Probing the rules of cell coordination in live tissues by interpretable machine learning based on graph neural networks. - Takaki Yamamoto; Katie Cockburn; Valentina Greco; Kyogo Kawaguchi (PLoS Comput. Biol., 2022)

LapTrack: linear assignment particle tracking with tunable metrics. - Yohsuke T. Fukai; Kyogo Kawaguchi (Bioinform., 2023)

A Percolation Model of Emergence: Analyzing Transformers Trained on a Formal Language. - Ekdeep Singh Lubana; Kyogo Kawaguchi; Robert P. Dick; Hidenori Tanaka (ICLR, 2025)