Professor Jonathan Miller



From cephalopod camouflage and covid pandemiology to human cognition, natural language processing, and genome evolution, the mission of the Physics and Biology unit is to enable data to find its own voice through analytical, numerical, and machine-learning methods.

1. Staff

  • Dr. Shotaro Funai, Staff Scientist
  • Dr. Reuven Pnini, Technician
  • John Parker, Technician
  • Dr. Zdenek Lajbner, Technician
  • Dr. Lucia Zifcakova, Postdoctoral Scholars  (Nov 2021-)
  • Dr. Giovanni Masucci (Sep 2021-)
  • Mayu Suzuki, Research Unit Administrative Assistant

2. Collaborations

2.1 Marine ecosystems and organisms under anthropogenic pressure

  • Type of collaboration: Joint research
  • Researchers:
    • Professor James Davis Reimer, University of the Ryukyus
    • Dr. Giovanni Diego Masucci, OIST

2.2 Comparison of neural activity in human brain and artificial intelligence

  • Type of collaboration: Joint research
  • Researchers:
    • Professor Satoshi Iso, KEK (High Energy Accelerator Research Organization)
    • Dr. Shotaro Shiba Funai, OIST
    • Professor Junichi Chikazoe, NIPS (National Institute for Physiological Sciences)
    • Professor Naokazu Goda, NIPS
    • Professor Teppei Matsui, Okayama University
    • Professor Daichi Mochihashi, ISM (The Institute of Statistical Mathematics)
    • Professor Masayuki Asahara, NINJAL (National Institute for Japanese Language and Linguistics)
    • Professor Yutaka Shikano, Gunma University
    • Hirono Kawashima, Keio University

2.3 Epidemic dynamics in inhomogeneous populations and the role of superspreaders

  • Type of collaboration: Joint Research
  • Researchers:
    • Kyle Kawagoe, Department of Physics, Kadanoff Center for Theoretical Physics, University of Chicago, Chicago, Illinois 60637, USA
    • Mark Rychbovsky, Department of Mathematics, Columbia University, New York, New York 10027, USA
    • Serena Chang, Department of Computer Science, Stanford University, Stanford, California 94305, USA
    • Greg Huber, Chan Zuckerberg Biohub, San Francisco, California 94158, USA
    • Lucy M Li, Chan Zuckerberg Biohub, San Francisco, California 94158, USA
    • Jonathan Miller, Okinawa Institute of Science and Technology, Onna-son, Okinawa 904-0495, Japan
    • Reuven Pnini, Okinawa Institute of Science and Technology, Onna-son, Okinawa 904-0495, Japan
    • Boris Veytsman,  Chan Zuckerberg Initiative, Redwood City, California 9 4063, USA and School of Systems Biology, George Mason University, Fairfax VA 20030
    • David Ylanes, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), 50018 Zaragoza, Spain and CZBiohub, San Francisco, California 94158, USA

3. Activities and Findings

3.1 Squid adjust their body color according to substrate

Contributors: Ryuta Nakajima, Zdeněk Lajbner, Michael J. Kuba, Tamar Gutnick, Teresa L. Iglesias, Keishu Asada, Takahiro Nishibayashi, Jonathan Miller

Coleoid cephalopods camouflage on timescales of seconds to match their visual surroundings. To date, studies of cephalopod camouflage-to-substrate have been focused primarily on benthic cuttlefish and octopus, because they are readily found sitting on the substrate. In contrast to benthic cephalopods, oval squid (Sepioteuthis lessoniana species complex) are semi-pelagic animals that spend most of their time in the water column. In this study, we demonstrate that in captivity, S. lessoniana Sp.2 (Shiro-ika, white-squid) from the Okinawa archipelago, Japan, adapts the coloration of their skin using their chromatophores according to the background substrate. We show that if the animal moves between substrates of different reflectivity, the body patterning is changed to match. Chromatophore matching to substrate has not been reported in any loliginid cephalopod under laboratory conditions. Adaptation of the chromatophore system to the bottom substrate in the laboratory is a novel experimental finding that establishes oval squid as laboratory model animals for further research on camouflage.



3.2 Local stressors and changes across coastal habitats and benthic diversity in Okinawa 

Within Japan and globally, there is now a great need to focus on environmental assessment of marine ecosystems. There is a clear need for scientific and neutral evaluation of the state of the marine costal ecosystems of Okinawa Main Island which has been interested by several land reclamation and industrial development projects We compared impacted and natural coastal ecosystems and their organisms on both the east and west coasts of Okinawa, documenting increased environmental degradation in conjunction with coastal development such as landfill and artificial beaches. 
Results suggest both potentially less impacting development strategies and methods to minimize future impacts via conservation, or reconciliatory/rehabilitation strategies.

Figure 1: Coastline alteration categories.

(A) Natural coastline (east Kunigami). Vegetation acts as buffer between shoreline and road. (B) Soft armoring (Odo). Beach and vegetation preserved but disconnected due to the presence of human-made structures above the intertidal zone. (C) Hard armoring (west Kunigami). Roads or buildings built next to the coastline. Presence of seawalls and/or breakwaters. (D) Land-filling (Agarihama/Agarizaki). The yellow line indicates the original shoreline before reclamation.

Figure 2: Human-made alterations to the Okinawa Island coastline.

The four main coastline alteration categories are represented by different colors and summarized in the pie chart, which shows their relative abundances (%). 


3.3 Comparison of neural activity for appreciation of Japanese tanka in human brain and artificial intelligence

Contributors: Shotaro Shiba Funai (OIST), Satoshi Iso (KEK), Junichi Chikazoe (NIPS), Naokazu Goda (NIPS), Teppei Matsui (Okayama Univ.), Daichi Mochihashi (ISM), Shinsuke Koyama (ISM), Masayuki Asahara (NINJAL), Yutaka Shikano (Gunma Univ.), Hirono Kawashima (Keio Univ.),  Nohiro Sadato (NIPS)

Recently machine learning methods in natural language processing (NLP) have been developing rapidly. A state-of-the-art machine learning such as BERT (Bidirectional Encoder Representations from Transformers) is able to comprehend semantics from such ordinary (nonverse) sentences at a level close to that of humans.

Apart from nonverse sentences, natural languages possess specialized formats for communicating aesthetic nuances. For example, a Japanese tanka is a short verse of only 31 syllables. A tanka often includes phrases with meaning beyond their literal sense to evoke emotion in the human reader.

However, it is unknown whether verse sentence comprehension is a simple extension of nonverse sentence comprehension. To investigate this question, we conducted fMRI experiments where subjects are asked to discriminate poetic sentences from non-poetic ones. In addition, we investigated whether a trained BERT appreciates a tanka like humans.

Comparing the fMRI data in reading tankas and nonverse sentences, we found that brain patterns show differences in several regions. Similarly, BERT representations of tankas also differ from those of nonverse sentences when we visualize them with the PCA (principal component analysis). These preliminary results suggest that both human brains and BERT have acquired distinguishable representations for tankas and nonverse sentences.

Figure 1: Correlation of human brain regions and BERT layers for reading tankas and nonverse sentences. We found that deeper layers (red colored) of BERT correspond to brain area correlated with the judgement (poetic or not).

3.4 Epidemic dynamics in inhomogeneous populations and the role of superspreaders

Contributors: Kyle Kawagoe (U Chicago), Mark Rychnovsky (Columbia U), Serena Chang (Stanford), Greg Huber (CZbiohub), Lucy M. Li (CZbiohub), Jonathan Miller (OIST), Reuven Pnini (OIST), Boris Veytsman (CZI, George Mason U), and David Yllanes (CZbiohub, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), 50018 Zaragoza, Spain)

A variant of the SIR model for an inhomogeneous population is introduced in order to account for the effect of variability in susceptibility and infectiousness across a population. An initial formulation of this dynamics leads to infinitely many differential equations. Our model, however, can be reduced to a single first-order one-dimensional differential equation. Using this approach, we provide quantitative solutions for different distributions. In particular, we use GPS data from $10^7$ cellphones to determine an empirical distribution of the number of individual contacts and use this to infer a possible distribution of susceptibility and infectivity. 

We quantify the effect of superspreaders on the early growth rate R0 of the infection and on the final epidemic size, the total number of people who are ever infected. We discuss the features of the distribution that contribute most to the dynamics of the infection. DOI:10.1103/PhysRevResearch.3.033283

4. Publications

4.1 Journals

  1. Greg Huber, Mason Kamb, Kyle Kawagoe, Lucy M Li, Aaron McGeever, Jonathan Miller, Boris Veytsman, Dan Zigmond, "A minimal model for household-based testing and tracing in epidemics​", Physical biology 18 (4), 045002, May 19, 2021,  DOI: https://iopscience.iop.org/article/10.1088/1478-3975/abdacd/meta
  2. Keishu Asada, Ryuta Nakajima, Takahiro Nishibayashi, Fabienne Ziadi-Künzli, Zdeněk Lajbner, Jonathan Miller, Tamar Gutnick, Michael J Kuba, "Improving Keeping for Octopuses by Testing Different Escape-Proof Designs on Tanks for “Big Blue Octopus”(Octopus cyanea)", Applied Sciences Vol. 11, Issue 18, 8547. September 14, 2021, DOI: https://doi.org/10.3390/app11188547  
  3. K. Kawagoe, M. Rychnovsky, S. Chang, G. Huber, L. M. Li, J. Miller, R. Pnini, B. Veytsman, and D. Yllanes, "Epidemic dynamics in inhomogeneous populations and the role of superspreaders", Physical Review Research, Vol 3, Issue 3, page 033283-1:16,  27 September 2021, DOI:10.1103/PhysRevResearch.3.033283
  4. Masucci, G. D., Biondi, P., & Reimer, J. D., “Impacts of coastal armouring on rubble mobile cryptofauna at shallow coral reefs in Okinawa”, Plankton and Benthos Research, 16(4), 237-248, November 2021, DOI: https://doi.org/10.3800/pbr.16.237, URL: https://www.jstage.jst.go.jp/article/pbr/16/4/16_B160404/_article/-char/ja/, File attachment: https://www.jstage.jst.go.jp/article/pbr/16/4/16_B160404/_pdf/-char/ja
  5. Masucci, G. D., Biondi, P., & Reimer, J. D., “A Comparison of Size, Shape, and Fractal Diversity Between Coral Rubble Sampled From Natural and Artificial Coastlines Around Okinawa Island, Japan”, Frontiers in Marine Science, 1653, November 08, 2021, DOI: https://doi.org/10.3389/fmars.2021.703698 ,URL: https://www.frontiersin.org/articles/10.3389/fmars.2021.703698/full, File attachment: https://www.frontiersin.org/articles/10.3389/fmars.2021.703698/pdf
  6. Das, R. R., Wada, H., Masucci, G. D., Singh, T., Tavakoli-Kolour, P., Wada, N., ... & Reimer, J. D., "Four-Year Field Survey of Black Band Disease and Skeletal Growth Anomalies in Encrusting Montipora spp. Corals around Sesoko Island, Okinawa", Diversity, 14(1), 32. Publication date: 4 January 2022 Type: Research, DOI: https://doi.org/10.3390/d14010032, URL: https://www.mdpi.com/1424-2818/14/1/32, File attachment: https://www.mdpi.com/1424-2818/14/1/32/pdf
  7. Carolina Diaz Arenas, Aleksandra Ardaševa, Jonathan Miller, Alexander S. Mikheyev & Yohei Yokobayashi, "Ribozyme Mutagenic Evolution: Mechanisms of Survival", Origins of Life and Evolution of Biospheres (2022), 07 January 2022, DOI: https://link.springer.com/article/10.1007/s11084-021-09617-0 
  8. Reimer JD, Albelda RL, Biondi P, Hardianto E, Huang S, Masucci GD, Sayco SLG, Wee HB, Zhu Y, "Literature review of coral reef Restoration in and around the coral triangle from the viewpoint of Marine Biodiversity", Arquivos de Ciências do Mar, v.55, pp. 413-431, 21 March 2022, DOI: https://doi.org/10.32360/acmar.v55iEspecial.78183, URL:  http://www.periodicos.ufc.br/arquivosdecienciadomar/article/view/78183, File attachment: http://www.periodicos.ufc.br/arquivosdecienciadomar/article/view/78183/218382
  9. Ryuta Nakajima, Zdeněk Lajbner, Michael J. Kuba, Tamar Gutnick, Teresa L. Iglesias, Keishu Asada, Takahiro Nishibayashi & Jonathan Miller, "Squid adjust their body color according to substrate", Scientific Reports 12, 5227. 28 March 2022, DOI: https://doi.org/10.1038/s41598-022-09209-6, URL: https://www.nature.com/articles/s41598-022-09209-6
  10. Tláskal, V., Pylro, V.S., Žifčáková, L., Baldrian, P., Ecological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood.  Frontiers in Microbiology, 2021, 12, 668644
  11. Arora, Jigyasa and Kinjo, Yukihiro and Šobotník, Jan and Buček, Aleš and Clitheroe, Crystal and Stiblik, Petr and Roisin, Yves and Žifčáková, Lucia and Park, Yung Chul and Kim, Ki Yoon and Sillam-Dussès, David and Hervé, Vincent and Lo, Nathan and Tokuda, Gaku and Brune, Andreas and Bourguignon, Thomas, The Functional Evolution of Termite Gut Microbiota. Microbiome 10, 78 (2022). https://doi.org/10.1186/s40168-022-01258-3

4.2 Books and other one-time publications

Nothing to report

4.3 Oral and Poster Presentations

[Poster Presentation]

  1. Shotaro Shiba Funai, “Comparison of neural activity for appreciation of Japanese tanka in human brain and artificial intelligence”, the 44th Annual Meeting of the Japan Neuroscience Society and the 1st CJK International meeting, Kobe Convention Center (Japan) and online, July 31, 2021
  2. Shotaro Shiba Funai, “Comparison of neural activity for appreciation of Japanese tanka in human brain and artificial intelligence”, RIKEN-OIST Joint Symposium: Kinds of Minds, Oct. 7, 2021,


  1. Shotaro Funai / 船井 正太郎, “Towards the development of AI to write sentences getting close to each person/「一人一人に寄り添う文章」が書けるAIの開発にむけて”, AI research society, Graduate School of Management, GLOBIS University / グロービス経営大学院人工知能研究会, August 13, 2021
  2. Shotaro Shiba Funai / 船井(柴)正太郎, “Toward AI that can write sentences for each person” / 一人一人に寄り添う文章が書けるAIを目指して, Tech BASE Okinawa (https://techbaseokinawa.com/), Dec. 18, 2021,
  3. Lucia Zifcakova, "Skill Pill Terminal", OIST, Feb. 7, Feb. 9, Feb. 14 2022
  4. Lucia Zifcakova, Zdenek Lajbner, Jonathan Miller, "Omni-C genome of Sepioteuthis lessoniana" CIAC2022/2/4 online meeting

[Conference Invited Lecture]

  1. Shotaro Shiba Funai, “Feature extraction of machine learning and phase transition point of Ising model”, ECT* workshop: Machine Learning for High Energy Physics on and off the Lattice, ECT* (Italy) and online, September 30, 2021
  2. Zdenek Lajbner, Ryuta Nakajima, Jonathan Miller, "Oval squids as model animals", 第四回 イカ・タコ研究会, on the web, October 23, 2021
  3. Rocktim Ramen DAS, Haruka WADA, Giovanni D. MASUCCI, Tanya SINGH, Parviz TAVAKOLI-KOLOUR, Naohisa WADA, Sen-Lin TANG, Hideyuki YAMASHIRO, James Davis REIMER, “Four-year field survey of Black Band Disease and Skeletal Growth Anomalies in encrusting Montipora spp. corals around Sesoko Island, Okinawa., JCRS (Japanese Coral Reef Society) 24th annual meeting, Location: Remote, November 28-29, 2021


  1. 船井 正太郎 / Shotaro Funai, “燃えよ!研究の志士たち”, CBC Radio/CBCラジオ https://hicbc.com/radio/kenkyu/ July 11 & 18, 2021

5. Intellectual Property Rights and Other Specific Achievements

Nothing to report

6. Meetings and Events

Nothing to report

6.1 Seminar Title in Full

Nothing to report

7. Other

Nothing to report.