Novel metric for hyperbolic phylogenetic tree embeddings

Hirotaka Matsumoto*, Takahiro Mimori, Tsukasa Fukunaga


研究成果: Article査読

7 被引用数 (Scopus)


Advances in experimental technologies, such as DNA sequencing, have opened up new avenues for the applications of phylogenetic methods to various fields beyond their traditional application in evolutionary investigations, extending to the fields of development, differentiation, cancer genomics, and immunogenomics. Thus, the importance of phylogenetic methods is increasingly being recognized, and the development of a novel phylogenetic approach can contribute to several areas of research. Recently, the use of hyperbolic geometry has attracted attention in artificial intelligence research. Hyperbolic space can better represent a hierarchical structure compared to Euclidean space, and can therefore be useful for describing and analyzing a phylogenetic tree. In this study, we developed a novel metric that considers the characteristics of a phylogenetic tree for representation in hyperbolic space. We compared the performance of the proposed hyperbolic embeddings, general hyperbolic embeddings, and Euclidean embeddings, and confirmed that our method could be used to more precisely reconstruct evolutionary distance. We also demonstrate that our approach is useful for predicting the nearest-neighbor node in a partial phylogenetic tree with missing nodes. Furthermore, we proposed a novel approach based on our metric to integrate multiple trees for analyzing tree nodes or imputing missing distances. This study highlights the utility of adopting a geometric approach for further advancing the applications of phylogenetic methods.

ジャーナルBiology Methods and Protocols
出版ステータスPublished - 2021

ASJC Scopus subject areas

  • 生化学、遺伝学、分子生物学(全般)
  • 農業および生物科学(全般)


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