FY2018 Annual Report


Cephalophysics: psychophysics in the tradition of Helmholtz, applied to cephalopod perception, camouflage and social interaction.

Compression, Inference, Machine learning: Quantum and Classical. AI via Reverse Engineering of Animal Intelligence. Theoretical Condensed Matter Physics.

Physics and Biology Unit
Associate Professor Jonathan Miller



By a fluke of evolution, cephalopods report their perceptions of their visual surroundings in real time through their skin color and texture. We adapt human natural vision concepts and technologies to cephalopod perception, supplemented by single-cell recording and transgenics.



1. Staff

  • Dr. Michael Kuba, Staff Scentist 
  • Dr. Shotaro Funai, Staff Scentist (July 2018 -  )
  • Dr. Tamar Gutnick, Postdoctoral Scholar 
  • Dr. Teresa Igelsias, Postdoctoral Scholar 
  • Dr. Jay Culligan, Postdoctoral Scholar (  - August 2018)
  • Dr. Fabienne Ziadi, Technician  (  - June 2018)
  • Dr. Zdenek Lajbner, Technician
  • Dr. Reuven Pnini, Technician
  • Keishu Asada, Technician
  • Takahiro Nishibayashi, Technician (December 2018 -  )
  • Midori Tanahara, Administrative Assistant

2. Collaborations

2.1 Thermal selection shapes mitochondrial genome evolution.

  • Type of collaboration: Joint research
  • Researchers:
    • Professor DK Dowling, Monash University.
    • MF Camus, Monash University.
    • Z Lajbner, R Pnini, J Miller, OIST.

3. Activities and Findings

3.1 Cephalopod Camoufalge

















































4. Publications

4.1 Journals

  1. Dornburg, A., Warren, D. L., Zapfe, K. L., Morris, R., Iglesias, T. L., Lamb, A., Hogue, G., Lukas, L. & Wong, R.  Testing ontogenetic patterns of sexual size dimorphism against expectations of the expensive tissue hypothesis, an intraspecific example using oyster toadfish (Opsanus tau). Ecol Evol8, 3609-3616, doi:10.1002/ece3.3835 (2018).
  2. Iglesias, T. L., Dornburg, A., Warren, D. L., Wainwright, P. C., Schmitz, L. & Economo, E. P.  Eyes Wide Shut: the impact of dim-light vision on neural investment in marine teleosts. J Evol Biol31, 1082-1092, doi:10.1111/jeb.13299 (2018).
  3. Lajbner, Z., Pnini, R., Camus, M. F., Miller, J. & Dowling, D. K.  Experimental evidence that thermal selection shapes mitochondrial genome evolution. Sci Rep 8, 9500, doi:10.1038/s41598-018-27805-3 (2018).
  4. Shiba Funai, S. & Giataganas, D. Thermodynamics and Feature Extraction by Machine Learning. arXiv (2018). https://arxiv.org/abs/1810.08179

4.2 Books and other one-time publications

  1. Kuba, M.  11 Vertebrate/Invertebrate – When do we start caring?, in Animal Wellfare in Changing World,Vol. 1  (ed Butterworth Andrew), Ch. 11, pages 108-113, CAB International(2018)
  2. Mather, J. A. & Kuba, M. J.  14 Octopuses – Mind in the Waters, in Field and Laboratory Methods in Animal Cognition: A Comparative Guide,  (eds Bueno-Guerra. Nereida. & Amici.Federica.), Ch. 14, pages 308-328, Cambridge University Press (2018).

4.3 Oral and Poster Presentations

[Conference invited Lecture]

  1. Shiba Funai, S. Renormalization, Thermodynamics, and Feature Extraction of Machine Learning, Nagoya University, JAPAN (2018).

[Oral Presentations]

  1. Miller, J.  Octopus hatchlings Flash Red When Exposing to Ketamine,  MBL (Marine Biological Laboratory), Woods Hole, MA, US. (2018).
  2. Miller, J.  Psychophysics of Cephalopod Camouflage,  Aspen Center for Physics, Aspen, CO, USA. (2018).

[Poster Presentations]

  1. Asada, K., Gutnick, T., Nishibayashi, T., Ziadi, F., Lajbner, Z., Iglesias, T. L., Miller, J. & Kuba, M.  Improving keeping and welfare for captive Octopus cyanea trough environmental enrichment St Petersburg, FL. (2018).
  2. Gutnick, T., Lajbner, Z., Iglesias, T. L., Nakajima, R., Miller, J. & Kuba, M. J.  Predatory behavior in the Broadclub Cuttlefish (Sepia latimanus),  Liverpool, England, UK (2018).
  3. Iglesias, T. L., Gutnick, T., Lajbner, Z., Miller, J. & Kuba, M.  Preliminary observations of the ‘sleep-like’ resting state in the broadclub cuttlefish, Sepia latimanus,  Liverpool, England, UK (2018).
  4. Lajbner, Z., Gutnick, T., Nishibayashi, T., Ziadi, F., Asada, K., Iglesias, T. L., Miller, J. & Kuba, M.  Captive breeding of the oval squid (Aori-ika; Sepioteuthis sp.),  St. Petersburg, FL. (2018).
  5. Nishibayashi, T., Miller, J., Kuba, M. J. & Gutnick, T. Social behaviour in big fin reef squid, Liverpool, England, UK (2018).
  6. 船井(柴)正太郎, 磯暁, 横尾純斗.平面図形の深層学習と複数の固定点を持つ繰り込み群との関係II. 日本物理学会2018年秋季大会. 長野(日本).Funai, S. S., Iso, S. & Yokoo, S. Presentation Relation of machine learning on plane figures and renormalization flow with multiple fixed points II,  Shinshu University, Nagano, Japan (2018). 


  1. Miller, J.  Psychophysics of Cephalopod Camouflage: Life as GIM in a GAN, CBM&M, Massachusetts Institute of Technology (MIT) (2018).
  2. Shiba Funai, S.  Renormalization, Thermodynamics, and Feature Extraction of Machine Learning, Tohoku University (2018).
  3. 船井(柴)正太郎. 認識の物理学にむけて.文教大学. 2018年12月21日. Shiba Funai, S. Towards physics of recognition. Bunkyo University (2018).

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

6.1 Seminar "Generalization in Deep Networks"

  • Date: June 21, 2018
  • Venue: OIST Campus Lab1
  • Speaker: Dr. Andrzej Banburski, Postdoctoral Researcher, MIT

6.2 Seminar "Random coefficients autoregressive processes and the PUCK model with fluctuating potential: application to the diffusion of market prices" 

  • Date: June 25, 2018
  • Venue: OIST Campus Lab1
  • Speaker: Mr. Arthur Yamashita, PhD student at Tokyo Institute of Technology

6.3 Seminar “Singular-Value-Decomposition Analysis of Holography and Renormalization Group” 

  • Date: January 11, 2019
  • Venue: OIST Campus Lab1
  • Speaker: Prof. Hiroaki Matsueda, Vice President (Advanced Course) in National Institute of Technology, Sendai College

6.4 Seminar "Statistical Challenge and Promise: Big Data, Sampling Bias" 

  • Date: January 28, 2019
  • Venue: OIST Campus Seminar Room C209
  • Speaker: Prof. Yu Shen, MD Anderson Cancer Center

6.5 Lecture to high school students “頭足類の世界 The world of cephalopod" 

  • Date: February 29, 2019
  • Venue: OIST
  • Visitors: Gushikawa High School students
  • Speaker: Takahiro Nishibayashi, Research Unit Technician, OIST

6.6 Lecture to high school students ““イカ・タコと私 - Squid, Octopus and my life -"  

  • Date: March 22, 2019
  • Venue: Yaeyama High School
  • Speaker: Takahiro Nishibayashi, Research Unit Technician, OIST

6.7 Lecture to high school students “イカ・タコの不思議な世界をのぞいてみよう - Let’s learn the wonderful world of cephalopod -" 

  • Date: March 23, 2019
  • Venue: Ishigaki island 
  • Speaker: Takahiro Nishibayashi, Research Unit Technician, OIST

7. Other

Nothing to report.