Publications

54.

Investigating Fine-and Coarse-grained Structural Correspondences Between Deep Neural Networks and Human Object Image Similarity Judgments Using Unsupervised Alignment

Soh Takahashi*, Sasaki Masaru*, Ken Takeda, Masafumi Oizumi

Neural Networks, 195, 108222, 2026.*: equal contribution.
53.

Qualia Structures Collapse for Geometric Shapes, but Not Faces, When Spatial Attention Is Withdrawn

Elise Rowe, Ken Takeda, Masafumi Oizumi, Joanita D'Souza, Jeroen van Boxtel, Naotsugu Tsuchiya

Neuroscience of Consciousness, in press, 2026.
52.

Single-cell resolution functional networks during sleep are segregated into spatially intermixed modules

Daiki Kiyooka*, Ikumi Oomoto*, Jun Kitazono, Midori Kobayashi, Chie Matsubara, Kenta Kobayashi, Masanori Murayama**, Masafumi Oizumi**

Cell Reports, in press. , 2026.*, **: equal contribution
51.

Unsupervised Neuronal Matching with Spontaneous Neuronal ActivityUnsupervised Neuronal Matching with Spontaneous Neuronal Activity

Shunsuke Kamiya, Taiga Mitamura, Muneki Ikeda, Masafumi Oizumi

In ICLR 2025 Workshop on Representational Alignment, 2025.
50.

Unsupervised alignment reveals structural commonalities and differences in neural representations of natural scenes across individuals and brain areas

Ken Takeda*, Kota Abe*, Jun Kitazono, Masafumi Oizumi

iScience, 28, 5112427. , 2025.*: equal contribution.
49.

Unsupervised Alignment in Neuroscience: Introducing a Toolbox for Gromov-Wasserstein Optimal Transport

Ken Takeda*, Masaru Sasaki*, Kota Abe, Masafumi Oizumi

Journal of Neuroscience Methods, 419, 110443, 2025.*: equal contribution. The Toolbox is available on GitHub
48.

Quantifying state-dependent control properties of brain dynamics from perturbation responses

Yumi Shikauchi, Mitsuaki Takemi, Leo Tomasevic, Jun Kitazono, Hartwig R. Siebner, Masafumi Oizumi

bioRxiv: 2025-02, 2025.
47.

Principal bundle geometry of qualia: Understanding the quality of consciousness from symmetry

Masafumi Oizumi, Chanseok Lim, Ryota Kanai

PsyArXiv, 2025.
46.

Koopman Mode Decomposition of Thermodynamic Dissipation in Nonlinear Langevin Dynamics

Daiki Sekizawa, Sosuke Ito, Masafumi Oizumi

arXiv, 2025.
45.

Is my "red" your "red"?: Evaluating structural correspondences between color similarity judgments using unsupervised alignment

Genji Kawakita*, Ariel Zeleznikow-Johnston*, Ken Takeda*, Naotsugu Tsuchiya**, Masafumi Oizumi**

iScience, 28, 3, 112029, 2025.*, **: equal contribution
44.

Exploring internal representation of self-supervised networks: few-shot learning abilities and comparison with human semantics and recognition of objects

Asaki Kataoka, Yoshihiro Nagano, Masafumi Oizumi

Frontiers in Computational Neuroscience, in press, 2025.
43.

Designing optimal perturbation inputs for system identification in neuroscience

Mikito Ogino, Daiki Sekizawa, Jun Kitazono, Masafumi Oizumi

bioRxiv, 2025.
42.

Correspondence of High-Dimensional Emotion Structures Elicited by Video Clips Between Humans and Multimodal LLMs

Haruka Asanuma, Naoko Koide-Majima, Ken Nakamura, Takato Horii, Shinji Nishimoto, Masafumi Oizumi

Scientific Reports, 15, 32175, 2025.
41.

Consciousness or pseudo-consciousness? A clash of two paradigms

Tononi G, Albantakis L, Barbosa L, Boly M, Cirelli C, Comolatti R, Ellia F, Findlay G, Girardi Casali A, Grasso M, Haun AM, Hendren J, Hoel E, Koch C, Maier A, Marshall W, Massimini M, Mayner WGP, Oizumi M, Szczotka J, Tsuchiya N, Zaeemzadeh A

Nature Neuroscience, 28, 694–702, 2025.
40.

Association of bidirectional network cores in the brain with conscious perception and cognition

Taguchi, Tomoya, Jun Kitazono, Shuntaro Sasai, Masafumi Oizumi

The Journal of Neuroscience, 45(17), e0802242025, 2025.
39.

Koopman Operator Based Dynamical Similarity Analysis for Data-driven Quantification of Distance between Dynamics

Shunsuke Kamiya, Jun Kitazono, Masafumi Oizumi

In ICLR 2024 Workshop on Representational Alignment, 2024.
38.

Gromov–Wasserstein unsupervised alignment reveals structural correspondences between the color similarity structures of humans and large language models

Genji Kawakita, Ariel Zeleznikow-Johnston, Naotsugu Tsuchiya, Masafumi Oizumi

Scientific Reports 14 (1), 15917, 2024.
37.

Decomposing thermodynamic dissipation of linear Langevin systems via oscillatory modes and its application to neural dynamics

Daiki Sekizawa, Sosuke Ito, Masafumi Oizumi

Physical Review X 14 (4), 041003, 2024.
36.

Constructive Approach to Bidirectional Causation between Qualia Structure and Language Emergence

Tadahiro Taniguchi, Masafumi Oizumi, Noburo Saji, Takato Horii, Naotsugu Tsuchiya

arXiv:2409.09413, 2024.
35.

Optimal Control Costs of Brain State Transitions in Linear Stochastic Systems

Shunsuke Kamiya, Genji Kawakita, Shuntaro Sasai, Jun Kitazono, Masafumi Oizumi

The Journal of Neuroscience, 43 (2), 270-281, 2023.
34.

Quantifying brain state transition cost via Schrödinger's bridge

Genji Kawakita, Shunsuke Kamiya, Shuntaro Sasai, Jun Kitazono, Masafumi Oizumi

Network Neuroscience, 6 (1), 118–134, 2022.
33.

Bidirectionally connected cores in a mouse connectome: Towards extracting the brain subnetworks essential for consciousness

Jun Kitazono, Yuma Aoki, Masafumi Oizumi

Cerebral Cortex, bhac143, 2022.
32.

Information flow in the rat thalamo-cortical system: spontaneous vs. stimulus-evoked activities

Kotaro Ishizu, Tomoyo I. Shiramatsu, Rie Hitsuyu, Masafumi Oizumi, Naotsugu Tsuchiya, Hirokazu Takahashi

Scientific Reports, 11(19252), 2021.
31.

Fast scanning high optical invariant two-photon microscopy for monitoring a large neural network activity with cellular resolution

Keisuke Ota, Yasuhiro Oisi, Takayuki Suzuki, Muneki Ikeda, Yoshiki Ito, Tsubasa Ito, Kenta Kobayashi, Midori Kobayashi, Maya Odagawa, Chie Matsubara, Yoshinori Kuroiwa, Masaru Horikoshi, Junya Matsushita, Hiroyuki Hioki, Masamichi Ohkura, Junichi Nakai, Masafumi Oizumi, Atsushi Miyawaki, Toru Aonishi, Takahiro Ode, Masanori Murayama

Neuron, 109(11), 1810-1824, 2021.
30.

Unified framework for the entropy production and the stochastic interaction based on information geometry

Sosuke Ito, Masafumi Oizumi, Shun-ichi Amari

Physical Review Research, 2, 033048, 2020.
29.

Efficient search for informational cores in complex systems: Application to brain networks

Jun Kitazono, Ryota Kanai, Masafumi Oizumi

Neural Networks, 132, 232-244, 2020.
28.

An Information Theoretic Approach to Reveal the Formation of Shared Representations

Akihiro Eguchi, Takato Horii, Takayuki Nagai, Ryota Kanai, Masafumi Oizumi

Frontiers in Computational Neuroscience, 2020.
27.

A general spectral decomposition of causal influences applied to integrated information

Dror Cohen, Shuntaro Sasai, Naotsugu Tsuchiya, Masafumi Oizumi

The Journal of Neuroscience Methods, 330, 108443, 2020.
26.

Statistical Neurodynamics of Deep Networks: Geometry of Signal Spaces

Shun-ichi Amari, Ryo Karakida, Masafumi Oizumi

Nonlinear Theory and Its Applications, IEICE, 10(4), 322-336, 2019.
25.

Information Geometry for Regularized Optimal Transport and Barycenters of Patterns

Shun-ichi Amari, Ryo Karakida, Masafumi Oizumi, Marco Cuturi

Neural Computation, 31(5), 827-848, 2019.
24.

Fisher Information and Natural Gradient Learning in Random Deep Networks

Shun-ichi Amari, Ryo Karakida, Masafumi Oizumi

Proceedings of Machine Learning Research, in PMLR 89:694-702, 2019.
23.

Information Geometry Connecting Wasserstein Distance and Kullback-Leibler Divergence via the Entropy-Relaxed Transportation Problem

Shun-ichi Amari, Ryo Karakida, Masafumi Oizumi

Information Geometry, 1(1), 1-25, 2018.
22.

Fast and exact search for the partition with minimal information loss

Shohei Hidaka, Masafumi Oizumi

PLoS ONE, 13(9), e0201126, 2018.
21.

Efficient Algorithms for Searching the Minimum Information Partition in Integrated Information Theory

Jun Kitazono, Ryota Kanai, Masafumi Oizumi

Entropy, 20(3), 173, 2018.
20.

Contents of Consciousness Investigated as Integrated Information in Direct Human Brain Recordings

Andrew M. Haun, Masafumi Oizumi, Christopher K Kovach, Hiroto Kawasaki, Hiroyuki Oya, Matthew A Howard, Ralph Adolphs, Naotsugu Tsuchiya

eNeuro, ENEURO-0085-17, 2017.
19.

Unified Framework for Information Integration Based on Information Geometry

Masafumi Oizumi, Naotsugu Tsuchiya, Shun-ichi Amari

Proceedings of the National Academy of Sciences, 113(51), 14817-14822, 2016.
18.

Measuring Integrated Information from the Decoding Perspective

Masafumi Oizumi, Shun-ichi Amari, Toru Yanagawa, Naotaka Fujii, Naotsugu Tsuchiya

PLoS Comput Biol, 12(1), e1004654, 2016.
17.

Geometry of information integration

Shun-ichi Amari, Naotsugu Tsuchiya, Masafumi Oizumi

Information Geometry and its Applications IV (pp. 3-17). Springer, Cham, 2016.
16.

Stimulus Set Meaningfulness and Neurophysiological Differentiation: A Functional Magnetic Resonance Imaging Study

Melanie Boly, Shuntaro Sasai, Olivia Gosseries, Masafumi Oizumi, Adenauer Casali, Marcello Massimini, Giulio Tononi

PLoS ONE, 10(5): e0125337, 2015.
15.

From the Phenomenology to the Mechanisms of Consciousness: Integrated Information Theory 3.0

Masafumi Oizumi*, Larissa Albantakis*, Giulio Tononi

PLoS Computational Biology, 10, e1003588, 2014.*: equal contribution
14.

A leaky-integrator model as a control mechanism underlying flexible decision making during task switching

Akinori Mitani, Ryo Sasaki, Masafumi Oizumi, Takanori Uka

PLoS ONE, 8, e59670, 2013.
13.

Theory of correlation in a network with synaptic depression

Yasuhiko Igarashi, Masafumi Oizumi, Masato Okada

Physical Review E 85, 016108, 2012.
12.

Functional differences between global pre- and postsynaptic inhibition in the Drosophila olfactory circuit

Masafumi Oizumi, Ryota Satoh, Hokto Kazama, Masato Okada

Frontiers in Computational Neuroscience, 6:14, 2012.
11.

Information loss associated with imperfect observation and mismatched decoding

Masafumi Oizumi, Masato Okada, Shun-ichi Amari

Frontiers in Computational Neuroscience, 5:9, 2011.
10.

Influence of synaptic depression on memory storage capacity

Yosuke Otsubo, Kenji Nagata, Masafumi Oizumi, Masato Okada

Journal of the Physical Society of Japan, 80, 084004, 2011.
9.

Mismatched decoding in the brain

Masafumi Oizumi, Toshiyuki Ishii, Kazuya Ishibashi, Toshihiko Hosoya, Masato Okada

The Journal of Neuroscience, 30, 4815-4826, 2010.
8.

Mechanisms of maximum information preservation in the Drosophila antennal lobe

Ryota Satoh*, Masafumi Oizumi*, Hokto Kazama, Masato Okada

PLoS ONE, 5, e10644, 2010. *: equal contribution, 2010.
7.

Mean field analysis of stochastic neural network models with synaptic depression

Yasuhiko Igarashi, Masafumi Oizumi, Masato Okada

Journal of the Physical Society of Japan, 79, 084001, 2010.
6.

Instabilities in associative memory model with synaptic depression and switching phenomena among attractors

Yosuke Otsubo, Kenji Nagata, Masafumi Oizumi, Masato Okada

Journal of the Physical Society of Japan, 79, 084002, 2010.
5.

Analytical investigation of the effects of lateral connections on the accuracy of population coding

Masafumi Oizumi, Keiji Miura, Masato Okada

Physical Review E, 81, 051905, 2010.
4.

Statistical mechanics of attractor neural network models with synaptic depression

Yasuhiko Igarashi, Masafumi Oizumi, Yosuke Otsubo, Kenji Nagata, Masato Okada

Journal of Physics Conference Series, 197, 012018, 2009.
3.

A general framework for investigating how far the decoding process in the brain can be simplified

Masafumi Oizumi, Toshiyuki Ishii, Kazuya Ishibashi, Toshihiko Hosoya, Masato Okada

Advances in Neural Information Processing Systems, 21, 1225-1232, 2009.
2.

Rate reduction for associative memory model in Hodgkin-Huxley-type network

Masafumi Oizumi, Yoichi Miyawaki, Masato Okada

Journal of the Physical Society of Japan, 77(6), 064802, 2008.
1.

Higher order effects on rate reduction for networks of Hodgkin-Huxley neurons

Masafumi Oizumi, Yoichi Miyawaki, Masato Okada

Journal of the Physical Society of Japan, 76(4), 044803, 2007.