Ruriko Yoshida

According to our database, Ruriko Yoshida authored at least 43 papers between 2004 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2025

Maximum inscribed and minimum enclosing tropical balls of tropical polytopes and applications to volume estimation and uniform sampling.

David Barnhill, Ruriko Yoshida, Keiji Miura

Comput. Geom., 2025

2024

Tropical Density Estimation of Phylogenetic Trees.

Ruriko Yoshida, David Barnhill, Keiji Miura, Daniel K. Howe

IEEE ACM Trans. Comput. Biol. Bioinform., 2024

Tropical Decision Boundaries for Neural Networks Are Robust Against Adversarial Attacks.

Kurt Pasque, Christopher Teska, Ruriko Yoshida, Keiji Miura, Jefferson Huang

CoRR, 2024

Tropical Neural Networks and Its Applications to Classifying Phylogenetic Trees.

Ruriko Yoshida, Georgios Aliatimis, Keiji Miura

Proceedings of the International Joint Conference on Neural Networks, 2024

2023

Tropical support vector machines: Evaluations and extension to function spaces.

Ruriko Yoshida, Misaki Takamori, Hideyuki Matsumoto, Keiji Miura

Neural Networks, 2023

Tropical Geometric Tools for Machine Learning: the TML package.

David Barnhill, Ruriko Yoshida, Georgios Aliatimis, Keiji Miura

CoRR, 2023

2022

SARS-CoV-2 Dissemination Using a Network of the US Counties.

Patrick Urrutia, David Wren, Chrysafis Vogiatzis, Ruriko Yoshida

Oper. Res. Forum, 2022

Solving Reward-Collecting Problems with UAVs: A Comparison of Online Optimization and Q-Learning.

Yixuan Liu, Chrysafis Vogiatzis, Ruriko Yoshida, Erich Morman

J. Intell. Robotic Syst., 2022

Tropical Geometric Variation of Tree Shapes.

Bo Lin, Anthea Monod, Ruriko Yoshida

Discret. Comput. Geom., 2022

Stochastic Safety Radius on UPGMA.

Ruriko Yoshida, Lillian Paul, Peter Nesbitt

Algorithms, 2022

2021

SARS-CoV-2 Dissemination using a Network of the United States Counties.

Patrick Urrutia, David Wren, Chrysafis Vogiatzis, Ruriko Yoshida

CoRR, 2021

Network Classification with Missing Information.

Ruriko Yoshida, Carolyne Vu

Proceedings of the Intelligent Systems and Applications, 2021

Tropical Data Science over the Space of Phylogenetic Trees.

Ruriko Yoshida

Proceedings of the Intelligent Systems and Applications, 2021

2020

imPhy: Imputing Phylogenetic Trees with Missing Information Using Mathematical Programming.

Niko Yasui, Chrysafis Vogiatzis, Ruriko Yoshida, Kenji Fukumizu

IEEE ACM Trans. Comput. Biol. Bioinform., 2020

CURatio: Genome-Wide Phylogenomic Analysis Method Using Ratios of Total Branch Lengths.

Qiwen Kang, Neil Moore, Christopher L. Schardl, Ruriko Yoshida

IEEE ACM Trans. Comput. Biol. Bioinform., 2020

Tropical Data Science.

Ruriko Yoshida

CoRR, 2020

Tropical principal component analysis on the space of phylogenetic trees.

Robert Page, Ruriko Yoshida, Leon Zhang

Bioinform., 2020

2019

Multilocus phylogenetic analysis with gene tree clustering.

Ruriko Yoshida, Kenji Fukumizu, Chrysafis Vogiatzis

Ann. Oper. Res., 2019

2018

Tropical Fermat-Weber Points.

Bo Lin, Ruriko Yoshida

SIAM J. Discret. Math., 2018

Estimating Tropical Principal Components Using Metropolis Hasting Algorithm.

Qiwen Kang, Ruriko Yoshida

Proceedings of the Mathematical Software - ICMS 2018, 2018

Network Similarity Using Distribution of Distance Matrices.

Ralucca Gera, Ruriko Yoshida

Proceedings of the IEEE/ACM 2018 International Conference on Advances in Social Networks Analysis and Mining, 2018

2017

Normalizing Kernels in the Billera-Holmes-Vogtmann Treespace.

Grady Weyenberg, Ruriko Yoshida, Daniel K. Howe

IEEE ACM Trans. Comput. Biol. Bioinform., 2017

Convexity in Tree Spaces.

Bo Lin, Bernd Sturmfels, Xiaoxian Tang, Ruriko Yoshida

SIAM J. Discret. Math., 2017

2015

The Characteristic Imset Polytope of Bayesian Networks with Ordered Nodes.

Jing Xi, Ruriko Yoshida

SIAM J. Discret. Math., 2015

2014

kdetrees: non-parametric estimation of phylogenetic tree distributions.

Grady Weyenberg, Peter Huggins, Christopher L. Schardl, Daniel K. Howe, Ruriko Yoshida

Bioinform., 2014

2013

Approximate Techniques in Solving Optimal Camera Placement Problems.

Jian Zhao, Ruriko Yoshida, Sen-ching Samson Cheung, David Haws

Int. J. Distributed Sens. Networks, 2013

Using HPC for teaching and learning bioinformatics software: Benefits and challenges.

Tyler Parke, Mark L. Farman, Elizabeth Farnsworth, Derek Fox, Jerzy W. Jaromczyk, Jolanta Jaromczyk, Neil Moore, Christopher L. Schardl, Ruriko Yoshida, Patrick Calie

BMC Bioinform., 2013

2012

A support vector machine based test for incongruence between sets of trees in tree space.

David C. Haws, Peter Huggins, Eric M. O'Neill, David W. Weisrock, Ruriko Yoshida

BMC Bioinform., 2012

2010

On connectivity of fibers with positive marginals in multiple logistic regression.

Hisayuki Hara, Akimichi Takemura, Ruriko Yoshida

J. Multivar. Anal., 2010

<i>Phylotree</i> - a toolkit for computing experiments with distance-based methods for genome coevolution.

Elissaveta G. Arnaoudova, Jerzy W. Jaromczyk, Neil Moore, Christopher L. Schardl, Ruriko Yoshida

BMC Bioinform., 2010

2009

A Markov basis for conditional test of common diagonal effect in quasi-independence model for square contingency tables.

Hisayuki Hara, Akimichi Takemura, Ruriko Yoshida

Comput. Stat. Data Anal., 2009

Bayes estimators for phylogenetic reconstruction

Peter Huggins, Wenbin Li, David Haws, Thomas Friedrich, Jinze Liu, Ruriko Yoshida

CoRR, 2009

Computing holes in semi-groups and its applications to transportation problems.

Raymond Hemmecke, Akimichi Takemura, Ruriko Yoshida

Contributions Discret. Math., 2009

2008

Indispensable monomials of toric ideals and Markov bases.

Satoshi Aoki, Akimichi Takemura, Ruriko Yoshida

J. Symb. Comput., 2008

A generalization of the integer linear infeasibility problem.

Akimichi Takemura, Ruriko Yoshida

Discret. Optim., 2008

On the optimality of the neighbor-joining algorithm.

Kord Eickmeyer, Peter Huggins, Lior Pachter, Ruriko Yoshida

Algorithms Mol. Biol., 2008

Holes in Semigroups and Their Applications to the Two-way Common Diagonal Effect Model.

Akimichi Takemura, Patrick Thomas, Ruriko Yoshida

Proceedings of the 2008 International Conference on Information Theory and Statistical Learning, 2008

The Geometry of the Neighbor-Joining Algorithm for Small Trees.

Kord Eickmeyer, Ruriko Yoshida

Proceedings of the Algebraic Biology, Third International Conference, 2008

2007

On the enumeration of certain weighted graphs.

Miklós Bóna, Hyeong-Kwan Ju, Ruriko Yoshida

Discret. Appl. Math., 2007

2005

A computational study of integer programming algorithms based on Barvinok's rational functions.

Jesús A. De Loera, David Haws, Raymond Hemmecke, Peter Huggins, Ruriko Yoshida

Discret. Optim., 2005

2004

Effective lattice point counting in rational convex polytopes.

Jesús A. De Loera, Raymond Hemmecke, Jeremiah Tauzer, Ruriko Yoshida

J. Symb. Comput., 2004

Short rational functions for toric algebra and applications.

Jesús A. De Loera, David Haws, Raymond Hemmecke, Peter Huggins, Bernd Sturmfels, Ruriko Yoshida

J. Symb. Comput., 2004

Three Kinds of Integer Programming Algorithms Based on Barvinok's Rational Functions.

Jesús A. De Loera, David Haws, Raymond Hemmecke, Peter Huggins, Ruriko Yoshida

Proceedings of the Integer Programming and Combinatorial Optimization, 2004