Ruriko Yoshida

Publication Activity (10 Years)

Years Active: 2004-2024
Publications (10 Years): 23

Top Topics

Principal Components

Triangular Inequality

Missing Information

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

SIAM J. Discret. Math.

Publications

Kurt Pasque, Christopher Teska, Ruriko Yoshida, Keiji Miura, Jefferson Huang
Tropical Decision Boundaries for Neural Networks Are Robust Against Adversarial Attacks. CoRR (2024)
Ruriko Yoshida, Georgios Aliatimis, Keiji Miura
Tropical neural networks and its applications to classifying phylogenetic trees. CoRR (2023)
Ruriko Yoshida, Misaki Takamori, Hideyuki Matsumoto, Keiji Miura
Tropical support vector machines: Evaluations and extension to function spaces. Neural Networks 157 (2023)
David Barnhill, Ruriko Yoshida, Georgios Aliatimis, Keiji Miura
Tropical Geometric Tools for Machine Learning: the TML package. CoRR (2023)
Bo Lin, Anthea Monod, Ruriko Yoshida
Tropical Geometric Variation of Tree Shapes. Discret. Comput. Geom. 68 (3) (2022)
Patrick Urrutia, David Wren, Chrysafis Vogiatzis, Ruriko Yoshida
SARS-CoV-2 Dissemination Using a Network of the US Counties. Oper. Res. Forum 3 (2) (2022)
Ruriko Yoshida, Lillian Paul, Peter Nesbitt
Stochastic Safety Radius on UPGMA. Algorithms 15 (12) (2022)
Yixuan Liu, Chrysafis Vogiatzis, Ruriko Yoshida, Erich Morman
Solving Reward-Collecting Problems with UAVs: A Comparison of Online Optimization and Q-Learning. J. Intell. Robotic Syst. 104 (2) (2022)
Yixuan Liu, Chrysafis Vogiatzis, Ruriko Yoshida, Erich Morman
Solving reward-collecting problems with UAVs: a comparison of online optimization and Q-learning. CoRR (2021)
Patrick Urrutia, David Wren, Chrysafis Vogiatzis, Ruriko Yoshida
SARS-CoV-2 Dissemination using a Network of the United States Counties. CoRR (2021)
Ruriko Yoshida, Carolyne Vu
Network Classification with Missing Information. IntelliSys (2) (2021)
Ruriko Yoshida, Misaki Takamori, Hideyuki Matsumoto, Keiji Miura
Tropical Support Vector Machines: Evaluations and Extension to Function Spaces. CoRR (2021)
Ruriko Yoshida
Tropical Data Science over the Space of Phylogenetic Trees. IntelliSys (2) (2021)
Qiwen Kang, Neil Moore, Christopher L. Schardl, Ruriko Yoshida
CURatio: Genome-Wide Phylogenomic Analysis Method Using Ratios of Total Branch Lengths. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (3) (2020)
Robert Page, Ruriko Yoshida, Leon Zhang
Tropical principal component analysis on the space of phylogenetic trees. Bioinform. 36 (17) (2020)
Ruriko Yoshida
Tropical Data Science. CoRR (2020)
Niko Yasui, Chrysafis Vogiatzis, Ruriko Yoshida, Kenji Fukumizu
imPhy: Imputing Phylogenetic Trees with Missing Information Using Mathematical Programming. IEEE ACM Trans. Comput. Biol. Bioinform. 17 (4) (2020)
Ruriko Yoshida, Kenji Fukumizu, Chrysafis Vogiatzis
Multilocus phylogenetic analysis with gene tree clustering. Ann. Oper. Res. 276 (1-2) (2019)
Bo Lin, Ruriko Yoshida
Tropical Fermat-Weber Points. SIAM J. Discret. Math. 32 (2) (2018)
Qiwen Kang, Ruriko Yoshida
Estimating Tropical Principal Components Using Metropolis Hasting Algorithm. ICMS (2018)
Ralucca Gera, Ruriko Yoshida
Network Similarity Using Distribution of Distance Matrices. ASONAM (2018)
Bo Lin, Bernd Sturmfels, Xiaoxian Tang, Ruriko Yoshida
Convexity in Tree Spaces. SIAM J. Discret. Math. 31 (3) (2017)
Grady Weyenberg, Ruriko Yoshida, Daniel K. Howe
Normalizing Kernels in the Billera-Holmes-Vogtmann Treespace. IEEE ACM Trans. Comput. Biol. Bioinform. 14 (6) (2017)
Jing Xi, Ruriko Yoshida
The Characteristic Imset Polytope of Bayesian Networks with Ordered Nodes. SIAM J. Discret. Math. 29 (2) (2015)
Bo Lin, Bernd Sturmfels, Xiaoxian Tang, Ruriko Yoshida
Convexity in Tree Spaces. CoRR (2015)
Grady Weyenberg, Peter Huggins, Christopher L. Schardl, Daniel K. Howe, Ruriko Yoshida
kdetrees: non-parametric estimation of phylogenetic tree distributions. Bioinform. 30 (16) (2014)
Tyler Parke, Mark L. Farman, Elizabeth Farnsworth, Derek Fox, Jerzy W. Jaromczyk, Jolanta Jaromczyk, Neil Moore, Christopher L. Schardl, Ruriko Yoshida, Patrick Calie
Using HPC for teaching and learning bioinformatics software: Benefits and challenges. BMC Bioinform. 14 (S-17) (2013)
Jian Zhao, Ruriko Yoshida, Sen-ching Samson Cheung, David Haws
Approximate Techniques in Solving Optimal Camera Placement Problems. Int. J. Distributed Sens. Networks 9 (2013)
David C. Haws, Peter Huggins, Eric M. O'Neill, David W. Weisrock, Ruriko Yoshida
A support vector machine based test for incongruence between sets of trees in tree space. BMC Bioinform. 13 (2012)
Jian Zhao, David Haws, Ruriko Yoshida, Sen-ching Samson Cheung
Approximate techniques in solving optimal camera placement problems. ICCV Workshops (2011)
Elissaveta G. Arnaoudova, Jerzy W. Jaromczyk, Neil Moore, Christopher L. Schardl, Ruriko Yoshida
- a toolkit for computing experiments with distance-based methods for genome coevolution. BMC Bioinform. 11 (S-4) (2010)
Hisayuki Hara, Akimichi Takemura, Ruriko Yoshida
On connectivity of fibers with positive marginals in multiple logistic regression. J. Multivar. Anal. 101 (4) (2010)
Peter Huggins, Wenbin Li, David Haws, Thomas Friedrich, Jinze Liu, Ruriko Yoshida
Bayes estimators for phylogenetic reconstruction CoRR (2009)
Hisayuki Hara, Akimichi Takemura, Ruriko Yoshida
A Markov basis for conditional test of common diagonal effect in quasi-independence model for square contingency tables. Comput. Stat. Data Anal. 53 (4) (2009)
Raymond Hemmecke, Akimichi Takemura, Ruriko Yoshida
Computing holes in semi-groups and its applications to transportation problems. Contributions Discret. Math. 4 (1) (2009)
Akimichi Takemura, Ruriko Yoshida
A generalization of the integer linear infeasibility problem. Discret. Optim. 5 (1) (2008)
Kord Eickmeyer, Ruriko Yoshida
The Geometry of the Neighbor-Joining Algorithm for Small Trees. AB (2008)
Kord Eickmeyer, Peter Huggins, Lior Pachter, Ruriko Yoshida
On the optimality of the neighbor-joining algorithm. Algorithms Mol. Biol. 3 (2008)
Satoshi Aoki, Akimichi Takemura, Ruriko Yoshida
Indispensable monomials of toric ideals and Markov bases. J. Symb. Comput. 43 (6-7) (2008)
Akimichi Takemura, Patrick Thomas, Ruriko Yoshida
Holes in Semigroups and Their Applications to the Two-way Common Diagonal Effect Model. ITSL (2008)
Miklós Bóna, Hyeong-Kwan Ju, Ruriko Yoshida
On the enumeration of certain weighted graphs. Discret. Appl. Math. 155 (11) (2007)
Jesús A. De Loera, David Haws, Raymond Hemmecke, Peter Huggins, Ruriko Yoshida
A computational study of integer programming algorithms based on Barvinok's rational functions. Discret. Optim. 2 (2) (2005)
Jesús A. De Loera, David Haws, Raymond Hemmecke, Peter Huggins, Ruriko Yoshida
Three Kinds of Integer Programming Algorithms Based on Barvinok's Rational Functions. IPCO (2004)
Jesús A. De Loera, David Haws, Raymond Hemmecke, Peter Huggins, Bernd Sturmfels, Ruriko Yoshida
Short rational functions for toric algebra and applications. J. Symb. Comput. 38 (2) (2004)
Jesús A. De Loera, Raymond Hemmecke, Jeremiah Tauzer, Ruriko Yoshida
Effective lattice point counting in rational convex polytopes. J. Symb. Comput. 38 (4) (2004)