Preprints

1. Jnanajyoti Bhaumik, Naoki Masuda.
   Constant-selection evolutionary dynamics on weighted networks.
   Preprint: arXiv:2403.17208
   Python codes
   
   
2. Lucas H. McCabe, Naoki Masuda, Shannon Casillas, Nathan Danneman, Alen Alic, Royal Law.
   Network analysis of U.S. non-fatal opioid-involved overdose journeys, 2018-2023.
   Preprint: arXiv:2402.03294
   
   
3. Chanon Thongprayoon, Naoki Masuda.
   Online landmark replacement for out-of-sample dimensionality reduction methods.
   Preprint: arXiv:2311.12646
   
   
4. Naoki Masuda, Zachary M. Boyd, Diego Garlaschelli, Peter J. Mucha.
   Correlation networks: Interdisciplinary approaches beyond thresholding.
   Preprint: arXiv:2311.09536
   
   
5. Aming Li, Yao Meng, Lei Zhou, Naoki Masuda, Long Wang.
   Temporal networks provide a unifying understanding of the evolution of cooperation.
   Preprint: arXiv:2309.12686
   
   
6. Pitambar Khanra, Johan Nakuci, Sarah Muldoon, Takamitsu Watanabe, Naoki Masuda.
   Reliability of energy landscape analysis of resting-state functional MRI data.
   Preprint: arXiv:2305.19573
   Codes
   
   
7. Penghang Liu, Rupam Acharyya, Robert E. Tillman, Shunya Kimura, Naoki Masuda, Ahmet Erdem Sarıyüce.
   Temporal motifs for financial networks: A Study on Mercari, JPMC, and Venmo platforms.
   Preprint: arXiv:2301.07791
   
   
8. Jun Miyata, Toby Winton-Brown, Thomas Sedlak, Toshihiko Aso, Nicola Cascella, Jennifer Coughlin, Nicolas A. Crossley, Emrah Duezel, Takahiro Ezaki, Masaki Fukunaga, Carolyn Howell, Masanori Isobe, Kouhei Kamiya, Kiyoto Kasai, Takanori Kochiyama, Shinsuke Koike, Akira Kunimatsu, Naoki Masuda, Susumu Mori, Yasuo Mori, Toshiya Murai, Kiyotaka Nemoto, Frederick Nucifora, Kazutaka Ohi, Naohiro Okada, Yuki Sakai, Nobukatsu Sawamoto, Tsutomu Takahashi, Shinichi Urayama, Yoshiyuki Watanabe, Crystal C. Watkins, Hidenaga Yamamori, Yuka Yasuda, Ryota Hashimoto, Hidehiko Takahashi, Akira Sawa, Philip McGuire.
   Functional alterations of salience-related networks are associated with traits, staging, and the state of psychosis.
   Preprint: https://doi.org/10.1101/2021.10.02.21264326
   
   

Journal papers (refereed papers only)

1. Ruodan Liu, Naoki Masuda.
   Fixation dynamics on multilayer networks.
   SIAM Journal on Applied Mathematics, in press (2024).
   Preprint: arXiv:2311.16457
   
   
2. Saiful Islam, Pitambar Khanra, Johan Nakuci, Sarah Muldoon, Takamitsu Watanabe, Naoki Masuda.
   State-transition dynamics of resting-state functional magnetic resonance imaging data: Model comparison and test-to-retest analysis.
   BMC Neuroscience, 25, 14 (2024). [open access]
   Preprint: arXiv:2308.11910
   Codes
   
   
3. Naoki Masuda, Kazuyuki Aihara, Neil G. MacLaren.
   Anticipating regime shifts by mixing early warning signals from different nodes.
   Nature Communications, 15, 1086 (2024). [open access]
   R and Python codes
   
   
4. Jun Miyata, Akihiko Sasamoto, Takahiro Ezaki, Masanori Isobe, Takanori Kochiyama, Naoki Masuda, Yasuo Mori, Yuki Sakai, Nobukatsu Sawamoto, Shisei Tei, Shiho Ubukata, Toshihiko Aso, Toshiya Murai, Hidehiko Takahashi.
   Associations of conservatism and jumping to conclusions biases with aberrant salience and default mode network.
   Psychiatry and Clinical Neurosciences, published online (2024). [open access]
   Preprint: https://doi.org/10.1101/2022.09.29.22280497
   
   
5. Shota Yonezawa, Takayuki Haruki, Keiichi Koizumi, Akinori Taketani, Yusuke Oshima, Makito Oku, Akinori Wada, Tsutomu Sato, Naoki Masuda, Jun Tahara, Noritaka Fujisawa, Shota Koshiyama, Makoto Kadowaki, Isao Kitajima, Shigeru Saito.
   Establishing monoclonal gammopathy of undetermined significance as an independent pre-disease state of multiple myeloma using Raman spectroscopy, dynamical network biomarker theory, and energy landscape analysis.
   International Journal of Molecular Sciences, 25, 1570 (2024). [open access]
   Press release (in Japanese; 富山大学)
   
   
6. Neil G. MacLaren, Lingqi Meng, Melissa Collier, Naoki Masuda.
   Cooperation and the social brain hypothesis in primate social networks.
   Frontiers in Complex Systems, 1, 1344094 (2024). [open access]
   Preprint: arXiv:2302.00075
   Python codes
   
   
7. Madison Russell, Alber Aqil, Marie Saitou, Omer Gokcumen, Naoki Masuda.
   Gene communities in co-expression networks across different tissues.
   PLoS Computational Biology, 19, e1011616 (2023). [open access]
   Preprint: arXiv:2305.12963
   Python codes
   
   
8. Kashin Sugishita, Naoki Masuda.
   Social network analysis of manga: Similarities to real-world social networks and trends over decades.
   Applied Network Science, 8, 79 (2023). [open access]
   Preprint: arXiv:2303.07208
   Manga network data
   
   
9. Kazuki Nakajima, Ruodan Liu, Kazuyuki Shudo, Naoki Masuda.
   Quantifying gender imbalance in East Asian academia: Research career and citation practice.
   Journal of Informetrics, 17, 101460 (2023). [open access]
   Preprint: arXiv:2302.07843
   Press release (in Japanese; 神戸大学)
   朝日新聞デジタルの記事 (in Japanese)
   ITMedia NEWS の記事 (in Japanese)
   
   
10. Ruodan Liu, Naoki Masuda.
    Fixation dynamics on hypergraphs.
    PLoS Computational Biology, 19, e1011494 (2023). [open access]
    Preprint: arXiv:2301.05343
    Python codes to produce the numerical results in the paper
    
    
11. Ruodan Liu, Masaki Ogura, Elohim Fonseca dos Reis, Naoki Masuda.
    Effects of concurrency on epidemic spreading in Markovian temporal networks.
    European Journal of Applied Mathematics, published online (2023). [open access]
    Preprint: arXiv:2201.00754
    
    
12. Jnanajyoti Bhaumik, Naoki Masuda.
    Fixation probability in evolutionary dynamics on switching temporal networks.
    Journal of Mathematical Biology, 87, 64 (2023). [open access]
    Preprint: arXiv:2304.00170
    Python codes
    
    
13. Maximilian B. Kloucek, Thomas Machon, Shogo Kajimura, C. Patrick Royall, Naoki Masuda, Francesco Turci.
    Biases in inverse Ising estimates of near-critical behavior.
    Physical Review E, 108, 014109 (2023). [open access]
    Preprint: arXiv:2301.05556
    
    
14. Lingqi Meng, Naoki Masuda.
    Perturbation theory for evolution of cooperation on networks.
    Journal of Mathematical Biology, 87, 12 (2023). [open access]
    Preprint: arXiv:2208.06584
    
    
15. Christelle Langley, Naoki Masuda, Simon Godwin, Giovanni De Marco, Angela Davies Smith, Rosemary Jones, Jared Bruce, Jade Ngoc Thai.
    Dysfunction of basal ganglia functional connectivity associated with subjective and cognitive fatigue in multiple sclerosis.
    Frontiers in Neuroscience, 17, 1194859 (2023). [open access]
    
    
16. Yiding Cao, Suraj Rajendran, Prathic Sundararajan, Royal K. Law, Sarah Bacon, Steven A. Sumner, Naoki Masuda.
    Web-based social networks of individuals with adverse childhood experiences: Quantitative study.
    Journal of Medical Internet Research, 25, e45171 (2023). [open access]
    Preprint:https://doi.org/10.1101/2022.12.19.22283651
    Codes
    
    
17. Chanon Thongprayoon, Lorenzo Livi, Naoki Masuda.
    Embedding and trajectories of temporal networks.
    IEEE Access, 11, 41426-41443 (2023). [open access]
    Preprint: arXiv:2208.02869
    
    
18. Neil G. MacLaren, Prosenjit Kundu, Naoki Masuda.
    Early warnings for multistage transitions in dynamics on networks.
    Journal of the Royal Society Interface, 20, 20220743 (2023). [open access]
    R codes to produce the numerical results in the paper
    Preprint: arXiv:2208.08961
    
    
19. Ik Soo Lim, Naoki Masuda.
    To trust or not to trust: Evolutionary dynamics of an asymmetric N-player trust game.
    IEEE Transactions on Evolutionary Computation, 28, 117-131 (2024). [open access]
    Preprint: arXiv:2305.01413
    
    
20. Kazuki Nakajima, Kazuyuki Shudo, Naoki Masuda.
    Higher-order rich-club phenomenon in collaborative research grants.
    Scientometrics, 128, 2429-2446 (2023). [open access]
    Preprint: arXiv:2206.11470
    
    
21. Yukiko Matsumoto, Satoshi Nishida, Ryusuke Hayashi, Shuraku Son, Akio Murakami, Naganobu Yoshikawa, Hiroyoshi Ito, Naoya Oishi, Naoki Masuda, Toshiya Murai, Karl Friston, Shinji Nishimoto, Hidehiko Takahashi.
    Disorganization of semantic brain networks in schizophrenia revealed by fMRI.
    Schizophrenia Bulletin, 49, 498--506 (2023). [open access]
    
    
22. Prosenjit Kundu, Neil G. MacLaren, Hiroshi Kori, Naoki Masuda.
    Mean-field theory for double-well systems on degree-heterogeneous networks.
    Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 478, 20220350 (2022). [open access]

    Correction to: `Mean-field theory for double-well systems on degree-heterogeneous networks' (2023) by Kundu et al.
    Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 479, 20230171 (2023).

    Python codes to produce the numerical results in the paper (mostly in MATLAB, partly in Python and R)
    Preprint: arXiv:2205.11592
    
    

23. Takao Sasaki, Naoki Masuda, Richard P. Mann, Dora Biro.
    Empirical test of the many-wrongs hypothesis reveals weighted averaging of individual routes in pigeon flocks.
    iScience, 25, 105076 (2022). [open access]
    
    
24. Naoki Masuda, Prosenjit Kundu.
    Dimension reduction of dynamical systems on networks with leading and non-leading eigenvectors of adjacency matrices.
    Physical Review Research, 4, 023257 (2022). [open access]
    Typo
    Python codes (numerical demonstration part is written in MATLAB)
    Preprint: arXiv:2203.13872
    
    
25. Prosenjit Kundu, Hiroshi Kori, Naoki Masuda.
    Accuracy of a one-dimensional reduction of dynamical systems on networks.
    Physical Review E, 105, 024305 (2022). [open access]
    Preprint: arXiv:2110.07140
    
    
26. Elohim Fonseca dos Reis, Naoki Masuda.
    Metapopulation models imply non-Poissonian statistics of interevent times.
    Physical Review Research, 4, 013050 (2022). [open access]
    Preprint: arXiv:2106.10348
    
    
27. Penghang Liu, Naoki Masuda, Tomomi Kito, Ahmet Erdem Sarıyüce.
    Temporal motifs in patent opposition and collaboration networks.
    Scientific Reports, 12, 1917 (2022). [open access]
    Preprint: arXiv:2110.11198
    
    
28. Kazuki Nakajima, Kazuyuki Shudo, Naoki Masuda.
    Randomizing hypergraphs preserving degree correlation and local clustering.
    IEEE Transactions on Network Science and Engineering, 9, 1139-1153 (2022). [open access]
    Preprint: arXiv:2106.12162
    
    
29. Lingqi Meng, Naoki Masuda.
    Epidemic dynamics on metapopulation networks with node2vec mobility.
    Journal of Theoretical Biology, 534, 110960 (2022). [open access]
    Preprint: arXiv:2106.08080
    
    
30. Arthur P. C. Spencer, Jonathan C. W. Brooks, Naoki Masuda, Hollie Byrne, Richard Lee-Kelland, Sally Jary, Marianne Thoresen, Marc Goodfellow, Frances M. Cowan, Ela Chakkarapani.
    Motor function and white matter connectivity in children cooled for neonatal encephalopathy.
    NeuroImage: Clinical, 32, 102872 (2021). [open access]
    Preprint: https://doi.org/10.1101/2021.04.30.21256369
    
    
31. Kashin Sugishita, Noha Abdel-Mottaleb, Qiong Zhang, Naoki Masuda.
    A growth model for water distribution networks with loops.
    Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 477, 20210528 (2021). [open access]
    arXiv:2106.13519
    
    
32. Marie Saitou, Naoki Masuda, Omer Gokcumen.
    Similarity-based analysis of allele frequency distribution among multiple populations identifies adaptive genomic structural variants.
    Molecular Biology and Evolution, 39, msab313 (2021). [open access]
    Preprint: https://doi.org/10.1101/2021.01.25.428140
    Codes
    
    
33. Takahiro Ezaki, Yu Himeno, Takamitsu Watanabe, Naoki Masuda.
    Modeling state-transition dynamics in resting-state brain signals by the hidden Markov and Gaussian mixture models.
    European Journal of Neuroscience, 54, 5404-5416 (2021). [open access]
    Preprint: arXiv:2001.08369
    Python codes
    
    
34. Hang-Hyun Jo, Naoki Masuda.
    Finite-size effects on the convergence time in continuous-opinion dynamics.
    Physical Review E, 104, 014309 (2021).
    Preprint: arXiv:2103.06055
    
    
35. Kashin Sugishita, Mason A. Porter, Mariano Beguerisse-Díaz, Naoki Masuda.
    Opinion dynamics on tie-decay networks.
    Physical Review Research, 3, 023249 (2021). [open access]
    Preprint: arXiv:2010.00143
    
    
36. Naoki Masuda, Joel C. Miller, Petter Holme.
    Concurrency measures in the era of temporal network epidemiology: A review.
    Journal of the Royal Society Interface, 18, 20210019 (2021). [open access]
    Preprint: arXiv:2012.13317
    
    
37. Christos Ellinas, Christos Nicolaides, Naoki Masuda.
    Mitigation strategies against cascading failures within a project activity network.
    Journal of Computational Social Science, 5, 383-400 (2022). [open access]
    Correction (only on the open access status): Journal of Computational Social Science, 5, 1097--1098 (2022). Preprint: arXiv:1810.07561
    Network data
    
    
38. Sadamori Kojaku, Giacomo Livan, Naoki Masuda.
    Detecting citation cartels in journal networks.
    Scientific Reports, 11, 14524 (2021). [open access]
    Author correction: Detecting anomalous citation groups in journal networks.
    Scientific Reports, 12, 14698 (2022).
    Preprint: arXiv:2009.09097
    Python codes
    
    
39. Kashin Sugishita, Naoki Masuda.
    Recurrence in the evolution of air transport networks.
    Scientific Reports, 11, 5514 (2021). [open access]
    Preprint: arXiv:2005.14392
    
    
40. Arthur P. C. Spencer, Jonathan C. W. Brooks, Naoki Masuda, Hollie Byrne, Richard Lee-Kelland, Sally Jary, Marianne Thoresen, James Tonks, Marc Goodfellow, Frances M. Cowan, Ela Chakkarapani.
    Disrupted brain connectivity in children treated with therapeutic hypothermia for neonatal encephalopathy.
    NeuroImage: Clinical, 30, 102582 (2021). [open access]
    Preprint: https://doi.org/10.1101/2020.09.23.20200014
    
    
41. Elohim Fonseca dos Reis, Mark Viney, Naoki Masuda.
    Network analysis of the immune state of mice.
    Scientific Reports, 11, 4306 (2021). [open access]
    Preprint: https://doi.org/10.1101/638445
    
    
42. Marinho A Lopes, Dominik Krzemiński, Khalid Hamandi, Krish D. Singh, Naoki Masuda, John R. Terry, Jiaxiang Zhang.
    A computational biomarker of juvenile myoclonic epilepsy from resting-state MEG.
    Clinical Neurophysiology, 132, 922-927 (2021). [open access]
    Preprint: https://doi.org/10.1101/2020.05.18.20102681
    
    
43. Lingqi Meng, Naoki Masuda.
    Analysis of node2vec random walks on networks.
    Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 476, 20200447 (2020). [open access]
    Preprint: arXiv:2006.04904
    Python code
    
    
44. Shun Kodate, Ryusuke Chiba, Shunya Kimura, Naoki Masuda.
    Detecting problematic transactions in a consumer-to-consumer e-commerce network.
    Applied Network Science, 5, 90 (2020). [open access]
    Preprint: arXiv:1906.07974
    Featured by Ledge.ai (in Japanese)
    Featured by impress (in Japanese)
    Press release (in Japanese; メルカリ)
    Press release (in Japanese; 東北大学)
    
    
45. Elohim Fonseca dos Reis, Aming Li, Naoki Masuda.
    Generative models of simultaneously heavy-tailed distributions of inter-event times on nodes and edges.
    Physical Review E, 102, 052303 (2020). [open access]
    Preprint: arXiv:2008.13034
    
    
46. Shogo Kajimura, Naoki Masuda, Johnny King L. Lau, Kou Murayama.
    Focused attention meditation changes the boundary and configuration of functional networks in the brain.
    Scientific Reports, 10, 18426 (2020). [open access]
    Preprint: https://doi.org/10.1101/664573
    
    
47. Xiu-Xiu Zhan, Ziyu Li, Naoki Masuda, Petter Holme, Huijuan Wang.
    Susceptible-infected-spreading-based network embedding in static and temporal networks.
    EPJ Data Science, 9, 30 (2020). [open access]
    Preprint: arXiv:2004.06750
    
    
48. Mengqiao Xu, Qian Pan, Haoxiang Xia, Naoki Masuda.
    Estimating international trade status of countries from global liner shipping networks.
    Royal Society Open Science, 7, 200386 (2020). [open access]
    Preprint: arXiv:2001.07688
    Data and Python codes
    
    
49. Marinho A. Lopes, Jiaxiang Zhang, Dominik Krzemiński, Khalid Hamandi, Qi Chen, Lorenzo Livi, Naoki Masuda.
    Recurrence quantification analysis of dynamic brain networks.
    European Journal of Neuroscience, 53, 1040-1059 (2021). [open access]
    Preprint: arXiv:2001.03761
    
    
50. Irene Malvestio, Alessio Cardillo, Naoki Masuda.
    Interplay between k-core and community structure in complex networks.
    Scientific Reports, 10, 14702 (2020). [open access]
    Preprint: arXiv:2005.01147
    
    
51. Genki Ichinose, Daiki Miyagawa, Junji Ito, Naoki Masuda.
    Winning by hiding behind others: An analysis of speed skating data.
    PLOS ONE, 15, e0237470 (2020). [open access]
    Preprint: arXiv:2004.06464
    日本語の研究紹介（Qiita）(in Japanese)
    研究ナビの記事 (in Japanese)（Qiita の記事と内容は同一）
    
    
52. Naoki Masuda, Takayuki Hiraoka.
    Waiting-time paradox in 1922.
    Northeast Journal of Complex Systems, 2, 1 (2020). [open access]
    Preprint: arXiv:2004.14081
    
    
53. Alessio Cardillo, Naoki Masuda.
    Critical mass effect in evolutionary games triggered by zealots.
    Physical Review Research, 2, 023305 (2020). [open access]
    Preprint: arXiv:1912.00400
    
    
54. Naoki Masuda, Petter Holme.
    Small inter-event times govern epidemic spreading on networks.
    Physical Review Research, 2, 023163 (2020). [open access]
    Preprint: arXiv:1911.04040
    
    
55. Takayuki Hiraoka, Naoki Masuda, Aming Li, Hang-Hyun Jo.
    Modeling temporal networks with bursty activity patterns of nodes and links.
    Physical Review Research, 2, 023073 (2020). [open access]
    Preprint: arXiv:1912.11212
    
    
56. Gabriele Valentini, Naoki Masuda, Zachary Shaffer, Jake R. Hanson, Takao Sasaki, Sara Imari Walker, Theodore P. Pavlic, Stephen C. Pratt.
    Division of labor promotes the spread of information in colony emigrations by the ant Temnothorax rugatulus.
    Proceedings of the Royal Society B: Biological Sciences, 287, 20192950 (2020).
    Request the paper
    Preprint: https://doi.org/10.1101/791996
    Featured by ASU Now
    Video
    
    
57. Makoto Okada, Kenji Yamanishi, Naoki Masuda.
    Long-tailed distributions of inter-event times as mixtures of exponential distributions.
    Royal Society Open Science, 7, 191643 (2020). [open access]
    Preprint: arXiv:1905.00699
    Python codes
    
    
58. Naoki Masuda, Victor M. Preciado, Masaki Ogura.
    Analysis of the susceptible-infected-susceptible epidemic dynamics in networks via the non-backtracking matrix.
    IMA Journal of Applied Mathematics, 85, 214-230 (2020). [open access]
    Preprint: arXiv:1906.04269
    C/C++ and MATLAB code
    
    
59. Takahiro Ezaki, Elohim Fonseca dos Reis, Takamitsu Watanabe, Michiko Sakaki, Naoki Masuda.
    Closer to critical resting-state neural dynamics in individuals with higher fluid intelligence.
    Communications Biology, 3, 52 (2020). [open access]
    Preprint: https://doi.org/10.1101/688655
    C code (the code to gather outputs stored in different files is in Python)
    
    
60. Dominik Krzemiński, Naoki Masuda, Khalid Hamandi, Krish D. Singh, Bethany Routley, Jiaxiang Zhang.
    Energy landscape of resting magnetoencephalography reveals fronto-parietal network impairments in epilepsy.
    Network Neuroscience, 4, 374-396 (2020).
    Request the paper
    Preprint: https://doi.org/10.1101/703074
    
    
61. Sadamori Kojaku, Naoki Masuda.
    Constructing networks by filtering correlation matrices: A null model approach.
    Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 475, 20190578 (2019).
    Request the paper
    Preprint: arXiv:1903.10805
    Python codes
    
    
62. Naoki Masuda, Fanlin Meng.
    Dynamical stability of water distribution networks.
    Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 475, 20190291 (2019).
    Request the paper
    Preprint: arXiv:1905.06132
    MATLAB code and water distribution network data
    
    
63. Masaki Ogura, Victor M. Preciado, Naoki Masuda.
    Optimal containment of epidemics over temporal activity-driven networks.
    SIAM Journal on Applied Mathematics, 79, 986-1006 (2019).
    Request the paper
    Preprint: arXiv:1802.08961
    
    
64. Takamitsu Watanabe, Geraint Rees, Naoki Masuda.
    Atypical intrinsic neural timescale in autism.
    eLife, 8, e42256 (2019). [open access]
    Download presentation slides
    Related insight article by Leonardo L. Gollo
    
    
65. Naoki Masuda, Petter Holme.
    Detecting sequences of system states in temporal networks.
    Scientific Reports, 9, 795 (2019). [open access]
    Preprint: arXiv:1803.04755
    Python and MATLAB codes
    Short introduction to this research
    日本語の研究紹介 (in Japanese)
    
    
66. Sadamori Kojaku, Mengqiao Xu, Haoxiang Xia, Naoki Masuda.
    Multiscale core-periphery structure in a global liner shipping network.
    Scientific Reports, 9, 404 (2019). [open access]
    Preprint: arXiv:1808.04549
    Python codes
    
    
67. Naoki Masuda, Sadamori Kojaku, Yukie Sano.
    Configuration model for correlation matrices preserving the node strength.
    Physical Review E, 98, 012312 (2018). [open access]
    Typo
    Preprint: arXiv:1806.08709
    MATLAB codes
    
    
68. Sadamori Kojaku, Giulio Cimini, Guido Caldarelli, Naoki Masuda.
    Structural changes in the interbank market across the financial crisis from multiple core-periphery analysis.
    Journal of Network Theory in Finance, 4, 33-51 (2018).
    Request the paper
    Preprint: arXiv:1802.05139
    
    
69. Takuya Sekiguchi, Kohei Tamura, Naoki Masuda.
    Population changes in residential clusters in Japan.
    PLOS ONE, 13, e0197144 (2018). [open access]
    Preprint: arXiv:1706.09439
    
    
70. Sadamori Kojaku, Naoki Masuda.
    A generalised significance test for individual communities in networks.
    Scientific Reports, 8, 7351 (2018). [open access]
    Preprint: arXiv:1712.00298
    Python codes
    
    
71. Sadamori Kojaku, Naoki Masuda.
    Core-periphery structure requires something else in the network.
    New Journal of Physics, 20, 043012 (2018). [open access]
    Preprint: arXiv:1710.07076
    C++ and MATLAB codes
    
    
72. Takahiro Ezaki, Michiko Sakaki, Takamitsu Watanabe, Naoki Masuda.
    Age-related changes in the ease of dynamical transitions in human brain activity.
    Human Brain Mapping, 39, 2673-2688 (2018). [open access]
    
    
73. Naoki Masuda, Michiko Sakaki, Takahiro Ezaki, Takamitsu Watanabe.
    Clustering coefficients for correlation networks.
    Frontiers in Neuroinformatics, 12, 7 (2018). [open access]
    Typo
    Preprint: arXiv:1806.10228
    Download presentation slides
    Python and C++ codes
    
    
74. Genki Ichinose, Naoki Masuda.
    Zero-determinant strategies in finitely repeated games.
    Journal of Theoretical Biology, 438, 61-77 (2018). [open access]
    Preprint: arXiv:1707.03097
    
    
75. Naoki Masuda, Luis E. C. Rocha.
    A Gillespie algorithm for non-Markovian stochastic processes.
    SIAM Review, 60, 95-115 (2018). [open access]
    Preprint: arXiv:1601.01490
    C/C++ codes for the Laplace Gillespie algorithm, one to generate positively correlated inter-event times etc.
    Short introduction to this research
    日本語の研究紹介 (in Japanese)
    
    
76. Takahiro Ezaki, Naoki Masuda.
    Reinforcement learning account of network reciprocity.
    PLOS ONE, 12, e0189220 (2017). [open access]
    Preprint: arXiv:1706.04310
    
    
77. Sadamori Kojaku, Naoki Masuda.
    Finding multiple core-periphery pairs in networks.
    Physical Review E, 96, 052313 (2017). [open access]
    Preprint: arXiv:1702.06903
    MATLAB codes
    日本語の研究紹介 (in Japanese)
    
    
78. Luis E. C. Rocha, Naoki Masuda, Petter Holme.
    Sampling of temporal networks: Methods and biases.
    Physical Review E, 96, 052302 (2017). [open access]
    Preprint: arXiv:1707.02108
    
    
79. Tomokatsu Onaga, James P. Gleeson, Naoki Masuda.
    Concurrency-induced transitions in epidemic dynamics on temporal networks.
    Physical Review Letters, 119, 108301 (2017). [open access]
    Preprint: arXiv:1702.05054
    Download presentation slides
    
    
80. Naoki Masuda, Mason A. Porter, Renaud Lambiotte.
    Random walks and diffusion on networks.
    Physics Reports, 716-717, 1-58 (2017). [open access]

    Corrigendum to ``Random walks and diffusion on networks'' [Phys. Rep. 716-717 (2017) 1-58].
    Physics Reports, 745, 96 (2018).

    Second corrigendum to ``Random walks and diffusion on networks'' [Phys. Rep. 716-717 (2017) 1-58].
    Physics Reports, 851, 37-39 (2020).

    Preprint: arXiv:1612.03281
    Download presentation slides
    
    

81. Kohei Tamura, Naoki Masuda.
    Effects of the distant population density on spatial patterns of demographic dynamics.
    Royal Society Open Science, 4, 170391 (2017). [open access]
    Typo
    Preprint: arXiv:1704.07523
    
    
82. Takahiro Ezaki, Takamitsu Watanabe, Masayuki Ohzeki, Naoki Masuda.
    Energy landscape analysis of neuroimaging data.
    Philosophical Transactions of the Royal Society A, 375, 20160287 (2017). [open access]
    Preprint: arXiv:1611.05137
    MATLAB code for calculating and visualizing energy landscapes is availble here.
    MATLAB code to calculate the maximum-likelihood estimator is also available as the supplementary material of the paper.
    
    
83. Thomas A. O'Shea-Wheller, Naoki Masuda, Ana Sendova-Franks, Nigel R. Franks.
    Variability in individual assessment behaviour and its implications for collective decision-making.
    Proceedings of the Royal Society B: Biological Sciences, 284, 20162237 (2017).
    Request the paper
    Featured by New Scientist
    
    
84. Yutaka Horita, Masanori Takezawa, Keigo Inukai, Toshimasa Kita, Naoki Masuda.
    Reinforcement learning accounts for moody conditional cooperation behavior: experimental results.
    Scientific Reports, 7, 39275 (2017). [open access]
    
    
85. Teruyoshi Kobayashi, Naoki Masuda.
    Fragmenting networks by targeting collective influencers at a mesoscopic level.
    Scientific Reports, 6, 37778 (2016). [open access]
    Preprint: arXiv:1605.03694
    MATLAB codes for the immunization algorithm
    
    
86. Luis E. C. Rocha, Naoki Masuda.
    Individual-based approach to epidemic processes on arbitrary dynamic contact networks.
    Scientific Reports, 6, 31456 (2016). [open access]
    Preprint: arXiv:1510.09179
    
    
87. Takahiro Ezaki, Yutaka Horita, Masanori Takezawa, Naoki Masuda.
    Reinforcement learning explains conditional cooperation and its moody cousin.
    PLOS Computational Biology, 12, e1005034 (2016). [open access]
    日本語の研究紹介 (in Japanese)
    
    
88. Leo Speidel, Konstantin Klemm, Víctor M. Eguíluz, Naoki Masuda.
    Temporal interactions facilitate endemicity in the susceptible-infected-susceptible epidemic model.
    New Journal of Physics, 18, 073013 (2016). [open access]
    Typos
    Preprint: arXiv:1602.00859
    Download presentation slides
    
    
89. Ryosuke Nishi, Taro Takaguchi, Keigo Oka, Takanori Maehara, Masashi Toyoda, Ken-ichi Kawarabayashi, Naoki Masuda.
    Reply trees in Twitter: data analysis and branching process models.
    Social Network Analysis and Mining, 6, 26 (2016). [open access]
    
    
90. Naoki Masuda.
    Accelerating coordination in temporal networks by engineering the link order.
    Scientific Reports, 6, 22105 (2016). [open access]
    Preprint: arXiv:1510.09085
    
    
91. Yutaka Horita, Masanori Takezawa, Takuji Kinjo, Yo Nakawake, Naoki Masuda.
    Transient nature of cooperation by pay-it-forward reciprocity.
    Scientific Reports, 6, 19471 (2016). [open access]
    
    
92. Jens Malmros, Naoki Masuda, Tom Britton.
    Random walks on directed networks: Inference and respondent-driven sampling.
    Journal of Official Statistics, 32, 433-459 (2016). [open access]
    Preprint: arXiv:1308.3600
    
    
93. Leo Speidel, Taro Takaguchi, Naoki Masuda.
    Community detection in directed acyclic graphs.
    European Physical Journal B, 88, 203 (2015). [open access]
    Preprint: arXiv:1503.05641
    Featured by Advances in Engineering
    
    
94. Kohei Tamura, Naoki Masuda.
    Win-stay lose-shift strategy in formation changes in football.
    EPJ Data Science, 4, 9 (2015). [open access]
    Preprint: arXiv:1503.02484
    Short introduction to this research
    日本語の研究紹介 (in Japanese)
    
    
95. Nigel Franks, Jonathan Stuttard, Carolina Doran, Julian Esposito, Maximillian Master, Ana Sendova-Franks, Naoki Masuda, Nicholas Britton.
    How ants use quorum sensing to estimate the average quality of a fluctuating resource.
    Scientific Reports, 5, 11890 (2015). [open access]
    
    
96. Naoki Masuda, Thomas A. O'Shea-Wheller, Carolina Doran, Nigel R. Franks.
    Computational model of collective nest selection by ants with heterogeneous acceptance thresholds.
    Royal Society Open Science, 2, 140533 (2015). [open access]
    C++ codes
    
    
97. Naoki Masuda, Feng Fu.
    Evolutionary models of in-group favoritism.
    F1000Prime Reports, 7, 27 (2015). [open access]
    
    
98. Naoki Masuda.
    Opinion control in complex networks.
    New Journal of Physics, 17, 033031 (2015). [open access]
    Preprint: arXiv:1412.2170
    
    
99. Petter Holme, Naoki Masuda.
    The basic reproduction number as a predictor for epidemic outbreaks in temporal networks.
    PLOS ONE, 10, e0120567 (2015). [open access]
    Preprint: arXiv:1407.6598
    
    
100. Víctor M. Eguíluz, Naoki Masuda, Juan Fernández-Gracia.
     Bayesian decision making in human collectives with binary choices.
     PLOS ONE, 10, e0121332 (2015). [open access]
     Preprint: arXiv:1502.01055
     Also available at SSRN
     
     
101. Leo Speidel, Renaud Lambiotte, Kazuyuki Aihara, Naoki Masuda.
     Steady state and mean recurrence time for random walks on stochastic temporal networks.
     Physical Review E, 91, 012806 (2015). [open access]
     Preprint: arXiv:1407.4582
     
     
102. Yohei Nakajima, Naoki Masuda.
     Evolutionary dynamics in finite populations with zealots.
     Journal of Mathematical Biology, 70, 465-484 (2015). [open access]
     Preprint: arXiv:1308.2273
     Preprint: METR (Mathematical Engineering Technical Reports) 2013-20, University of Tokyo
     
     
103. Takamitsu Watanabe, Naoki Masuda, Fukuda Megumi, Ryota Kanai, Geraint Rees.
     Energy landscape and dynamics of brain activity during human bistable perception.
     Nature Communications, 5, 4765 (2014). [open access]
     MATLAB code for calculating and visualizing energy landscapes is availble here.
     MATLAB code to calculate the maximum-likelihood estimator is also available as the supplementary material of one of our papers.
     日本語の研究紹介 (in Japanese)
     
     
104. Hiroyuki Shimoji, Masato S. Abe, Kazuki Tsuji, Naoki Masuda.
     Global network structure of dominance hierarchy of ant workers.
     Journal of the Royal Society Interface, 11, 20140599 (2014). [open access]
     Preprint: arXiv:1407.4277
     Download presentation slides
     Dominance network data are available at the journal's website.
     日本語の研究紹介 (in Japanese)
     
     
105. Ryosuke Nishi, Naoki Masuda.
     Dynamics of social balance under temporal interaction.
     EPL, 107, 48003 (2014). [open access]
     Preprint: arXiv:1403.4891
     
     
106. Yuni Iwamasa, Naoki Masuda.
     Networks maximizing the consensus time of voter models.
     Physical Review E, 90, 012816 (2014).
     Preprint: arXiv:1404.6360
     Preprint: METR (Mathematical Engineering Technical Reports) 2014-11, University of Tokyo
     
     
107. Naoki Masuda.
     Voter model on the two-clique graph.
     Physical Review E, 90, 012802 (2014). [open access]
     Preprint: arXiv:1403.4763
     
     
108. Takamitsu Watanabe, Shigeyuki Kan, Takahiko Koike, Masaya Misaki, Seiki Konishi, Satoru Miyauchi, Yasushi Miyashita, Naoki Masuda.
     Network-dependent modulation of brain activity during sleep.
     NeuroImage, 98, 1-10 (2014). [open access]
     
     
109. Luis E. C. Rocha, Naoki Masuda.
     Random walk centrality for temporal networks.
     New Journal of Physics, 16, 063023 (2014). [open access]
     Preprint: arXiv:1401.5648
     
     
110. Takamitsu Watanabe, Masanori Takezawa, Yo Nakawake, Akira Kunimatsu, Hidenori Yamasue, Mitsuhiro Nakamura, Yasushi Miyashita, Naoki Masuda.
     Two distinct neural mechanisms underlying indirect reciprocity.
     Proceedings of the National Academy of Sciences of the United States of America, 111, 3990-3995 (2014). [open access]
     Featured by Le Scienze (in Italian)
     Press release (in Japanese)
     
     
111. Naoki Masuda.
     Evolution via imitation among like-minded individuals.
     Journal of Theoretical Biology, 349, 100-108 (2014). [open access]
     Preprint: arXiv:1307.4141
     
     
112. Koji Oishi, Manuel Cebrian, Andres Abeliuk, Naoki Masuda.
     Iterated crowdsourcing dilemma game.
     Scientific Reports, 4, 4100 (2014). [open access]
     Preprint: arXiv:1401.4267
     
     
113. Takamitsu Watanabe, Satoshi Hirose, Hiroyuki Wada, Yoshio Imai, Toru Machida, Ichiro Shirouzu, Seiki Konishi, Yasushi Miyashita, Naoki Masuda.
     Energy landscapes of resting-state brain networks.
     Frontiers in Neuroinformatics, 8, 12 (2014). [open access]
     
     
114. Kodai Saito, Naoki Masuda.
     Two types of well followed users in the followership networks of Twitter.
     PLOS ONE, 9, e84265 (2014). [open access]
     Preprint: arXiv:1302.0677
     
     
115. Shoma Tanabe, Naoki Masuda.
     Complex dynamics of a nonlinear voter model with contrarian agents.
     Chaos, 23, 043136 (2013). [open access]
     Preprint: arXiv:1308.2795
     Preprint: METR (Mathematical Engineering Technical Reports) 2013-21, University of Tokyo
     
     
116. Naoki Masuda, Konstantin Klemm, Víctor M. Eguíluz.
     Temporal networks: slowing down diffusion by long lasting interactions.
     Physical Review Letters, 111, 188701 (2013). [open access]
     Preprint: arXiv:1305.2938
     
     
117. Naoki Masuda.
     Voter models with contrarian agents.
     Physical Review E, 88, 052803 (2013). [open access]
     Preprint: arXiv:1306.4401
     
     
118. Takehisa Hasegawa, Taro Takaguchi, Naoki Masuda.
     Observability transitions in correlated networks.
     Physical Review E, 88, 042809 (2013). [open access]
     Preprint: arXiv:1309.1862
     
     
119. Makoto Hiroi, Masamichi Ohkura, Junichi Nakai, Naoki Masuda, Koichi Hashimoto, Kiichi Inoue, André Fiala, Tetsuya Tabata.
     Principal component analysis of odor coding at the level of third order olfactory neurons in Drosophila.
     Genes to Cells, 18, 1070-1081 (2013).
     Request the paper
     
     
120. Ryosuke Nishi, Naoki Masuda.
     Collective opinion formation model under Bayesian updating and confirmation bias.
     Physical Review E, 87, 062123 (2013). [open access]
     Preprint: arXiv:1302.3949
     Preprint: METR (Mathematical Engineering Technical Reports) 2013-22, University of Tokyo
     
     
121. Taro Takaguchi, Naoki Masuda, Petter Holme.
     Bursty communication patterns facilitate spreading in a threshold-based epidemic dynamics.
     PLOS ONE, 8, e68629 (2013). [open access]
     Preprint: arXiv:1206.2097
     
     
122. Naoki Masuda, Issei Kurahashi, Hiroko Onari.
     Suicide ideation of individuals in online social networks.
     PLOS ONE, 8, e62262 (2013). [open access]
     Preprint: arXiv:1207.0561
     Featured by MIT Technology Review
     Featured by I Programmer news
     日本語の研究紹介 (in Japanese)
     
     
123. Masayoshi Ito, Naoki Masuda, Kazunori Shinomiya, Keita Endo, Kei Ito.
     Systematic analysis of neural projections reveals clonal composition of the Drosophila brain.
     Current Biology, 23, 644-655 (2013).
     Request the paper
     
     
124. Naoki Masuda, Petter Holme.
     Predicting and controlling infectious disease epidemics using temporal networks.
     F1000Prime Reports, 5, 6 (2013). [open access]
     
     
125. Shun-ichi Amari, Hiroyasu Ando, Taro Toyoizumi, Naoki Masuda.
     State concentration exponent as a measure of quickness in Kauffman-type networks.
     Physical Review E, 87, 022814 (2013). [open access]
     Preprint: arXiv:1202.6526
     Preprint: METR (Mathematical Engineering Technical Reports) 2013-19, University of Tokyo
     
     
126. Takamitsu Watanabe, Satoshi Hirose, Hiroyuki Wada, Yoshio Imai, Toru Machida, Ichiro Shirouzu, Seiki Konishi, Yasushi Miyashita, Naoki Masuda.
     A pairwise maximum entropy model accurately describes resting-state human brain networks.
     Nature Communications, 4, 1370 (2013). [open access]
     Unofficial errata
     MATLAB code to calculate the maximum-likelihood estimator is also available as the supplementary material of one of our papers.
     
     
127. Ryo Fujie, Kazuyuki Aihara, Naoki Masuda.
     A model of competition among more than two languages.
     Journal of Statistical Physics, 151, 289-303 (2013). [open access]
     Preprint: arXiv:1206.4557
     
     
128. Shoma Tanabe, Hideyuki Suzuki, Naoki Masuda.
     Indirect reciprocity with trinary reputations.
     Journal of Theoretical Biology, 317, 338-347 (2013). [open access]
     

     Corrigendum to ``Indirect reciprocity with trinary reputations'' [J. Theor. Biol. 317 (2013) 338--347].
     Journal of Theoretical Biology, 328, 100-101 (2013).
     

     Preprint: arXiv:1205.3547
     Preprint: METR (Mathematical Engineering Technical Reports) 2012-10, University of Tokyo
     
     

129. Mitsuhiro Nakamura, Naoki Masuda.
     Groupwise information sharing promotes ingroup favoritism in indirect reciprocity.
     BMC Evolutionary Biology, 12, 213 (2012). [open access]
     Preprint: arXiv:1207.5663
     Download presentation slides
     Preprint: METR (Mathematical Engineering Technical Reports) 2012-19, University of Tokyo
     
     
130. Shun Motegi, Naoki Masuda.
     A network-based dynamical ranking system for competitive sports.
     Scientific Reports, 2, 904 (2012). [open access]
     Featured by Nature Japan (in Japanese)
     Preprint: arXiv:1203.2228
     Download presentation slides (in Japanese)
     Preprint: METR (Mathematical Engineering Technical Reports) 2012-21, University of Tokyo
     
     
131. Naoki Masuda.
     Evolution of cooperation driven by zealots.
     Scientific Reports, 2, 646 (2012). [open access]
     Featured by Nature Japan (in Japanese)
     Preprint: arXiv:1207.2548
     Preprint: METR (Mathematical Engineering Technical Reports) 2012-22, University of Tokyo
     
     
132. Taro Takaguchi, Nobuo Sato, Kazuo Yano, Naoki Masuda.
     Importance of individual events in temporal networks.
     New Journal of Physics, 14, 093003 (2012). [open access]
     Preprint: arXiv:1205.4808
     Download presentation slides
     Preprint: METR (Mathematical Engineering Technical Reports) 2012-20, University of Tokyo
     
     
133. Naoki Masuda, Mitsuhiro Nakamura.
     Coevolution of trustful buyers and cooperative sellers in the trust game.
     PLOS ONE,7(9), e44169 (2012). [open access]
     Preprint: arXiv:1103.2648
     
     
134. Naoki Masuda.
     Ingroup favoritism and intergroup cooperation under indirect reciprocity based on group reputation.
     Journal of Theoretical Biology, 311, 8-18 (2012). [open access]
     Preprint: arXiv:1205.2825
     
     
135. Taro Ueno, Naoki Masuda, Shoen Kume, Kazuhiko Kume.
     Dopamine modulates the rest period length without perturbation of its power law distribution in Drosophila melanogaster.
     PLOS ONE, 7 (2), e32007 (2012). [open access]
     
     
136. Hiroshi Kori, Yoji Kawamura, Naoki Masuda.
     Structure of cell networks critically determines oscillation regularity.
     Journal of Theoretical Biology, 297, 61-72 (2012). [open access]
     Preprint: arXiv:1108.4790
     
     
137. Shoma Tanabe, Naoki Masuda.
     Evolution of cooperation facilitated by reinforcement learning with adaptive aspiration levels.
     Journal of Theoretical Biology, 293, 151-160 (2012). [open access]
     Preprint: arXiv:1106.6107
     Preprint: METR (Mathematical Engineering Technical Reports) 2011-21, University of Tokyo
     
     
138. Naoki Masuda.
     Clustering in large networks does not promote upstream reciprocity.
     PLOS ONE, 6 (10), e25190 (2011). [open access]
     Preprint: arXiv:1108.1440
     
     
139. Taro Takaguchi, Naoki Masuda.
     Voter model with non-Poissonian inter-event intervals.
     Physical Review E, 84, 036115 (2011). [open access]
     Preprint: arXiv:1011.4445
     Preprint: METR (Mathematical Engineering Technical Reports) 2011-20, University of Tokyo
     
     
140. Takehisa Hasegawa, Naoki Masuda.
     Robustness of networks against propagating attacks under vaccination strategies.
     Journal of Statistical Mechanics, P09014 (2011).
     Request the paper
     Preprint: arXiv:1102.4878
     
     
141. Taro Takaguchi, Mitsuhiro Nakamura, Nobuo Sato, Kazuo Yano, Naoki Masuda.
     Predictability of conversation partners.
     Physical Review X, 1, 011008 (2011). [open access]
     Preprint: arXiv:1104.5344
     Download presentation slides
     Preprint: METR (Mathematical Engineering Technical Reports) 2011-22, University of Tokyo
     
     
142. Mitsuhiro Nakamura, Naoki Masuda.
     Indirect reciprocity under incomplete observation.
     PLOS Computational Biology, 7 (7), e1002113 (2011). [open access]
     
     
143. C.-K. Yun, N. Masuda, B. Kahng.
     Diversity and critical behavior in prisoner's dilemma game.
     Physical Review E, 83, 057102 (2011).
     Preprint: arXiv:1006.3607
     
     
144. Naoki Masuda, Mitsuhiro Nakamura.
     Numerical analysis of a reinforcement learning model with the dynamic aspiration level in the iterated Prisoner's Dilemma.
     Journal of Theoretical Biology, 278, 55-62 (2011). [open access]
     Preprint: arXiv:1012.0121
     
     
145. Takehisa Hasegawa, Norio Konno, Naoki Masuda.
     Numerical study of a three-state host-parasite system on the square lattice.
     Physical Review E, 83, 046102 (2011).
     Preprint: arXiv:1006.4428
     
     
146. Yuri Ogiso, Kazuhide Tsuneizumi, Naoki Masuda, Makoto Sato, Tetsuya Tabata.
     Robustness of the Dpp morphogen activity gradient depends on negative feedback regulation by the inhibitory Smad, Dad.
     Development Growth and Differentiation, 53, 668-678 (2011).
     Request the paper
     
     
147. Naoki Masuda, S. Redner.
     Can partisan voting lead to truth?
     Journal of Statistical Mechanics, L02002 (2011). [open access]
     Preprint: arXiv:1012.2462
     
     
148. Naoki Masuda, Hiroshi Kori.
     Dynamics-based centrality for directed networks.
     Physical Review E, 82, 056107 (2010).
     Preprint: arXiv:1006.3138
     
     
149. Takamitsu Watanabe, Naoki Masuda.
     Enhancing the spectral gap of networks by node removal.
     Physical Review E, 82, 046102 (2010).
     Preprint: arXiv:1003.4340
     Download presentation slides [pdf only]
     
     
150. Jun Ohkubo, Kazushi Yoshida, Yuichi Iino, Naoki Masuda.
     Long-tail behavior in locomotion of Caenorhabditis elegans.
     Journal of Theoretical Biology, 267, 213-222 (2010).
     Request the paper
     Preprint: arXiv:1008.3014
     日本語の研究紹介 (in Japanese)
     
     
151. Naoki Masuda.
     Effects of diffusion rates on epidemic spreads in metapopulation networks.
     New Journal of Physics, 12, 093009 (2010). [open access]
     Preprint: arXiv:1004.2391
     
     
152. Naoki Masuda, Yoji Kawamura, Hiroshi Kori.
     Collective fluctuations in networks of noisy components.
     New Journal of Physics, 12, 093007 (2010). [open access]
     Preprint: arXiv:0911.5013
     Preprint: METR (Mathematical Engineering Technical Reports) 2010-24, University of Tokyo
     
     
153. Ralf Tönjes, Naoki Masuda, Hiroshi Kori.
     Synchronization transition of identical phase oscillators in a directed small-world network.
     Chaos, 20, 033108 (2010). [open access]
     Preprint: arXiv:1003.2020
     
     
154. Naoki Masuda, N. Gibert, S. Redner.
     Heterogeneous voter models.
     Physical Review E, 82, 010103(R) (2010).
     Preprint: arXiv:1003.0768
     
     
155. Akio Iwagami, Naoki Masuda.
     Upstream reciprocity in heterogeneous networks.
     Journal of Theoretical Biology, 265, 297-305 (2010). [open access]
     Preprint: arXiv:0905.4007
     Preprint: METR (Mathematical Engineering Technical Reports) 2010-25, University of Tokyo
     
     
156. Yusuke Ide, Norio Konno, Naoki Masuda.
     Statistical properties of a generalized threshold network model.
     Methodology & Computing in Applied Probability, 12, 361-377 (2010).
     Request the paper
     Preprint: arXiv:0707.1744
     Download presentation slides
     
     
157. Naoki Masuda.
     Immunization of networks with community structure.
     New Journal of Physics, 11, 123018 (2009). [open access]
     Preprint: arXiv:0909.1945
     
     
158. Naoki Masuda, Yoji Kawamura, Hiroshi Kori.
     Impact of hierarchical modular structure on ranking of individual nodes in directed networks.
     New Journal of Physics, 11, 113002 (2009). [open access]
     Preprint: arXiv:0907.0900
     
     
159. Naoki Masuda, Yoji Kawamura, Hiroshi Kori.
     Analysis of relative influence of nodes in directed networks.
     Physical Review E, 80, 046114 (2009).
     Preprint: arXiv:0907.0901
     Preprint: METR (Mathematical Engineering Technical Reports) 2009-40, University of Tokyo
     
     
160. Naoki Masuda, Hisashi Ohtsuki.
     A theoretical analysis of temporal difference learning in the iterated Prisoner's Dilemma game.
     Bulletin of Mathematical Biology, 71, 1818-1850 (2009).
     Request the paper
     
     
161. Naoki Masuda.
     Selective population rate coding: a possible computational role of gamma oscillations in selective attention.
     Neural Computation, 21, 3335-3362 (2009).
     Request the paper
     
     
162. Yuko K. Takahashi, Hiroshi Kori, Naoki Masuda.
     Self-organization of feedforward structure and entrainment in excitatory neural networks with spike-timing-dependent plasticity.
     Physical Review E, 79, 051904 (2009).
     Preprint: arXiv:0809.1127
     Preprint: METR (Mathematical Engineering Technical Reports) 2009-07, University of Tokyo
     
     
163. Naoki Masuda, Hisashi Ohtsuki.
     Evolutionary dynamics and fixation probabilities in directed networks.
     New Journal of Physics, 11, 033012 (2009). [open access]
     Preprint: arXiv:0812.1075
     
     
164. Naoki Masuda.
     Directionality of contact networks suppresses selection pressure in evolutionary dynamics.
     Journal of Theoretical Biology, 258, 323-334 (2009). [open access]
     Preprint: arXiv:0812.1076
     
     
165. N. Masuda, J. S. Kim, B. Kahng.
     Priority queues with bursty arrivals of incoming tasks.
     Physical Review E, 79, 036106 (2009).
     Preprint: arXiv:0805.0841
     
     
166. Taro Ueno, Naoki Masuda.
     Controlling nosocomial infection based on structure of hospital social networks.
     Journal of Theoretical Biology, 254, 655-666 (2008). [open access]
     Preprint: arXiv:0803.1879
     Download presentation slides
     
     
167. Naoki Masuda.
     Oscillatory dynamics in evolutionary games are suppressed by heterogeneous adaptation rates of players.
     Journal of Theoretical Biology, 251,181-189 (2008). [open access]
     Preprint: arXiv:0803.1023
     
     
168. Naoki Masuda, Shun-ichi Amari.
     A computational study of synaptic mechanisms of partial memory transfer in cerebellar vestibulo-ocular-reflex learning.
     Journal of Computational Neuroscience, 24, 137-156 (2008).
     Request the paper
     
     
169. Nobuaki Sugimine, Naoki Masuda, Norio Konno, Kazuyuki Aihara.
     On global and local critical points of extended contact process on homogeneous trees.
     Mathematical Biosciences, 213, 13-17 (2008).
     Request the paper
     
     
170. Naoki Masuda, Brent Doiron.
     Gamma oscillations of spiking neural populations enhance signal discrimination.
     PLOS Computational Biology, 3 (11), e236, 2348-2355 (2007). [open access]
     
     
171. Naoki Masuda.
     Participation costs dismiss the advantage of heterogeneous networks in evolution of cooperation.
     Proceedings of the Royal Society B: Biological Sciences, 274, 1815-1821 (2007).
     Request the paper
     Preprint: arXiv:physics/0702017
     Download presentation slides
     
     
172. Naoki Masuda, Hiroshi Kori.
     Formation of feedforward networks and frequency synchrony by spike-timing-dependent plasticity.
     Journal of Computational Neuroscience, 22, 327-345 (2007).
     Preprint: arXiv:1207.2816
     Preprint: HUSCAP, Hokkaido University (no article number)
     
     
173. Naoki Masuda, Masato Okada, Kazuyuki Aihara.
     Filtering of spatial bias and noise inputs by spatially structured neural networks.
     Neural Computation, 19, 1854-1870 (2007).
     
     
174. Naoki Masuda, Kazuyuki Aihara.
     Dual coding hypotheses for neural information representation.
     Mathematical Biosciences, 207, 312-321 (2007).
     
     
175. Naoki Masuda, Hisashi Ohtsuki.
     Tag-based indirect reciprocity by incomplete social information.
     Proceedings of the Royal Society B: Biological Sciences, 274, 689-695 (2007). [open access]
     Request the paper
     Download presentation slides
     
     
176. Yong-Yeol Ahn, Hawoong Jeong, Naoki Masuda, Jae Dong Noh.
     Epidemic dynamics of two species of interacting particles on scale-free networks.
     Physical Review E, 74, 066113 (2006).
     Preprint: arXiv:cont-mat/0608461
     
     
177. Naoki Masuda, Norio Konno.
     Networks with dispersed degrees save stable coexistence of species in cyclic competition.
     Physical Review E, 74, 066102 (2006).
     Preprint: arXiv:cond-mat/0603114
     
     
178. Yuichi Katori, Naoki Masuda, Kazuyuki Aihara.
     Dynamic switching of optimal neural codes in networks with gap junctions.
     Neural Networks, 19, 1463-1466 (2006).
     
     
179. Naoki Masuda, Norio Konno.
     Multi-state epidemic processes on complex networks.
     Journal of Theoretical Biology, 243, 64-75 (2006).
     Preprint: arXiv:cond-mat/0504329
     
     
180. Kazumichi Ohtsuka, Norio Konno, Naoki Masuda, Kazuyuki Aihara.
     Phase diagrams and correlation inequalities of a three-state stochastic epidemic model on the square lattice.
     International Journal of Bifurcation and Chaos, 16(12), 3687-3693 (2006).
     Preprint: METR (Mathematical Engineering Technical Reports) 2005-33, University of Tokyo
     
     
181. Naoki Masuda, Goce Jakimoski, Kazuyuki Aihara, Ljupco Kocarev.
     Chaotic block ciphers: from theory to practical algorithms.
     IEEE Transactions on Circuits and Systems Part I, 53(6), 1341-1352 (2006).
     
     
182. Naoki Masuda, Norio Konno.
     VIP-club phenomenon: emergence of elites and masterminds in social networks.
     Social Networks, 28, 297-309 (2006).
     Preprint: arXiv:cond-mat/0501129
     Download presentation slides
     
     
183. Naoki Masuda.
     Simultaneous rate-synchrony codes in populations of spiking neurons.
     Neural Computation, 18, 45-59 (2006).
     
     
184. N. Masuda, K.-I. Goh, B. Kahng.
     Extremal dynamics on complex networks: analytic solutions.
     Physical Review E, 72, 066106 (2005).
     Preprint: arXiv:cond-mat/0508623
     
     
185. Norio Konno, Naoki Masuda, Rahul Roy, Anish Sarkar.
     Rigorous results on the threshold network model.
     Journal of Physics A: Mathematical and General, 38, 6277-6291 (2005).
     Preprint: arXiv:math.PR/0505681
     Download presentation slides
     
     
186. Naoki Masuda, Brent Doiron, André Longtin, Kazuyuki Aihara.
     Coding of temporally varying signals in networks of spiking neurons with global delayed feedback.
     Neural Computation, 17, 2139-2175 (2005).
     
     
187. Naoki Masuda, Hiroyoshi Miwa, Norio Konno.
     Geographical threshold graphs with small-world and scale-free properties.
     Physical Review E, 71, 036108 (2005).
     Preprint: arXiv:cond-mat/0409378
     Download presentation slides
     
     
188. Naoki Masuda, Hiroyoshi Miwa, Norio Konno.
     Analysis of scale-free networks based on a threshold graph with intrinsic vertex weights.
     Physical Review E, 70, 036124 (2004).
     Preprint: arXiv:cond-mat/0403524
     Download presentation slides
     
     
189. Naoki Masuda, Norio Konno.
     Subcritical behavior in the alternating supercritical Domany-Kinzel dynamics.
     European Physical Journal B, 40, 313-319 (2004).
     Preprint: arXiv:cond-mat/0407745
     
     
190. Naoki Masuda, Norio Konno.
     Return times of random walk on generalized random graphs.
     Physical Review E, 69, 066113 (2004).
     Preprint: arXiv:cond-mat/0401255
     Download presentation slides
     
     
191. Naoki Masuda, Kazuyuki Aihara.
     Dual coding and effects of global feedback in multilayered neural networks.
     Neurocomputing, 58-60, 33-39 (2004).
     
     
192. Naoki Masuda, Norio Konno, Kazuyuki Aihara.
     Transmission of severe acute respiratory syndrome in dynamical small-world networks.
     Physical Review E, 69, 031917 (2004).
     Preprint: arXiv:cond-mat/0401598
     
     
193. Naoki Masuda, Kazuyuki Aihara.
     Self-organizing dual coding based on spike-time-dependent plasticity.
     Neural Computation, 16, 627-663 (2004).
     
     
194. Naoki Masuda, Kazuyuki Aihara.
     Global and local synchrony of coupled neurons in small-world networks.
     Biological Cybernetics, 90, 302-309 (2004).
     
     
195. Naoki Masuda, Kazuyuki Aihara.
     Spatial prisoner's dilemma optimally played in small-world networks.
     Physics Letters A, 313, 55-61 (2003).
     Download presentation slides
     
     
196. Naoki Masuda, Kazuyuki Aihara.
     Filtered interspike interval encoding by class II neurons.
     Physics Letters A, 311, 485-490 (2003).
     
     
197. Naoki Masuda, Kazuyuki Aihara.
     Ergodicity of spike trains: when does trial averaging make sense?
     Neural Computation, 15, 1341-1372 (2003).
     Request the paper
     
     
198. Naoki Masuda, Kazuyuki Aihara.
     Duality of rate coding and temporal spike coding in multilayered feedforward networks.
     Neural Computation, 15, 103-125 (2003).
     Request the paper
     
     
199. Naoki Masuda, Kazuyuki Aihara.
     Bridging rate coding and temporal spike coding by effect of noise.
     Physical Review Letters, 88, 248101 (2002).
     
     
200. Naoki Masuda, Kazuyuki Aihara.
     Spatiotemporal spike encoding of a continuous external signal.
     Neural Computation, 14, 1599-1628 (2002).
     Request the paper
     
     
201. Naoki Masuda, Kazuyuki Aihara.
     Dynamical characteristics of discretized chaotic permutations.
     International Journal of Bifurcation and Chaos, 12, 2087-2103 (2002).
     Request the paper
     
     
202. Naoki Masuda, Kazuyuki Aihara.
     Cryptosystems with discretized chaotic maps.
     IEEE Transactions on Circuits and Systems Part I, 49, 28-40 (2002).
     Request the paper
     
     
203. Naoki Masuda, Kazuyuki Aihara.
     Synchronization of pulse-coupled excitable neurons.
     Physical Review E, 64, 051906 (2001).
     
     
204. Henry D. I. Abarbanel, Naoki Masuda, M. I. Rabinovich, Evren Tumer.
     Distribution of mutual information.
     Physics Letters A, 281, 368-373 (2001).
     Request the paper
     Preprint: arXiv:nlin/0011016
     
     
205. Naoki Masuda, Yasunori Okabe.
     Time series analysis with wavelet coefficients.
     Japan Journal of Industrial and Applied Mathematics, 18, 129-158 (2001).
     Request the paper
     
     
The following copyright notices apply to the papers published in Physical Review Letters, Physical Review E, and Chaos, which can be downloaded on this webpage: Copyright American Institute of Physics as of the publication year. This article may be downloaded for personal use only. Any other use requires prior permission of the author and the American Institute of Physics.

Refereed conference papers

1. Masaki Ogura, Junpei Tagawa, Naoki Masuda.
   Distributed agreement on activity driven networks.
   Preprint: arXiv:1801.07412
   Presented in: 2018 American Control Conference.
   Wisconsin Center, Milwaukee, USA, June 27-29, 2018.
   
   
2. Xia Cui, Sadamori Kojaku, Naoki Masuda, Danushka Bollegala.
   Solving feature spareness in text classification using core-periphery decomposition.
   The Seventh Joint Conference on Lexical and Computational Semantics (*SEM 2018).
   New Orleans, USA, June 5-6 (2018).
   In: Proceedings, 255-264.
   
   
3. Naoki Masuda, Konstantin Klemm, Víctor M. Eguíluz.
   Slowing down of linear consensus dynamics on temporal networks: some theoretical extensions.
   4th IFAC Conference on Analysis and Control of Chaotic Systems.
   Tokyo, Japan, August 26-28 (2015).
   In: IFAC-PapersOnLine, 48-18, 187-192 (2015). [open access]
   Typos
   
   
4. Kodai Saito, Naoki Masuda.
   Two types of Twitter users with equally many followers.
   The 2013 IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM 2013).
   Niagara, Canada, August 25-28 (2013).
   In: Proceedings, 1425-1426.
   
   
5. Naoki Masuda, Tetsuya Fujie, Kazuo Murota.
   Application of semidefinite programming to maximize the spectral gap produced by node removal.
   4th Workshop on Complex Networks (CompleNet 2013).
   Berlin, March 13-15 (2013).
   In: Complex Networks IV, Studies in Computational Intelligence, 476, 155-163 (2013).
   Preprint: arXiv:1301.1503
   Preprint: METR (Mathematical Engineering Technical Reports) 2011-37, University of Tokyo
   Download presentation slides [pdf only]
   
   
6. Jin Seop Kim, Naoki Masuda, Byungnam Kahng.
   A priority queue model of human dynamics with bursty input tasks.
   First International Conference on Complex Sciences: Theory and Applications (Complex' 2009).
   Shanghai, China, February 23-25 (2009).
   In: Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, 5, 2402-2410 (2009).
   
   
7. Naoki Masuda, Hiroshi Kori.
   STDP enhances frequency synchrony in neural networks with a pacemaker.
   International Joint Conference on Neural Networks (IJCNN 2007).
   Orlando, Florida, USA, August 12-17 (2007).
   In: Proceedings of International Joint Conference on Neural Networks, 96-101 (2007).
   
   
8. Naoki Masuda, Shun-ichi Amari.
   Modeling memory transfer and savings in cerebellar motor learning.
   Neural Information Processing Systems (NIPS) 2005.
   Vancouver, Canada, December 5-10 (2005).
   In: Advances in Neural Information Processing Systems (Eds. Y. Weiss, B. Scholkopf, J. Platt), 18, 859-866 (2006).
   
   
9. Naoki Masuda, Kazuyuki Aihara.
   Collective behavior of pulse-coupled FitzHugh-Nagumo neurons.
   The 8th International Conference on Neural Information Processing (ICONIP 2001).
   Shanghai, China, November 14-18 (2001).
   In: Proceedings of ICONIP2001, Vol. 2, 910-915.
   
   
10. Naoki Masuda, Kazuyuki Aihara.
    Cryptosystems based on space-discretization of chaotic maps.
    The IEEE International Symposium on Circuits and Systems, 2001 (ISCAS 2001).
    Sydney, Australia, May 6-9 (2001).
    In: Proceedings of ISCAS 2001, III, 321-324.
    
    
11. Naoki Masuda, Kazuyuki Aihara.
    Cryptosystem based on a finite-state baker's map and its security analysis.
    1999 International Symposium on Nonlinear Theory and its Applications (NOLTA99).
    Hilton Waikoloa Village, Waikoloa, Hawaii, USA, November 28 - December 2 (1999).
    In: Proceedings of NOLTA'99, 613-616.
    
    

Books

1. Naoki Masuda, Christian L. Vestergaard.
   Gillespie algorithms for stochastic multiagent dynamics in populations and networks.
   Cambridge Elements, Cambridge University Press, Cambridge, UK (2022). [open access]
   Preprint: arXiv:2112.05293
   Python and C/C++ codes
   
   
2. Naoki Masuda, Renaud Lambiotte.
   A Guide to Temporal Networks.
   World Scientific, Singapore (2020).
   (The first edition was published in 2016.)
   
   
3. Naoki Masuda, Kwang-Il Goh, Tao Jia, Junichi Yamanoi, Hiroki Sayama. (Editors)
   Proceedings of NetSci-X 2020: Sixth International Winter School and Conference on Network Science.
   Springer, Cham, Switzerland (2020). On Amazon
   
   
4. Naoki Masuda, Petter Holme. (Editors)
   Temporal Network Epidemiology.
   Springer, Singapore (2017).
   On Amazon
   
   

Book chapters

1. Tomokatsu Onaga, James P. Gleeson, Naoki Masuda.
   The effect of concurrency on epidemic threshold in time-varying networks.
   In: Temporal Network Theory, Petter Holme and Jari Saramäki (Eds.), Springer, Cham (2019), pp. 253-267.
   The same chapter is in pp. 259--274 of Second Edition (2023).
   Request the paper
   
   
2. Naoki Masuda, Petter Holme.
   Introduction to temporal network epidemiology.
   In: Temporal Network Epidemiology, Naoki Masuda and Petter Holme (Eds.), Springer, Singapore (2017), pp. 1-16.
   Request the paper
   
   
3. Leo Speidel, Konstantin Klemm, Víctor M. Eguíluz, Naoki Masuda.
   Epidemic threshold in temporally-switching networks.
   In: Temporal Network Epidemiology, Naoki Masuda and Petter Holme (Eds.), Springer, Singapore (2017), pp. 161-177.
   Request the paper
   
   
4. Naoki Masuda, Taro Takaguchi, Nobuo Sato, Kazuo Yano.
   Self-exciting point process modeling of conversation event sequences.
   In: Temporal Networks, Petter Holme and Jari Saramäki (Eds.), Springer-Verlag, Berlin (2013), pp. 245-264.
   Preprint: arXiv:1205.5109
   
   

Editorials, commentaries, papers in institutional journals, papers for young adults, reports, English translation of Japanese papers, etc.

1. Aoi Naito, Naoki Masuda, Tatsuya Kameda.
   Collective intelligence under a volatile task environment: A behavioral experiment using social networks and computer simulations.
   Interdisciplinary Information Sciences, 30, 1-12 (2024). [open access]
   Preprint: https://doi.org/10.21203/rs.3.rs-1230730/v1
   
   
2. Naoki Masuda, Mason A. Porter.
   The waiting-time paradox.
   Frontiers for Young Minds, 8, 582433 (2021). [open access]
   Translation into Arabic
   Preprint: arXiv:2007.05883
   Also posted to: https://doi.org/10.31235/osf.io/uem6d
   
   
3. Teruyoshi Kobayashi, Naoki Masuda.
   Introduction to the special issue “Economics and Complex Networks”.
   Japanese Economic Review,72, 1-4 (2021). [open access]
   
   
4. Naoki Masuda, Francisco C. Santos.
   A mathematical look at empathy.
   eLife, 8, e47036 (2019). [open access]
   
   
5. Yoshimi Yoshino, Naoki Masuda.
   Evolution of cooperation is a robust outcome in the prisoner's dilemma on dynamic networks.
   Preprint: arXiv:1006.5791
   Presented in a domestic workshop on networks in Japan.
   
   
6. Akihiro Fujihara, Yusuke Ide, Norio Konno, Naoki Masuda, Hiroyoshi Miwa, Masato Uchida.
   Limit theorems for the average distance and the degree distribution of the threshold network model.
   Interdisciplinary Information Sciences, 15, 361-366 (2010). [open access]
   
   
7. Yusuke Ide, Norio Konno, Naoki Masuda.
   Limit theorems for some statistics of a generalized threshold network model.
   RIMS Kôkyûroku, 1551, 81-86 (2007). [open access]
   
   
8. Naoki Masuda, Kazuyuki Aihara.
   The prediction of chaotic time series with wavelet coefficients.
   Electronics and Communications in Japan, Part III (Fundamental Electronic Science), 84(6), 50-59 (2001).
   
   

Referee activities (論文査読者としての活動)

1. American Journal of Physical Anthropology
2. American Naturalist
3. Animal Behaviour
4. Annals of Applied Probability
5. Artificial Life and Robotics
6. Automatica
7. Behavioral Ecology
8. Bioinformatics
9. Biological Cybernetics
10. Biology Letters
11. BMC Evolutionary Biology
12. BMC Infectious Diseases
13. BMC Medical Genomics
14. Brain and Cognition
15. Bulletin of Mathematical Biology
16. Cerebral Cortex
17. Chaos
18. Chaos, Solitons & Fractals
19. Cognitive Neurodynamics
20. Communications Biology
21. Communications Physics
22. Communications in Nonlinear Science and Numerical Simulation
23. Complexity
24. Computational Social Networks
25. Current Zoology
26. Differential Equations and Dynamical Systems
27. Discrete Mathematics
28. Dynamic Games and Applications
29. Ecological Modelling
30. Ecological Research
31. Ecology and Evolution
32. eLife
33. Entropy
34. European Journal of Applied Mathematics
35. European Journal of Combinatorics
36. European Journal of Neuroscience
37. European Physical Journal B
38. Europhysics Letters
39. Evolutionary Bioinformatics
40. Fractals
41. Frontiers in Physics
42. Genome Biology
43. Human Brain Mapping
44. IEEE Journal on Selected Areas in Communications
45. IEEE Transactions on Circuits and Systems I
46. IEEE Transactions on Circuits and Systems II
47. IEEE Transactions on Control of Network Systems
48. IEEE Transactions on Evolutionary Computation
49. IEEE Transactions on Information Theory
50. IEEE Transactions on Network Science and Engineering
51. IEICE (an elec. engg. journal issued in Japan)
52. IET Control Theory & Applications
53. IET Systems Biology
54. International Journal of Behavioral Development
55. International Journal of Bifurcation and Chaos
56. International Journal of Environmental Research and Public Health
57. International Journal of Modern Physics C
58. Journal of Circuits, Systems, and Computers
59. Journal of Complex Networks
60. Journal of Conflict Resolution
61. Journal of Mathematical Biology
62. Journal of Neurophysiology
63. Journal of Physics A
64. Journal of Quantitative Analysis of Sports
65. Journal of Signal Transduction
66. Journal of Statistical Mechanics
67. Journal of Systems and Software
68. Journal of the Physical Society of Japan
69. Journal of the Royal Society Interface
70. Journal of Theoretical Biology
71. Mathematical Biosciences
72. Mathematical Problems in Engineering
73. Methods in Ecology and Evolution
74. Myrmecological News
75. Nature Communications
76. Nature Machine Intelligence
77. Nature Physics
78. Neural Networks
79. Neurocomputing
80. NeuroImage: Clinical
81. Neuropsychologia
82. New Journal of Physics
83. Nonlinearity
84. Physica A
85. Physica D
86. Physical Review E
87. Physical Review Letters
88. Physical Review Research
89. Physical Review X
90. Physics Letters A
91. PLoS Biology
92. PLoS Complex Systems
93. PLoS Computational Biology
94. PLoS ONE
95. Proceedings of the National Academy of Sciences of the United States of America
96. Proceedings of the Royal Society A
97. Proceedings of the Royal Society B
98. Royal Society Open Science
99. Science Advances
100. Scientific Reports
101. SIAM Journal on Applied Dynamical Systems
102. SIAM Journal on Applied Mathematics
103. SIAM Review
104. Social Network Analysis and Mining
105. Sociological Methodology
106. Stochastic Processes and their Applications
107. Trends in Neurosciences