba solves computationally demanding problems. Our dynamical system model, AmoebaSAT, runs on conventional digital computers and functions as an algorithm for searching for a solution to the satisfiability problem (SAT). Moreover, AmoebaSAT can be implemented using na-noelectronic and nanophotonic devices. In this study, performing Monte Carlo simulations using a digital computer, we show that AmoebaSAT outperforms a randomized version of the GSAT algorithm for randomly generated 10000 variable 3-SAT instances. Thus, when implemented using the nanodevices, AmoebaSAT will open up a new computing paradigm that might enable high-speed problem solving with low power consumption.

Amoeba-inspired nanoarchitectonic computing implemented using electrical Brownian ratchets

by Masashi Aono and Song-Ju Kim

In this study, we extracted the essential spatiotemporal dynamics that allow an amoeboid organism... more In this study, we extracted the essential spatiotemporal dynamics that allow an amoeboid organism to solve a computationally demanding problem and adapt to its environment, thereby proposing a nature-inspired nanoarchitectonic computing system, which we implemented using a network of nanowire devices called 'electrical Brownian ratchets (EBRs)'. By utilizing the fluctuations generated from thermal energy in nanowire devices, we used our system to solve the satisfiability problem, which is a highly complex combinatorial problem related to a wide variety of practical applications. We evaluated the dependency of the solution search speed on its exploration parameter, which characterizes the fluctuation intensity of EBRs, using a simulation model of our system called 'AmoebaSAT-Brownian'. We found that AmoebaSAT-Brownian enhanced the solution searching speed dramatically when we imposed some constraints on the fluctuations in its time series and it outperformed a well-known stochastic local search method. These results suggest a new computing paradigm, which may allow high-speed problem solving to be implemented by interacting nanoscale devices with low power consumption.

Decision Maker using Coupled Incompressible-Fluid Cylinders

by Masashi Aono and Song-Ju Kim

The multi-armed bandit problem (MBP) is the problem of finding, as accurately and quickly as poss... more The multi-armed bandit problem (MBP) is the problem of finding, as accurately and quickly as possible, the most profitable option from a set of options that gives stochastic rewards by referring to past experiences. Inspired by fluctuated movements of a rigid body in a tug-of-war game, we formulated a unique search algorithm that we call the ‘tug-of-war (TOW) dynamics’ for solving the MBP efficiently [1-5]. The cognitive medium access, which refers to multi-user channel allocations in cognitive radio, can be interpreted as the competitive multi-armed bandit problem (CMBP); the problem is to determine the optimal strategy for allocating channels to users which yields maximum total rewards gained by all users [6]. Here we show that it is possible to construct a physical device for solving the CMBP, which we call the ‘TOW Bombe’, by exploiting the TOW dynamics existed in coupled incompressible-fluid cylinders. This analog computing device achieves the ‘socially-maximum’ resource allocation that maximizes the total rewards in cognitive medium access without paying a huge computational cost that grows exponentially as a function of the problem size.

Amoeba-inspired Spatiotemporal Dynamics for Solving the Satisfiability Problem

by Song-Ju Kim and Masashi Aono

Inspired by spatiotemporal oscillatory dynamics of an amoeboid organism that exhibits sophisticat... more Inspired by spatiotemporal oscillatory dynamics of an amoeboid organism that exhibits sophisticated computing capabilities in adapting to its environment, we propose a dynamical system model that is applied to solving an NP-complete problem, the Boolean satisfiability problem (SAT). Our model, called AmoebaSAT, utilizes the fluctuation that is generated from chaotic oscillatory dynamics (the logistic map) and finds a SAT solution at a speed that is dramatically faster than one of the conventionally known fastest stochastic local search methods for randomly generated 3-SAT instances. We show that the solution searching speed of AmoebaSAT degrades significantly when its fluctuation generator is replaced with uncorrelated random noise that simulates Brownian motion. These results suggest that the performance of AmoebaSAT is enhanced by its temporally correlated fluctuation produced from the chaotic oscillatory dynamics.

Return map structure and entrainment in a time-state-scale re-entrant system

Physica D-nonlinear Phenomena, 2007

From the perspective of a heterarchy, endo-physics, or internal measurement, a time-state-scale r... more

Interface of global and local semantics in a self-navigating system based on the concept lattice

Chaos Solitons & Fractals, 2002

If the syntaxsemantics interaction is driven by the interface, it also interrupts the interactio... more

Dynamical infomorphism: form of endo-perspective

Chaos Solitons & Fractals, 2004

The essential feature of the endo-perspective is examined, and a formal model of the endo-perspec... more The essential feature of the endo-perspective is examined, and a formal model of the endo-perspective is proposed by introducing the mixture of intra-and inter-operations. Because such a mixture in its naive realization entails a paradox within a formal system, we weaken the inter-operation in order to allow the formal system to be endowed with that mixture without a contradiction. The weakened inter-operation is related to the infomorphism proposed by Barwise [Information Flow, The Logic of Distributed Systems, Cambridge Univ. Press, 1997]. The formal model of the endoperspective is thereby expressed as the dynamical infomorphism driven by that mixture. The endo-perspective is described as a formal system that includes the outside of the occupied perspective. If such an inclusion is applied to the common definition of a set, it entails Russel's paradox. Retaining the outside can be expressed as the mixture of the intent and the extent of a set together with the mixture of intra-operations within the intent (or the extent) and interoperations between the intent and the extent. The endo-perspective, therefore, consists of two subsystems corresponding to the intent and the extent, respectively, and is defined as a system involving a particular mathematical tool (i.e., infomorphism) that allows for retaining the outside without a contradiction. Within that framework, the mixture of the intra-and the inter-operation drives the dynamical transition of the system, however, it can be terminated by its collapse. This collapse can be predicted from the internal logic defined within the system. The model is constructed through the verification of ''a weakened paradox''. Because the definition of the system involves a weakened paradox only, it does not always lead to a contradiction, although the collapse of the system corresponds to a contradiction. The double standards can be embedded into the system, the domain with truth-values (the inside) and the domain in which the collapse of the logic can occur (the outside).

Information physics fundamentals of nanophotonics

Spatiotemporal dynamics in optical energy transfer on the nanoscale and its application to constraint satisfaction problems

Nature-inspired devices and architectures are attracting considerable attention for various purpo... more Nature-inspired devices and architectures are attracting considerable attention for various purposes, including developing novel computing based on spatiotemporal dynamics, exploiting stochastic processes for computing, and reducing energy dissipation. This paper demonstrates that the optical energy transfer between quantum nanostructures mediated by optical near-field interactions occurring at scales far below the wavelength of light could be utilized for solving constraint satisfaction problems (CSPs). The optical energy transfer from smaller quantum dots to larger ones, which is a quantum stochastic process, depends on the existence of resonant energy levels between the quantum dots or a state-filling effect occurring at the larger quantum dots. Such a spatiotemporal mechanism yields different evolutions of energy transfer patterns in multi-quantum-dot systems. We numerically demonstrate that optical energy transfer processes can be used to solve a CSP. The work described in this paper is a first step in showing the applicability and potential of nanometer-scale optical near-field processes toward solving computationally demanding problems.

Amoeba-based computing for traveling salesman problem: Long-term correlations between spatially separated individual cells of Physarum polycephalum

A single-celled, multi-nucleated amoeboid organism, a plasmodium of the true slime mold Physarum ... more A single-celled, multi-nucleated amoeboid organism, a plasmodium of the true slime mold Physarum polycephalum, can perform sophisticated computing by exhibiting complex spatiotemporal oscillatory dynamics while deforming its amorphous body. We previously devised an “amoeba-based computer (ABC)” to quantitatively evaluate the optimization capability of the amoeboid organism in searching for a solution to the traveling salesman problem (TSP) under optical feedback control. In ABC, the organism changes its shape to find a high quality solution (a relatively shorter TSP route) by alternately expanding and contracting its pseudopod-like branches that exhibit local photoavoidance behavior. The quality of the solution serves as a measure of the optimality of which the organism maximizes its global body area (nutrient absorption) while minimizing the risk of being illuminated (exposure to aversive stimuli). ABC found a high quality solution for the 8-city TSP with a high probability. However, it remains unclear whether intracellular communication among the branches of the organism is essential for computing. In this study, we conducted a series of control experiments using two individual cells (two single-celled organisms) to perform parallel searches in the absence of intercellular communication. We found that ABC drastically lost its ability to find a solution when it used two independent individuals. However, interestingly, when two individuals were prepared by dividing one individual, they found a solution for a few tens of minutes. That is, the two divided individuals remained correlated even though they were spatially separated. These results suggest the presence of a long-term memory in the intrinsic dynamics of this organism and its significance in performing sophisticated computing.

Amoeba-Inspired Nanoarchitectonic Computing: Solving Intractable Computational Problems Using Nanoscale Photoexcitation Transfer Dynamics

Biologically inspired computing devices and architectures are expected to overcome the limitation... more Biologically inspired computing devices and architectures are expected to overcome the limitations of conventional technologies in terms of solving computationally demanding problems, adapting to complex environments, reducing energy consumption, and so on. We previously demonstrated that a primitive single-celled amoeba (a plasmodial slime mold), which exhibits complex spatiotemporal oscillatory dynamics and sophisticated computing capabilities, can be used to search for a solution to a very hard combinatorial optimization problem. We successfully extracted the essential spatiotemporal dynamics by which the amoeba solves the problem. This amoeba-inspired computing paradigm can be implemented by various physical systems that exhibit suitable spatiotemporal dynamics resembling the amoeba's problem-solving process. In this Article, we demonstrate that photoexcitation transfer phenomena in certain quantum nanostructures mediated by optical near-field interactions generate the amoebalike spatiotemporal dynamics and can be used to solve the satisfiability problem (SAT), which is the problem of judging whether a given logical proposition (a Boolean formula) is self-consistent. SAT is related to diverse application problems in artificial intelligence, information security, and bioinformatics and is a crucially important nondeterministic polynomial time (NP)-complete problem, which is believed to become intractable for conventional digital computers when the problem size increases. We show that our amoeba-inspired computing paradigm dramatically outperforms a conventional stochastic search method. These results indicate the potential for developing highly versatile nanoarchitectonic computers that realize powerful solution searching with low energy consumption.

Adaptive Tug-of-war Model for Two-armed Bandit Problem

The "tug-of-war (TOW) model" proposed in our previous studies ] is a unique dynamical system insp... more The "tug-of-war (TOW) model" proposed in our previous studies ] is a unique dynamical system inspired by the photoavoidance behavior of a single-celled amoeba of the true slime mold Physarum polycephalum. The TOW model is applied to solving the "multi-armed bandit problem," a problem of finding the most rewarding one from multiple options as accurately and speedy as possible. We showed that the model exhibits better performances compared with other well-known algorithms. However, in order to maximize its performance, the TOW model is required an optimized parameter w. In this study, we propose a new TOW model which adaptively produces the estimates to determine w in its own way and thus has no parameter. We show that in some asymmetric problems the new model is more efficient than the UCB1tuned algorithm , which is known as the best algorithm.

Robust and emergent Physarum logical-computing

BioSystems, Jan 1, 2004

Amoeba-based neurocomputing with chaotic dynamics

Communications of the ACM, Jan 1, 2007

Beyond input-output computings: Error-driven emergence with parallel non-distributed slime mold computer

BioSystems, Jan 1, 2003

Amoeba-based nonequilibrium neurocomputer utilizing fluctuations and instability

Unconventional Computation, Jan 1, 2007

Abstract. We employ a photosensitive amoeboid cell known as a model organism for studying cellula... more

Spontaneous deadlock breaking on amoeba-based neurocomputer

BioSystems, Jan 1, 2008

Resolution of infinite-loop in hyperincursive and nonlocal cellular automata: Introduction to slime mold computing

AIP conference proceedings, Jan 1, 2004