Taichi Haruna

Abstract We propose a class of generalized multiplicative stochastic processes obtained by introducing an endo-perspective into one-dimensional maps with additive noise. We define an internal state for the noisy dynamics of a given one-dimensional map and study its statistical behavior. We found intermittency characterized by two power-laws in the dynamics of the internal state for the logistic map and the BZ map with noise which exhibit different noise-induced phenomena, namely, noise-induced chaos and noise-induced order, respectively. We show that the power-laws can be explained in a unified way from the theory of generalized multiplicative stochastic processes.

Abstract Human decision-making is relevant for concept formation and cognitive illusions. Cognitive illusions can be explained by quantum probability, while the reason for introducing quantum mechanics is based on ad hoc bounded rationality (BR). Concept formation can be explained in a set-theoretic way, although such explanations have not been extended to cognitive illusions. We naturally expand the idea of BR to incomplete BR and introduce the key notion of nonlocality in cognition without any attempts on quantum theory. We define incomplete bounded rationality and nonlocality as a binary relation, construct a lattice from the relation by using a rough-set technique, and define probability in concept formation. By using probability defined in concept formation, we describe various cognitive illusions, such as the guppy effect, conjunction fallacy, order effect, and so on. It implies that cognitive illusions can be explained by changes in the probability space relevant to concept formation.

Abstract We propose a growing network model that can generate dense scale-free networks with an almost neutral degree−degree correlation and a negative scaling of local clustering coefficient. The model is obtained by modifying an existing model in the literature that can also generate dense scale-free networks but with a different higher-order network structure. The modification is mediated by category theory. Category theory can identify a duality structure hidden in the previous model. The proposed model is built so that the identified duality is preserved. This work is a novel application of category theory for designing a network model focusing on a universal algebraic structure.

Burst suppression on electroencephalogram (EEG) is defined as suppression periods longer than 0.5 s during which the amplitude does not exceed 5 μV in human. The aims of this study were; 1) an attempt of creating new criteria of burst suppression in dogs; and 2) a survey on accuracy of sub-parameter of Bispectral index (BIS). Using a BIS monitor, suppression ratio (SRBIS) and raw-EEG data were recorded at 2.0%, 2.5%, 3.0%, 3.5%, 4.0%, and 5.0% end-tidal sevoflurane concentration (ETSEV) in 6 beagle dogs. The minimum ETSEV at which burst suppression was visually confirmed (ETSEVBS) was determined. By applying various duration and voltage threshold to criteria, suppression ratio was calculated (SR). Using the minimum balanced error rate (BER), new criteria consisting of the minimum duration of 0.35 s and the maximum threshold of 2.25 μV that provided SR > 0 above ETSEVBS was screened. SR was set by these criteria (SRBER) and by manual inspection (SRTRUE). The median detection rate of SRBER/SRTRUE was a statistically significant increase (p < .01) compared to that of SRBIS/SRTRUE (77% and 17% at 3.5% ETSEV, 89% and 19% at 4.0% ETSEV, and 86% and 84% at 5.0% ETSEV, respectively). In addition, between SRBER and SRTRUE evaluated by regression and Bland-Altman analyses, there was a strong correlation (r = 0.967, p < .001) and a moderate agreement (Limits of agreement: -7.14 ± 13.95). The method using BER may help to establish new criteria of burst suppression to grasp the excessive deep level of anesthesia.

To overcome the dualism between mind and matter and to implement consciousness in science, a physical entity has to be embedded with a measurement process. Although quantum mechanics have been regarded as a candidate for implementing consciousness, nature at its macroscopic level is inconsistent with quantum mechanics. We propose a measurement-oriented inference system comprising Bayesian and inverse Bayesian inferences. While Bayesian inference contracts probability space, the newly defined inverse one relaxes the space. These two inferences allow an agent to make a decision corresponding to an immediate change in their environment. They generate a particular pattern of joint probability for data and hypotheses, comprising multiple diagonal and noisy matrices. This is expressed as a nondistributive orthomodular lattice equivalent to quantum logic. We also show that an orthomodular lattice can reveal information generated by inverse syllogism as well as the solutions to the frame and symbol-grounding problems. Our model is the first to connect macroscopic cognitive processes with the mathematical structure of quantum mechanics with no additional assumptions. (C) 2016 Elsevier Ireland Ltd. All rights reserved.

Living systems such as gene regulatory networks and neuronal networks have been supposed to work close to dynamical criticality, where their information-processing ability is optimal at the whole-system level. We investigate how this global information-processing optimality is related to the local information transfer at each individual-unit level. In particular, we introduce an internal adjustment process of the local information transfer and examine whether the former can emerge from the latter. We propose an adaptive random Boolean network model in which each unit rewires its incoming arcs from other units to balance stability of its information processing based on the measurement of the local information transfer pattern. First, we show numerically that random Boolean networks can self-organize toward near dynamical criticality in our model. Second, the proposed model is analyzed by a mean-field theory. We recognize that the rewiring rule has a bootstrapping feature. The stationary indegree distribution is calculated semi-analytically and is shown to be close to dynamical criticality in a broad range of model parameter values.

We investigate the influence of the small-world topology on the composition of information flow on networks. By appealing to the combinatorial Hodge theory, we decompose information flow generated by random threshold networks on the Watts-Strogatz model into three components: gradient, harmonic and curl flows. The harmonic and curl flows represent globally circular and locally circular components, respectively. The Watts-Strogatz model bridges the two extreme network topologies, a lattice network and a random network, by a single parameter that is the probability of random rewiring. The small-world topology is realized within a certain range between them. By numerical simulation we found that as networks become more random the ratio of harmonic flow to the total magnitude of information flow increases whereas the ratio of curl flow decreases. Furthermore, both quantities are significantly enhanced from the level when only network structure is considered for the network close to a random network and a lattice network, respectively. Finally, the sum of these two ratios takes its maximum value within the small-world region. These findings suggest that the dynamical information counterpart of global integration and that of local segregation are the harmonic flow and the curl flow, respectively, and that a part of the small-world region is dominated by internal circulation of information flow.

Coherence of a network means that it is made up of functions of nodes glued together. In our previous work [Haruna, T., 2013. BioSystems 114, 125-148], we showed that coherence of directed networks can be captured by the lateral path which is dual to the usual directed path. In this paper, we study coherence along lateral paths emerging from random Boolean network dynamics. A s

The effect of discreteness on stochastic dynamics of chemically reacting systems is studied analytically. We apply the scheme bridging the chemical master equation and the chemical Fokker-Planck equation by a parameter representing the degree of discreteness previously proposed by the author for two concrete systems. One is an autocatalytic reaction system, and the other is a branching-annihilation reaction system. It is revealed that the change in characteristic time scales when discreteness is decreased is yielded between the two systems for different reasons. In the former system, it originates from the boundaries where one of the chemical species is zero, whereas in the latter system, it is due to modification of the most probable extinction path caused by discreteness loss.

Biological networks have two modes. The first mode is static: a network is a passage on which something flows. The second mode is dynamic: a network is a pattern constructed by gluing functions of entities constituting the network. In this paper, first we discuss that these two modes can be associated with the category theoretic duality (adjunction) and derive a natural network structure (a path notion) for each mode by appealing to the category theoretic universality. The path notion corresponding to the static mode is just the usual directed path. The path notion for the dynamic mode is called lateral path which is the alternating path considered on the set of arcs. Their general functionalities in a network are transport and coherence, respectively. Second, we introduce a betweenness centrality of arcs for each mode and see how the two modes are embedded in various real biological network data. We find that there is a trade-off relationship between the two centralities: if the value of one is large then the value of the other is small. This can be seen as a kind of division of labor in a network into transport on the network and coherence of the network. Finally, we propose an optimization model of networks based on a quality function involving intensities of the two modes in order to see how networks with the above trade-off relationship can emerge through evolution. We show that the trade-off relationship can be observed in the evolved networks only when the dynamic mode is dominant in the quality function by numerical simulations. We also show that the evolved networks have features qualitatively similar to real biological networks by standard complex network analysis. (C) 2013 Elsevier Ireland Ltd. All rights reserved.

Recently, the duality between values (words) and orderings (permutations) has been proposed by the authors as a basis to discuss the relationship between information theoretic measures for finite-alphabet stationary stochastic processes and their permutation analogues. It has been used to give a simple proof of the equality between the entropy rate and the permutation entropy rate for any finite-alphabet stationary stochastic process and to show some results on the excess entropy and the transfer entropy for finite-alphabet stationary ergodic Markov processes. In this paper, we extend our previous results to hidden Markov models and show the equalities between various information theoretic complexity and coupling measures and their permutation analogues. In particular, we show the following two results within the realm of hidden Markov models with ergodic internal processes: the two permutation analogues of the transfer entropy, the symbolic transfer entropy and the transfer entropy on rank vectors, are both equivalent to the transfer entropy if they are considered as the rates, and the directed information theory can be captured by the permutation entropy approach.

Recently, the permutation-information theoretic approach has been used in a broad range of research fields. In particular, in the study of high-dimensional dynamical systems, it has been shown that this approach can be effective in characterizing global properties, including the complexity of their spatiotemporal dynamics. Here, we show that this approach can also be applied to reveal local spatiotemporal profiles of distributed computations existing at each spatiotemporal point in the system. J. T. Lizier et al. have recently introduced the concept of local information dynamics, which consists of information storage, transfer, and modification. This concept has been intensively studied with regard to cellular automata, and has provided quantitative evidence of several characteristic behaviors observed in the system. In this paper, by focusing on the local information transfer, we demonstrate that the application of the permutation-information theoretic approach, which introduces natural symbolization methods, makes the concept easily extendible to systems that have continuous states. We propose measures called symbolic local transfer entropies, and apply these measures to two test models, the coupled map lattice (CML) system and the Bak-Sneppen model (BS-model), to show their relevance to spatiotemporal systems that have continuous states. In the CML, we demonstrate that it can be successfully used as a spatiotemporal filter to stress a coherent structure buried in the system. In particular, we show that the approach can clearly stress out defect turbulences or Brownian motion of defects from the background, which gives quantitative evidence suggesting that these moving patterns are the information transfer substrate in the spatiotemporal system. We then show that these measures reveal qualitatively different properties from the conventional approach using the sliding window method, and are also robust against external noise. In the BS-model, we demonstrate that these measures can provide novel insight to the model, featuring how symbolic local information transfer is related to the dynamical properties of the elements involved in a spatiotemporal dynamics.

The duality between values and orderings is a powerful tool to discuss relationships between various information-theoretic measures and their permutation analogues for discrete-time finite-alphabet stationary stochastic processes (SSPs). Applying it to output processes of hidden Markov models with ergodic internal processes, we have shown in our previous work that the excess entropy and the transfer entropy rate coincide with their permutation analogues. In this paper, we discuss two permutation characterizations of the two measures for general ergodic SSPs not necessarily having the Markov property assumed in our previous work. In the first approach, we show that the excess entropy and the transfer entropy rate of an ergodic SSP can be obtained as the limits of permutation analogues of them for the N-th order approximation by hidden Markov models, respectively. In the second approach, we employ the modified permutation partition of the set of words which considers equalities of symbols in addition to permutations of words. We show that the excess entropy and the transfer entropy rate of an ergodic SSP are equal to their modified permutation analogues, respectively. © 2013 EDP Sciences and Springer.

Transfer entropy is a measure of the magnitude and the direction of information flow between jointly distributed stochastic processes. In recent years, its permutation analogues are considered in the literature to estimate the transfer entropy by counting the number of occurrences of orderings of values, not the values themselves. It has been suggested that the method of permutation is easy to implement, computationally low cost and robust to noise when applying to real world time series data. In this paper, we initiate a theoretical treatment of the corresponding rates. In particular, we consider the transfer entropy rate and its permutation analogue, the symbolic transfer entropy rate, and show that they are equal for any bivariate finite-alphabet stationary ergodic Markov process. This result is an illustration of the duality method introduced in [T. Haruna, K. Nakajima, Physica D 240, 1370 (2011)]. We also discuss the relationship among the transfer entropy rate, the time-delayed mutual information rate and their permutation analogues.

In this paper, we propose a new class of cellular automata based on the modification of its state space. It is introduced to model a computation which is exposed to an environment. We formalized the computation as extension and projection processes of its state space and resulting misidentifications of the state. This is motivated to embed the role of an environment into the system itself, which naturally induces self-organized internal perturbations rather than the usual external perturbations. Implementing this structure into the elementary cellular automata, we characterized its effect by means of input entropy and power spectral analysis. As a result, the cellular automata with this structure showed robust class IV behavior and a 1/f power spectrum in a wide range of rule space comparative to the notion of the edge of chaos. (C) 2011 Elsevier Ireland Ltd. All rights reserved.

We study the permutation complexity of finite-state stationary stochastic processes based on a duality between values and orderings between values. First, we establish a duality between the set of all words of a fixed length and the set of all permutations of the same length. Second, on this basis, we give an elementary alternative proof of the equality between the permutation entropy rate and the entropy rate for a finite-state stationary stochastic processes first proved in [J.M. Amigo, M.B. Kennel, L Kocarev, The permutation entropy rate equals the metric entropy rate for ergodic information sources and ergodic dynamical systems, Physica D 210 (2005) 77-95]. Third, we show that further information on the relationship between the structure of values and the structure of orderings for finite-state stationary stochastic processes beyond the entropy rate can be obtained from the established duality. In particular, we prove that the permutation excess entropy is equal to the excess entropy, which is a measure of global correlation present in a stationary stochastic process, for finite-state stationary ergodic Markov processes. (C) 2011 Elsevier B.V. All rights reserved.

We explore lattice theoretic aspects in rough set theory in terms of the duality between algebra and representation. Approximation spaces are dual to complete atomic Boolean algebras in the sense that there is an adjunction between corresponding suitable categories. This is an analogy with the adjunction between the category of topological spaces and the opposite of the category of frames in pointless topology. In this paper we consider a generalization of approximation spaces called double approximation systems. A double approximation system consists of a set and two equivalence relations on it. We construct an adjunction generalizing this concept for approximation spaces. To achieve this goal, we first introduce a natural generalization of complete atomic Boolean algebras called complete prime lattices. Then we select double approximation systems that can be dual to complete prime lattices and prove the adjunction.

One slogan of science of complex networks is "functionality from network topology". In order to achieve this slogan, many characteristics such as degree distributions, average path length, clustering coefficients, network motifs etc have been introduced. However, these are all based on the "real view" on networks, that is, nodes are just points and an arc or an edge between two nodes indicates existence of some interaction between the two nodes and nothing more. In this paper we introduce "dual views" on networks in contrast to the "real view" in order to promote further achievement of the slogan. In a "dual view" we interpret objects as processes. This is an abstraction from real systems in which each component has its own process. There are infinitely many "dual views", however, we can show that there is a canonical "dual view" among all possible ones. We explain mathematical idea to formulate "dual views" and discuss its application to the study of complex networks.

The aim of this paper is to investigate the discrete nature of chemically reacting systems. In order to achieve our purpose we propose a systematic method to compare the discrete stochastic model of chemically reacting systems with the continuous stochastic model. We adopt the chemical master equation (CME) as the discrete stochastic model and the chemical Fokker-Planck equation (CFPE) as the continuous stochastic model. By making use of the well-known idea of approximating diffusion processes by birth-death processes, we construct a family of master equations parameterized by the degree of discreteness. This family of master equations bridges CME and CFPE. With full degree of discreteness we obtain CME and as decreasing discreteness the family of master equations converges to CFPE. Our strategy is not to study CME directly but to distinguish the properties of CME by putting CME into the family of master equations bridging CME and CFPE. We examine the usefulness of our construction by two simple examples.

The central notion of a rough set is the indiscernibility that is based on an equivalence relation. Because an equivalence relation shows strong bondage in an equivalence class, it forms a Galois connection and the difference between the upper and lower approximations is lost. Here, we introduce two different equivalence relations, one for the upper approximation and one for the lower approximation, and construct a composite approximation operator consisting of different equivalence relations. We show that a collection of fixed points with respect to the operator is a lattice and there exists a representation theorem for that construction. © 2010 Springer-Verlag.

The internal description of spacetime can reveal ambiguity regarding an observer&apos;s perception of the present, where an observer can refer to the present as if he were outside spacetime while actually existing in the present. This ambiguity can be expressed as the compatibility between an element and a set, and is here called a/{a}-compatibility. We describe a causal set as a lattice and a causal history as a quotient lattice, and implement the a/{a}-compatibility in the framework of a causal histories approach. This leads to a perpetual change or a pair of causal set and causal history, and can be used to describe subjective spacetime including the deja vu experience and/or schizophrenic time. (C) 2009 Elsevier B.V. All rights reserved.

In this paper we address balancing process of ecological flow networks. In existing approaches, macroscopic objectives to which systems organize are assumed. Flow balance provides only constraints for the optimization. Since flow balance and objectives are separated from each other, it is impossible to address how the appearance of objectives is related to flow balance. Therefore, we take an alternative approach, in which we directly describe a dynamics of balancing process. We propose a simple mathematical formula for local balancing dynamics and show that it can generate a self-organizing property, which could be seen as a primitive objective. (C) 2008 Elsevier B.V. All rights reserved.

We here concentrate on equivalence relation, and show that the composition of upper approximation of one equivalence relation and the lower one of the other equivalence relation can form a lattice. We also show that this method can be used to define computational complementarity in automata.

In this paper we address network motifs found in information processing biological networks. Network motifs are local structures hi a whole network on one hand, they are materializations of a kind of wholeness to have biological functions oil the other hand. We formalize the wholeness by the notion of sheaf. We also formalize a, feature of information processing by considering an internal structure of nodes ill terms of their information processing ability. We show that two network motifs called bi-fan (BF) and feed-forward loop (FFL) can be obtained by purely algebraic considerations.

A representation theorem for complete lattices by double approximation systems proved in [Gunji, Y-P., Haruna, T., submitted] is analyzed in terms of category theory. A double approximation system consists of two equivalence relations on a, set. One equivalence relation defines the lower approximation and the other defines the upper approximation. It is proved that the representation theorem can be extended to an equivalence of categories.

A cell is a minimal self-sustaining system that can move and compute. Previous work has shown that a unicellular slime mold, Physarum, can be utilized as a biological computer based on cytoplasmic flow encapsulated by a membrane. Although the interplay between the modification of the boundary of a cell and the cytoplasmic flow surrounded by the boundary plays a key role in Physarum computing, no model of a cell has been developed to describe this interplay. Here we propose a toy model of a cell that shows amoebic motion and can solve a maze, Steiner minimum tree problem and a spanning tree problem. Only by assuming that cytoplasm is hardened after passing external matter (or softened part) through a cell, the shape of the cell and the cytoplasmic flow can be changed. Without cytoplasm hardening, a cell is easily destroyed. This suggests that cytoplasmic hardening and/or sol-gel transformation caused by external perturbation can keep a cell in a critical state leading to a wide variety of shapes and motion. (C) 2008 Elsevier Ltd. All rights reserved.