Peer-reviewed journal papers

• Taichi Haruna, 2026. Subpattern matching persistent homology for coupling complexity analysis of multivariate time series. Chaos 36, 083106. (journal webpage)
• Taichi Haruna, Kohei Nakajima, 2026. Memory uncertainty relation and harmonic memory in random recurrent networks. Physical Review E 113, 055304. (journal webpage, download)
• Taichi Haruna, 2025. Analysis of coupling complexity in echo state networks via ordinal persistent homology. Artificial Life and Robotics 30, 417-423. (fulltext)
• Taichi Haruna, 2023. Complexity of couplings in multivariate time series via ordinal persistent homology. Chaos 33, 043115. (journal webpage)
• Taichi Haruna, Tomohiro Shirakawa, 2023. Noise-induced bistability in a simple mutual inhibition system. Physical Review E 108, 024108. (journal webpage)
• Taichi Haruna, Kohei Nakajima, 2022. Generalized multiplicative stochastic processes arising from one-dimensional maps with noise. Artificial Life and Robotics. (fulltext)
• Yukio-Pegio Gunji, Taichi Haruna, 2022. Concept Formation and Quantum-like Probability from Nonlocality in Cognition. Cognitive Computation 14, 1328–1349.(fulltext)
• Taichi Haruna, Yukio-Pegio Gunji, 2020. Analysis and synthesis of a growing network model generating dense scale-free networks via category theory. Scientific Reports 10, 22351. (fulltext)
• Taichi Haruna, Kohei Nakajima, 2019. Optimal short-term memory before the edge of chaos in driven random recurrent networks. Physical Review E 100, 062312. (journal webpage, download)
• Taichi Haruna, 2019. Partially ordered permutation entropies. European Physical Journal B 92, 81. (journal webpage, download)
• Taichi Haruna, Yukio-Pegio Gunji, 2019. Ordinal preferential attachment: a self-organizing principle generating dense scale-free networks. Scientific Reports 9, 4130. (fulltext)
• Taichi Haruna, 2019. Uncertainty of the second order: Quasispecies model with inverse Bayesian inference. Artificial Life and Robotics 24, 297-303. (journal webpage, download)
• Kohei Nakajima, Taichi Haruna, 2019. Spatiotemporal dynamics driven by the maximization of local information transfer. New Journal of Physics 21, 013034. (fulltext)
• Chika Koyama, Taichi Haruna, Satoshi Hagihira, Kazuto Yamashita, 2019. New criteria of burst suppression on electroencephalogram in dogs anesthetized with sevoflurane. Research in Veterinary Science 123, 171-177. (journal webpage)
• Taichi Haruna, 2019. Partially ordered permutation complexity of coupled time series. Physica D 388, 40-44. (journal webpage, download)
• Taichi Haruna, Kohei Nakajima, 2018. Maximizing local information transfer in Boolean networks. New Journal of Physics 20, 083046. (fulltext)
• Igor Balaz, Taichi Haruna, 2018. Evolution of influenza A nucleotide segments through the lens of different complexity measures. Advances in Complex Systems 21, 1850009. (journal webpage)
• Taichi Haruna, 2018. Open networks from within: input or output betweenness centrality of nodes in directed networks. Applied Network Science 3:15. (fulltext)
• Taichi Haruna, 2018. Evolution of activity-dependent adaptive Boolean networks towards criticality: an analytic approach. Journal of Complex Networks 6, 914-926. (journal webpage, download)
• Taichi Haruna, 2017. Adaptive local information transfer on random Boolean networks. Artificial Life 23, 105-118. (journal webpage, download)
• Yukio-Pegio Gunji, Shuji Shinohara, Taichi Haruna, Vasileios Basios, 2017. Inverse Bayesian inference as a key of consciousness featuring a macroscopic quantum logical structure. BioSystems 152, 44-65. journal webpage)
• Taichi Haruna, Yuuya Fujiki, 2016. Hodge decomposition of information flow on small-world networks. Frontiers in Neural Circuits 10, 77. (fulltext)
• Taichi Haruna, 2016. Coherence of directed complex networks. Transactions of the Society of Instrument and Control Engineers Vol. 52 No. 3, 180-187. (fulltext, in Japanese)
• Taichi Haruna, 2015. Distinguishing between discreteness effects in stochastic reaction processes. Physical Review E 91, 052814. (download)
• Taichi Haruna, Kohei Nakajima, 2014. Permutation Excess Entropy and Mutual Information between the Past and Future. International Journal of Computing Anticipatory Systems 26, 197-209. (download)
• Taichi Haruna, 2013. Theory of Interface: Category Theory, Directed Networks and Evolution of Biological Networks. BioSystems 114, 125-148. (download)
• Taichi Haruna, Kohei Nakajima, 2013. Permutation complexity and coupling measures in hidden Markov models. Entropy 15, 3910-3930. (download)
• Taichi Haruna, Kohei Nakajima, 2013. Symbolic transfer entropy rate is equal to transfer entropy rate for bivariate finite-alphabet stationary ergodic Markov processes. European Physical Journal B 86, 230. (download)
• Taichi Haruna, Kohei Nakajima, 2013. Permutation Approach to Finite-Alphabet Stationary Stochastic Processes Based on the Duality between Values and Orderings. European Physical Journal Special Topics 222, 383-399. (download)
• Kohei Nakajima, Taichi Haruna, 2013. Symbolic Local Information Transfer. European Physical Journal Special Topics 222, 437-455.
• Taichi Haruna, Kohei Nakajima, 2011. Permutation Complexity via Duality between Values and Orderings. Physica D 240, 1370-1377. (download)
• Taichi Haruna, Yukio-Pegio Gunji, 2011. Double Approximation and Complete Lattices. Fundamenta Informaticae 111, 1-14.
• Kohei Nakajima, Taichi Haruna, 2011. Self-organized perturbations enhance class IV behavior and 1/f power spectrum in elementary cellular automata. BioSystems 105, 216-224.
• Taichi Haruna, 2010. An Application of Category Theory to the Study of Complex Networks. International Journal of Computing Anticipatory Systems 23, 146-157. (download)
• Taichi Haruna, 2010. Investigating the Gap between Discrete and Continuous Models of Chemically Reacting Systems. Journal of Computer Chemistry, Japan 9, 135-142. (download)
• Yukio-Pegio Gunji, Taichi Haruna, 2010. A Non-Boolean Lattice Derived by Double Indiscernibility. In: J. F. Peters et al. (Eds.) Transactions on Rough Sets XII, Lecture Notes in Computer Science 6190, pp. 211-225. (download)
• Taichi Haruna and Yukio-Pegio Gunji, 2009. Imbalance and balancing: Development of ecological flow networks. Ecological Complexity 6, 208-218. (download)
• Yukio-Pegio Gunji, Taichi Haruna, Daisuke Uragami and Asaki Nishikawa, 2009. Subjective Spacetime Derived from a Causal Histories Approach. Physica D 238, 2016-2023. (download)
• Taichi Haruna and Yukio-Pegio Gunji, 2008. An Algebraic Description of Development of Hierarchy. International Journal of Computing Anticipatory Systems 20, 131-143. (download)
• Yukio-Pegio Gunji, Tomohiro Shirakawa, Takayuki Niizato, Taichi Haruna and Igor Balaz, 2008. Life driven by damaged damage. Progress of Theoretical Physics Supplement 173, 26-37.
• Yukio-Pegio Gunji, Tomohiro Shirakawa, Takayuki Niizato and Taichi Haruna, 2008. Minimal model of a cell connecting amoebic motion and adaptive transport networks. Journal of Theoretical Biology 253, 659-667. (download)
• Taichi Haruna and Yukio-Pegio Gunji, 2007. Duality between decomposition and gluing: A theoretical biology via adjoint functors. BioSystems 90, 716-727. (download)
• Taichi Haruna and Yukio-Pegio Gunji, 2007. Identity and its Robustness According to Second Person Descriptions. Physica D 236, 75-80. (download)
• Yukio-Pegio Gunji, Taichi Haruna and Koji Sawa, 2006. Principles of Biological Organization: Local-Global Negotiation Based on ``Material Cause''. Physica D 219, 152-167. (download)
• Taichi Haruna and Yukio-Pegio Gunji, 2006. A Generalization of Formal Model of Internal Measurement: A Construction on One-Dimensional Maps. International Journal of Unconventional Computing 2, 231-248. (download)
• Taichi Haruna and Yukio-Pegio Gunji, 2005. Autonomous indefiniteness versus external indefiniteness: Theory of weak topped ∩-structure and its application to elementary local cellular automaton. Physica D 202, 71-94. (download)

Peer-reviewed international conference papers

• Taichi Haruna, 2015. An Anticipatory Model for Self-Organization of Random Boolean Networks toward Criticality. In: D. Dubois and G. Lasker, (Eds.) Proceedings of 1st Special Focus Symposium on Open Problems in Anticipative Models of Physical and Living Systems, pp. 1-5.
• Yuuya Fujiki, Taichi Haruna, 2014. Hodge Decomposition of Information Flow on Complex Networks. In: J. Suzuki and T. Nakano, (Eds.) Proceedings of 8th International Conference on Bio-inspired Information and Communications Technologies, pp. 103-112. (download)
• Taichi Haruna, Sayaka Tanaka, 2014. On the Relationship between Local Rewiring Rules and Stationary Out-degree Distributions in Adaptive Random Boolean Network Models. In: H. Sayama et al. (Eds.) Artificial Life 14, Proceedings of the Fourteenth International Conference on the Synthesis and Simulation of Living Systems, pp. 420-426. (download)
• Taichi Haruna, 2013. Robustness and Directed Structures in Ecological Flow Networks. In: P. Lio et al. (Eds.) Advances in Artificial Life, ECAL 2013, Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems, pp. 175-181. (download)
• Taichi Haruna, Junya Shiozaki, Sayaka Tanaka, 2012. How Does Thermal Gradient Contribute to Microcapsule Formation by Proteinoids? In: M. Umano et al. (Eds.) Proceedings of the 6th International Conference on Soft Computing and Intelligent Systems, pp. 2314-2316. (short paper) (download)
• Taichi Haruna, Itsuki Kunita, Shigeru Sakurazawa, 2011. Microcapsule Formation by Thermal Heterocomplex Molecules from Amino Acids in a Thermal Gradient Microcapillary. In: R. Pfeifer et al. (Eds.) Proceedings of the Second International Conference on Morphological Computation, pp. 60-62. (extended abstract) (download)
• Taichi Haruna, 2011. Global Structure of Directed Networks Emerging from a Category Theoretical Formulation of the Idea “Objects as Processes, Interactions as Interfaces”. In: T. Lenaerts et al. (Eds.) Advances in Artificial Life, ECAL 2011, Proceedings of the Eleventh European Conference on the Synthesis and Simulation of Living Systems, pp. 310-317. (download)
• Yukio-Pegio Gunji, Taichi Haruna and Eugene Schneider Kitamura, 2009. Lattice Derived by Double Indiscernibility and Computational Complementarity. In: P. Wen et al. (Eds.) Rough Sets and Knowledge Technology, 4th International Conference, RSKT 2009, Gold Coast, Australia, July 2009, Proceedings, pp. 46-51.
• Taichi Haruna and Yukio-Pegio Gunji, 2009. Double Approximation and Complete Lattices. In: P. Wen et al. (Eds.) Rough Sets and Knowledge Technology, 4th International Conference, RSKT 2009, Gold Coast, Australia, July 2009, Proceedings, pp. 52-59.
• Taichi Haruna, Yukio-Pegio Gunji, 2009. Wholeness and Information Processing in Biological Networks: An Algebraic Study of Network Motifs. In: Y. Suzuki et al. (Eds.) Natural Computing, 2nd Internal Workshop on Natural Computing, Nagoya, Japan, December 2007, PICT1, pp. 70-80. (download)
• Taichi Haruna, 2008. Being Arranged in Advance: Quantum Entanglement and Biological Feedback. In: S. Bullock, J. Noble, R. Watson, and M. A. Bedau (eds.) Artificial Life XI: Proceedings of the Eleventh International Conference on the Simulation and Synthesis of Living Systems, pp.220-226. MIT Press, Cambridge, MA. (download)
• Yuka Tauchi, Moto Kamiura, Taichi Haruna and Yukio-Pegio Gunji, 2008. Origin of Money: Dynamic Duality between Necessity and Unnecessity. AIP Conference Proceedings 1051: Computing Anticipatory Systems: CASYS’07, 390-400.
• Taichi Haruna and Yukio-Pegio Gunji, 2006. Local Cellular Automata as an Abstract Model of Self-Organizing Process. AIP Conference Proceedings 839: Computing Anticipatory Systems: CASYS’05, 371-380. (download)

Awards

• Best Paper Award, Taichi Haruna, Analysis of coupling complexity in echo state networks via ordinal persistenthomology. The 29th International Symposium on Artificial Life and Robotics / The 9th International Symposium on Biocomplexity, B-Con PLAZA, Beppu, Japan and ONLINE, January 25, 2024.
• Best Paper Award, Taichi Haruna, Uncertainty of the Second Order: Quasispecies model with inverse Bayesian inference. The 23rd International Symposium on Artificial Life and Robotics / The 3rd International Symposium on Biocomplexity, B-Con PLAZA, Beppu, Japan, January 18, 2018.
• Best Poster Award, Taichi Haruna, Junya Shiozaki and Sayaka Tanaka, How Does Thermal Gradient Contribute to Microcapsule Formation by Proteinoid? The 6th International Conference on Soft Computing and Intelligent Systems / The 13th International Symposium on Advanced Intelligent Systems, Kobe, Japan, November 22, 2012.
• Best Paper Award, Taichi Haruna and Yukio-Pegio Gunji, Double Approximation and Complete Lattices. The Fourth International Conference on Rough Set and Knowledge Technology, Gold Coast, Australia, July 15, 2009.
• Best Paper Award, Taichi Haruna and Yukio-Pegio Gunji, Local Cellular Automata as an Abstract Model of Self-Organizing Process. 7th International Conference on Computing Anticipatory Systems, Liege, Belgium, August 13, 2005.

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