Ruriko Yoshida

53 papers B 4Journal 43Unranked 6

Year	Rank	Type	Title / Venue / Authors
2026	J	`jnl`	Adversarially robust neural network decision boundaries via tropical geometry. Neural Networks Kurt Pasque, Christopher Teska, Ruriko Yoshida, Keiji Miura, Jefferson Huang
2026	J	`jnl`	Tropical Fréchet means: a polyhedral approach to exact optimization. J. Symb. Comput. Kamillo Ferry, Bo Lin, Carlos Améndola, Anthea Monod, Ruriko Yoshida
2025	J	`jnl`	Inference for max-linear Bayesian networks with noise. CoRR Mark Adams, Kamillo Ferry, Ruriko Yoshida
2025	J	`jnl`	Maximum inscribed and minimum enclosing tropical balls of tropical polytopes and applications to volume estimation and uniform sampling. Comput. Geom. David Barnhill, Ruriko Yoshida, Keiji Miura
2025	J	`jnl`	Tropical Attention: Neural Algorithmic Reasoning for Combinatorial Algorithms. CoRR Baran Hashemi, Kurt Pasque, Christopher Teska, Ruriko Yoshida
2025	J	`jnl`	Tropical Bisectors and Carlini-Wagner Attacks. CoRR Gillian Grindstaff, Julia Lindberg, Daniela Schkoda, Miruna-Stefana Sorea, Ruriko Yoshida
2025	B	`conf`	Tropical Fréchet Means. ISSAC Bo Lin, Kamillo Ferry, Carlos Améndola, Anthea Monod, Ruriko Yoshida
2024	J	`jnl`	Tropical Decision Boundaries for Neural Networks Are Robust Against Adversarial Attacks. CoRR Kurt Pasque, Christopher Teska, Ruriko Yoshida, Keiji Miura, Jefferson Huang
2024	J	`jnl`	Tropical Density Estimation of Phylogenetic Trees. IEEE ACM Trans. Comput. Biol. Bioinform. Ruriko Yoshida, David Barnhill, Keiji Miura, Daniel K. Howe
2024	B	`conf`	Tropical Neural Networks and Its Applications to Classifying Phylogenetic Trees. IJCNN Ruriko Yoshida, Georgios Aliatimis, Keiji Miura
2023	J	`jnl`	Tropical Geometric Tools for Machine Learning: the TML package. CoRR David Barnhill, Ruriko Yoshida, Georgios Aliatimis, Keiji Miura
2023	J	`jnl`	Tropical neural networks and its applications to classifying phylogenetic trees. CoRR Ruriko Yoshida, Georgios Aliatimis, Keiji Miura
2023	J	`jnl`	Tropical support vector machines: Evaluations and extension to function spaces. Neural Networks Ruriko Yoshida, Misaki Takamori, Hideyuki Matsumoto, Keiji Miura
2022	J	`jnl`	SARS-CoV-2 Dissemination Using a Network of the US Counties. Oper. Res. Forum Patrick Urrutia, David Wren, Chrysafis Vogiatzis, Ruriko Yoshida
2022	J	`jnl`	Solving Reward-Collecting Problems with UAVs: A Comparison of Online Optimization and Q-Learning. J. Intell. Robotic Syst. Yixuan Liu, Chrysafis Vogiatzis, Ruriko Yoshida, Erich Morman
2022	J	`jnl`	Stochastic Safety Radius on UPGMA. Algorithms Ruriko Yoshida, Lillian Paul, Peter Nesbitt
2022	J	`jnl`	Tropical Geometric Variation of Tree Shapes. Discret. Comput. Geom. Bo Lin, Anthea Monod, Ruriko Yoshida
2021	—	`conf`	Network Classification with Missing Information. IntelliSys (2) Ruriko Yoshida, Carolyne Vu
2021	J	`jnl`	SARS-CoV-2 Dissemination using a Network of the United States Counties. CoRR Patrick Urrutia, David Wren, Chrysafis Vogiatzis, Ruriko Yoshida
2021	J	`jnl`	Solving reward-collecting problems with UAVs: a comparison of online optimization and Q-learning. CoRR Yixuan Liu, Chrysafis Vogiatzis, Ruriko Yoshida, Erich Morman
2021	—	`conf`	Tropical Data Science over the Space of Phylogenetic Trees. IntelliSys (2) Ruriko Yoshida
2021	J	`jnl`	Tropical Support Vector Machines: Evaluations and Extension to Function Spaces. CoRR Ruriko Yoshida, Misaki Takamori, Hideyuki Matsumoto, Keiji Miura
2020	J	`jnl`	CURatio: Genome-Wide Phylogenomic Analysis Method Using Ratios of Total Branch Lengths. IEEE ACM Trans. Comput. Biol. Bioinform. Qiwen Kang, Neil Moore, Christopher L. Schardl, Ruriko Yoshida
2020	J	`jnl`	Tropical Data Science. CoRR Ruriko Yoshida
2020	J	`jnl`	Tropical principal component analysis on the space of phylogenetic trees. Bioinform. Robert Page, Ruriko Yoshida, Leon Zhang
2020	J	`jnl`	imPhy: Imputing Phylogenetic Trees with Missing Information Using Mathematical Programming. IEEE ACM Trans. Comput. Biol. Bioinform. Niko Yasui, Chrysafis Vogiatzis, Ruriko Yoshida, Kenji Fukumizu
2019	J	`jnl`	Multilocus phylogenetic analysis with gene tree clustering. Ann. Oper. Res. Ruriko Yoshida, Kenji Fukumizu, Chrysafis Vogiatzis
2018	—	`conf`	Estimating Tropical Principal Components Using Metropolis Hasting Algorithm. ICMS Qiwen Kang, Ruriko Yoshida
2018	B	`conf`	Network Similarity Using Distribution of Distance Matrices. ASONAM Ralucca Gera, Ruriko Yoshida
2018	J	`jnl`	Tropical Fermat-Weber Points. SIAM J. Discret. Math. Bo Lin, Ruriko Yoshida
2017	J	`jnl`	Convexity in Tree Spaces. SIAM J. Discret. Math. Bo Lin, Bernd Sturmfels, Xiaoxian Tang, Ruriko Yoshida
2017	J	`jnl`	Normalizing Kernels in the Billera-Holmes-Vogtmann Treespace. IEEE ACM Trans. Comput. Biol. Bioinform. Grady Weyenberg, Ruriko Yoshida, Daniel K. Howe
2015	J	`jnl`	Convexity in Tree Spaces. CoRR Bo Lin, Bernd Sturmfels, Xiaoxian Tang, Ruriko Yoshida
2015	J	`jnl`	The Characteristic Imset Polytope of Bayesian Networks with Ordered Nodes. SIAM J. Discret. Math. Jing Xi, Ruriko Yoshida
2014	J	`jnl`	kdetrees: non-parametric estimation of phylogenetic tree distributions. Bioinform. Grady Weyenberg, Peter Huggins, Christopher L. Schardl, Daniel K. Howe, Ruriko Yoshida
2013	J	`jnl`	Approximate Techniques in Solving Optimal Camera Placement Problems. Int. J. Distributed Sens. Networks Jian Zhao, Ruriko Yoshida, Sen-ching Samson Cheung, David Haws
2013	J	`jnl`	Using HPC for teaching and learning bioinformatics software: Benefits and challenges. BMC Bioinform. Tyler Parke, Mark L. Farman, Elizabeth Farnsworth, Derek Fox, Jerzy W. Jaromczyk, Jolanta Jaromczyk, Neil Moore, Christopher L. Schardl, Ruriko Yoshida, Patrick Calie
2012	J	`jnl`	A support vector machine based test for incongruence between sets of trees in tree space. BMC Bioinform. David C. Haws, Peter Huggins, Eric M. O'Neill, David W. Weisrock, Ruriko Yoshida
2011	—	`conf`	Approximate techniques in solving optimal camera placement problems. ICCV Workshops Jian Zhao, David Haws, Ruriko Yoshida, Sen-ching Samson Cheung
2010	J	`jnl`	On connectivity of fibers with positive marginals in multiple logistic regression. J. Multivar. Anal. Hisayuki Hara, Akimichi Takemura, Ruriko Yoshida
2009	J	`jnl`	A Markov basis for conditional test of common diagonal effect in quasi-independence model for square contingency tables. Comput. Stat. Data Anal. Hisayuki Hara, Akimichi Takemura, Ruriko Yoshida
2009	J	`jnl`	Bayes estimators for phylogenetic reconstruction CoRR Peter Huggins, Wenbin Li, David Haws, Thomas Friedrich, Jinze Liu, Ruriko Yoshida
2009	J	`jnl`	Computing holes in semi-groups and its applications to transportation problems. Contributions Discret. Math. Raymond Hemmecke, Akimichi Takemura, Ruriko Yoshida
2008	J	`jnl`	A generalization of the integer linear infeasibility problem. Discret. Optim. Akimichi Takemura, Ruriko Yoshida
2008	—	`conf`	Holes in Semigroups and Their Applications to the Two-way Common Diagonal Effect Model. ITSL Akimichi Takemura, Patrick Thomas, Ruriko Yoshida
2008	J	`jnl`	Indispensable monomials of toric ideals and Markov bases. J. Symb. Comput. Satoshi Aoki, Akimichi Takemura, Ruriko Yoshida
2008	J	`jnl`	On the optimality of the neighbor-joining algorithm. Algorithms Mol. Biol. Kord Eickmeyer, Peter Huggins, Lior Pachter, Ruriko Yoshida
2008	—	`conf`	The Geometry of the Neighbor-Joining Algorithm for Small Trees. AB Kord Eickmeyer, Ruriko Yoshida
2007	J	`jnl`	On the enumeration of certain weighted graphs. Discret. Appl. Math. Miklós Bóna, Hyeong-Kwan Ju, Ruriko Yoshida
2005	J	`jnl`	A computational study of integer programming algorithms based on Barvinok's rational functions. Discret. Optim. Jesús A. De Loera, David Haws, Raymond Hemmecke, Peter Huggins, Ruriko Yoshida
2004	J	`jnl`	Effective lattice point counting in rational convex polytopes. J. Symb. Comput. Jesús A. De Loera, Raymond Hemmecke, Jeremiah Tauzer, Ruriko Yoshida
2004	J	`jnl`	Short rational functions for toric algebra and applications. J. Symb. Comput. Jesús A. De Loera, David Haws, Raymond Hemmecke, Peter Huggins, Bernd Sturmfels, Ruriko Yoshida
2004	B	`conf`	Three Kinds of Integer Programming Algorithms Based on Barvinok's Rational Functions. IPCO Jesús A. De Loera, David Haws, Raymond Hemmecke, Peter Huggins, Ruriko Yoshida