Three Kinds of Integer Programming Algorithms Based on Barvinok's Rational Functions. - Jesús A. De Loera; David Haws; Raymond Hemmecke; Peter Huggins; Ruriko Yoshida (IPCO, 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)

Effective lattice point counting in rational convex polytopes. - Jesús A. De Loera; Raymond Hemmecke; Jeremiah Tauzer; Ruriko Yoshida (J. Symb. Comput., 2004)

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)

On the enumeration of certain weighted graphs. - Miklós Bóna; Hyeong-Kwan Ju; Ruriko Yoshida (Discret. Appl. Math., 2007)

The Geometry of the Neighbor-Joining Algorithm for Small Trees. - Kord Eickmeyer; Ruriko Yoshida (AB, 2008)

Holes in Semigroups and Their Applications to the Two-way Common Diagonal Effect Model. - Akimichi Takemura; Patrick Thomas; Ruriko Yoshida (ITSL, 2008)

On the optimality of the neighbor-joining algorithm. - Kord Eickmeyer; Peter Huggins; Lior Pachter; Ruriko Yoshida (Algorithms Mol. Biol., 2008)

A generalization of the integer linear infeasibility problem. - Akimichi Takemura; Ruriko Yoshida (Discret. Optim., 2008)

Indispensable monomials of toric ideals and Markov bases. - Satoshi Aoki; Akimichi Takemura; Ruriko Yoshida (J. Symb. Comput., 2008)

Computing holes in semi-groups and its applications to transportation problems. - Raymond Hemmecke; Akimichi Takemura; Ruriko Yoshida (Contributions Discret. Math., 2009)

Bayes estimators for phylogenetic reconstruction - Peter Huggins; Wenbin Li; David Haws; Thomas Friedrich 004; Jinze Liu; Ruriko Yoshida (CoRR, 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)

Phylotree - 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)

On connectivity of fibers with positive marginals in multiple logistic regression. - Hisayuki Hara; Akimichi Takemura; Ruriko Yoshida (J. Multivar. Anal., 2010)

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)

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)

Approximate Techniques in Solving Optimal Camera Placement Problems. - Jian Zhao 003; Ruriko Yoshida; Sen-ching Samson Cheung; David Haws (Int. J. Distributed Sens. Networks, 2013)

kdetrees: non-parametric estimation of phylogenetic tree distributions. - Grady Weyenberg; Peter Huggins; Christopher L. Schardl; Daniel K. Howe; Ruriko Yoshida (Bioinform., 2014)

The Characteristic Imset Polytope of Bayesian Networks with Ordered Nodes. - Jing Xi; Ruriko Yoshida (SIAM J. Discret. Math., 2015)

Convexity in Tree Spaces. - Bo Lin; Bernd Sturmfels; Xiaoxian Tang; Ruriko Yoshida (SIAM J. Discret. Math., 2017)

Normalizing Kernels in the Billera-Holmes-Vogtmann Treespace. - Grady Weyenberg; Ruriko Yoshida; Daniel K. Howe (IEEE ACM Trans. Comput. Biol. Bioinform., 2017)

Network Similarity Using Distribution of Distance Matrices. - Ralucca Gera; Ruriko Yoshida (ASONAM, 2018)

Estimating Tropical Principal Components Using Metropolis Hasting Algorithm. - Qiwen Kang; Ruriko Yoshida (ICMS, 2018)

Tropical Fermat-Weber Points. - Bo Lin; Ruriko Yoshida (SIAM J. Discret. Math., 2018)

Multilocus phylogenetic analysis with gene tree clustering. - Ruriko Yoshida; Kenji Fukumizu; Chrysafis Vogiatzis (Ann. Oper. Res., 2019)

Tropical principal component analysis on the space of phylogenetic trees. - Robert Page; Ruriko Yoshida; Leon Zhang (Bioinform., 2020)

Tropical Data Science. - Ruriko Yoshida (CoRR, 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)

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)

Tropical Data Science over the Space of Phylogenetic Trees. - Ruriko Yoshida (IntelliSys (2), 2021)

Network Classification with Missing Information. - Ruriko Yoshida; Carolyne Vu (IntelliSys (2), 2021)

SARS-CoV-2 Dissemination using a Network of the United States Counties. - Patrick Urrutia; David Wren; Chrysafis Vogiatzis; Ruriko Yoshida (CoRR, 2021)

Stochastic Safety Radius on UPGMA. - Ruriko Yoshida; Lillian Paul; Peter Nesbitt (Algorithms, 2022)

Tropical Geometric Variation of Tree Shapes. - Bo Lin; Anthea Monod; Ruriko Yoshida (Discret. Comput. Geom., 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)

SARS-CoV-2 Dissemination Using a Network of the US Counties. - Patrick Urrutia; David Wren; Chrysafis Vogiatzis; Ruriko Yoshida (Oper. Res. Forum, 2022)

Tropical Geometric Tools for Machine Learning: the TML package. - David Barnhill; Ruriko Yoshida; Georgios Aliatimis; Keiji Miura (CoRR, 2023)

Tropical support vector machines: Evaluations and extension to function spaces. - Ruriko Yoshida; Misaki Takamori; Hideyuki Matsumoto; Keiji Miura (Neural Networks, 2023)

Tropical Neural Networks and Its Applications to Classifying Phylogenetic Trees. - Ruriko Yoshida; Georgios Aliatimis; Keiji Miura (IJCNN, 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 Density Estimation of Phylogenetic Trees. - Ruriko Yoshida; David Barnhill; Keiji Miura; Daniel K. Howe (IEEE ACM Trans. Comput. Biol. Bioinform., 2024)

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)

Tropical Bisectors and Carlini-Wagner Attacks. - Gillian Grindstaff; Julia Lindberg; Daniela Schkoda; Miruna-Stefana Sorea; Ruriko Yoshida (CoRR, 2025)

Inference for max-linear Bayesian networks with noise. - Mark Adams; Kamillo Ferry; Ruriko Yoshida (CoRR, 2025)

Tropical Attention: Neural Algorithmic Reasoning for Combinatorial Algorithms. - Baran Hashemi; Kurt Pasque; Christopher Teska; Ruriko Yoshida (CoRR, 2025)