42 citations · 208 across the 51 of their papers we have counts for
52 papers
Tropical neural networks and its applications to classifying phylogenetic trees
Ruriko Yoshida, Georgios Aliatimis, Keiji Miura
Deep neural networks show great success when input vectors are in an Euclidean space. However, those classical neural networks show a poor performance when inputs are phylogenetic…
Imputing phylogenetic trees using tropical polytopes over the space of phylogenetic trees
Ruriko Yoshida
When we apply comparative phylogenetic analyses to genome data, it is a well-known problem and challenge that some of given species (or taxa) often have missing genes. In such a ca…
Tropical Logistic Regression Model on Space of Phylogenetic Trees
Georgios Aliatimis, Ruriko Yoshida, Burak Boyaci +1
Classification of gene trees is an important task both in the analysis of multi-locus phylogenetic data, and assessment of the convergence of Markov Chain Monte Carlo (MCMC) analys…
Maximum Inscribed and Minimum Enclosing Tropical Balls of Tropical Polytopes and Applications to Volume Estimation and Uniform Sampling
David Barnhill, Ruriko Yoshida, Keiji Miura
We consider a minimum enclosing and maximum inscribed tropical balls for any given tropical polytope over the tropical projective torus in terms of the tropical metric with the max…
Hit and Run Sampling from Tropically Convex Sets
Ruriko Yoshida, Keiji Miura, David Barnhill
In this paper we propose Hit and Run (HAR) sampling from a tropically convex set. The key ingredient of HAR sampling from a tropically convex set is sampling uniformly from a tropi…
Tropical Density Estimation of Phylogenetic Trees
Ruriko Yoshida, David Barnhill, Keiji Miura +1
Much evidence from biological theory and empirical data indicates that, gene tree, phylogenetic trees reconstructed from different genes (loci), do not have to have exactly the sam…