Publications

📚 Peer-reviewed Papers

2025

Disentanglement of batch effects and biological signals across conditions in the single-cell transcriptome
Shunta Sakaguchi, Masato Tsutsumi, Kentaro Nishi, Honda Naoki
bioRxiv (April 16, 2025) PDF

2024

Deciphering the origin of developmental stability: The role of intracellular expression variability in evolutionary conservation
Yui Uchida, Masato Tsutsumi, Shunsuke Ichii, Naoki Irie, Chikara Furusawa
Evolution & Development (March 2024) PDF | Code

2023

A deep learning approach for morphological feature extraction based on variational auto-encoder: an application to mandible shape
Masato Tsutsumi, Nen Saito, Daisuke Koyabu, Chikara Furusawa
npj Systems Biology and Applications (July 6, 2023) PDF | Code

2022

A method for morphological feature extraction based on variational auto-encoder : an application to mandible shape
Masato Tsutsumi, Nen Saito, Daisuke Koyabu, Chikara Furusawa
Preprint (May 19, 2022)

2024

Development of quantitative analysis methods for biological morphology using deep learning
Japan Society for Industrial and Applied Mathematics Annual Meeting 2024 (September 16, 2024)
Development of quantitative analysis methods for biological morphology using deep learning
Online Seminar Series “Future of Evolutionary Biology with AI” (March 9, 2024)
Development of quantitative analysis methods for biological morphology using deep learning
8th Theoretical Immunology Workshop (February 14, 2024)

2022

Quantification of various biological morphologies using machine learning
Hiroshima University Mathematical Life Sciences Program Seminar (November 10, 2022)

2021

Quantification and application of biological morphology using machine learning: Focusing on primate mandibles
National Institute for Basic Biology Departmental Seminar (October 2021)

2025

Behavioral analysis of double mutant Drosophila larvae using DOLO (Drosophila tracking with YOLO)
1st Systems Behavioral Science Workshop (May 30, 2025)
Estimation of psychological state transitions during/after emergency declarations using energy landscape analysis
SSTB2025 - Spring School for Theoretical Biology 2025- (February 20, 2025)

2024

Proposal of morphological quantitative analysis methods using deep learning
Annual Meeting of the Japanese Society for Mathematical Biology 2024 (September 12, 2024)
Quantification of mouse behavior under social defeat stress using mathematical models
CPSY TOKYO 2024 (March 28, 2024)
Mathematical model of rumination in the brain using Bayesian inference
Spring School for Theoretical Biology 2024 (February 20, 2024)
Mathematical model of rumination in the brain using free energy principle
11th Annual Meeting of the Quantitative Biology Society (January 6, 2024)

2023

Unveiling the enigmatic Middle Devonian vertebrate, Palaeospondylus
The 3rd Asia Evo Conference Symposium (December 16, 2023)
Co-authors: Tatsuya Hirasawa, Masato Tsutsumi, Shunsuke Ichii, Shigeru Kuratani
Development of a quantitative analysis method for biological morphology using deep learning
Statphys28 Satellite meeting Statistical Physics and Information-Processing in Living Systems (August 8, 2023)

2022

Morphological feature extraction of primate mandibles using variational autoencoders
10th Annual Meeting of the Quantitative Biology Society (December 15, 2022)
A method for morphological feature extraction based on variational auto-encoder
60th Annual Meeting of the Biophysical Society of Japan (September 30, 2022)
A Deep learning approach for the shape analysis of the primates mandible
Euro Evo Devo 2022 (June 1, 2022)

Reviews & Commentary

Quantification of biological morphology using machine learning
Proceedings of the Physical Society of Japan 75.1 2878-2878 (2020)

Medical AI Related

Verification of classification methods for 2D OCT images using two-stage networks
2nd Japanese Society for Medical AI Academic Conference (January 31, 2020)
Co-authors: Masahiko Takemura, Masato Tsutsumi, Hiroki Kawai, Kazumi Hakamata, Hideyoshi Fuji