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ORCIDRuriko Yoshida
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2020 – today
- 2024
[c9]Ruriko Yoshida, Georgios Aliatimis, Keiji Miura:
Tropical Neural Networks and Its Applications to Classifying Phylogenetic Trees. IJCNN 2024: 1-9- [i9]Kurt Pasque, Christopher Teska, Ruriko Yoshida, Keiji Miura, Jefferson Huang:
Tropical Decision Boundaries for Neural Networks Are Robust Against Adversarial Attacks. CoRR abs/2402.00576 (2024) - 2023
- [j28]Ruriko Yoshida, Misaki Takamori, Hideyuki Matsumoto
, Keiji Miura:
Tropical support vector machines: Evaluations and extension to function spaces. Neural Networks 157: 77-89 (2023) - [i8]David Barnhill, Ruriko Yoshida, Georgios Aliatimis, Keiji Miura:
Tropical Geometric Tools for Machine Learning: the TML package. CoRR abs/2309.01082 (2023) - [i7]Ruriko Yoshida, Georgios Aliatimis, Keiji Miura:
Tropical neural networks and its applications to classifying phylogenetic trees. CoRR abs/2309.13410 (2023) - 2022
- [j27]Ruriko Yoshida, Lillian Paul, Peter Nesbitt:
Stochastic Safety Radius on UPGMA. Algorithms 15(12): 483 (2022) - [j26]Bo Lin, Anthea Monod, Ruriko Yoshida:
Tropical Geometric Variation of Tree Shapes. Discret. Comput. Geom. 68(3): 817-849 (2022) - [j25]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): 35 (2022) - [j24]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) - 2021
- [c8]Ruriko Yoshida, Carolyne Vu:
Network Classification with Missing Information. IntelliSys (2) 2021: 166-183 - [c7]Ruriko Yoshida:
Tropical Data Science over the Space of Phylogenetic Trees. IntelliSys (2) 2021: 340-361 - [i6]Ruriko Yoshida, Misaki Takamori, Hideyuki Matsumoto, Keiji Miura:
Tropical Support Vector Machines: Evaluations and Extension to Function Spaces. CoRR abs/2101.11531 (2021) - [i5]Patrick Urrutia, David Wren, Chrysafis Vogiatzis, Ruriko Yoshida:
SARS-CoV-2 Dissemination using a Network of the United States Counties. CoRR abs/2111.13723 (2021) - [i4]Yixuan Liu, Chrysafis Vogiatzis, Ruriko Yoshida, Erich Morman:
Solving reward-collecting problems with UAVs: a comparison of online optimization and Q-learning. CoRR abs/2112.00141 (2021) - 2020
- [j23]Robert Page, Ruriko Yoshida, Leon Zhang:
Tropical principal component analysis on the space of phylogenetic trees. Bioinform. 36(17): 4590-4598 (2020) - [j22]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): 981-989 (2020) - [j21]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): 1222-1230 (2020) - [i3]Ruriko Yoshida:
Tropical Data Science. CoRR abs/2005.06586 (2020)
2010 – 2019
- 2019
- [j20]Ruriko Yoshida, Kenji Fukumizu, Chrysafis Vogiatzis:
Multilocus phylogenetic analysis with gene tree clustering. Ann. Oper. Res. 276(1-2): 293-313 (2019) - 2018
- [j19]Bo Lin, Ruriko Yoshida:
Tropical Fermat-Weber Points. SIAM J. Discret. Math. 32(2): 1229-1245 (2018) - [c6]Ralucca Gera, Ruriko Yoshida:
Network Similarity Using Distribution of Distance Matrices. ASONAM 2018: 1176-1183 - [c5]Qiwen Kang, Ruriko Yoshida:
Estimating Tropical Principal Components Using Metropolis Hasting Algorithm. ICMS 2018: 272-279 - 2017
- [j18]Bo Lin, Bernd Sturmfels, Xiaoxian Tang, Ruriko Yoshida:
Convexity in Tree Spaces. SIAM J. Discret. Math. 31(3): 2015-2038 (2017) - [j17]Grady Weyenberg, Ruriko Yoshida, Daniel K. Howe:
Normalizing Kernels in the Billera-Holmes-Vogtmann Treespace. IEEE ACM Trans. Comput. Biol. Bioinform. 14(6): 1359-1365 (2017) - 2015
- [j16]Jing Xi, Ruriko Yoshida:
The Characteristic Imset Polytope of Bayesian Networks with Ordered Nodes. SIAM J. Discret. Math. 29(2): 697-715 (2015) - [i2]Bo Lin, Bernd Sturmfels, Xiaoxian Tang, Ruriko Yoshida:
Convexity in Tree Spaces. CoRR abs/1510.08797 (2015) - 2014
- [j15]Grady Weyenberg, Peter Huggins, Christopher L. Schardl, Daniel K. Howe, Ruriko Yoshida:
kdetrees: non-parametric estimation of phylogenetic tree distributions. Bioinform. 30(16): 2280-2287 (2014) - 2013
- [j14]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): A18 (2013) - [j13]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) - 2012
- [j12]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: 210 (2012) - 2011
- [c4]Jian Zhao, David Haws, Ruriko Yoshida, Sen-ching Samson Cheung:
Approximate techniques in solving optimal camera placement problems. ICCV Workshops 2011: 1705-1712 - 2010
- [j11]Elissaveta G. Arnaoudova, Jerzy W. Jaromczyk, Neil Moore, Christopher L. Schardl, Ruriko Yoshida:
Phylotree - a toolkit for computing experiments with distance-based methods for genome coevolution. BMC Bioinform. 11(S-4): P6 (2010) - [j10]Hisayuki Hara, Akimichi Takemura, Ruriko Yoshida:
On connectivity of fibers with positive marginals in multiple logistic regression. J. Multivar. Anal. 101(4): 909-925 (2010)
2000 – 2009
- 2009
- [j9]Raymond Hemmecke, Akimichi Takemura, Ruriko Yoshida:
Computing holes in semi-groups and its applications to transportation problems. Contributions Discret. Math. 4(1) (2009) - [j8]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): 1006-1014 (2009) - [i1]Peter Huggins, Wenbin Li, David Haws, Thomas Friedrich, Jinze Liu, Ruriko Yoshida:
Bayes estimators for phylogenetic reconstruction. CoRR abs/0911.0645 (2009) - 2008
- [j7]Kord Eickmeyer, Peter Huggins, Lior Pachter, Ruriko Yoshida:
On the optimality of the neighbor-joining algorithm. Algorithms Mol. Biol. 3 (2008) - [j6]Akimichi Takemura, Ruriko Yoshida:
A generalization of the integer linear infeasibility problem. Discret. Optim. 5(1): 36-52 (2008) - [j5]Satoshi Aoki, Akimichi Takemura, Ruriko Yoshida:
Indispensable monomials of toric ideals and Markov bases. J. Symb. Comput. 43(6-7): 490-507 (2008) - [c3]Kord Eickmeyer, Ruriko Yoshida:
The Geometry of the Neighbor-Joining Algorithm for Small Trees. AB 2008: 81-95 - [c2]Akimichi Takemura, Patrick Thomas, Ruriko Yoshida:
Holes in Semigroups and Their Applications to the Two-way Common Diagonal Effect Model. ITSL 2008: 67-72 - 2007
- [j4]Miklós Bóna, Hyeong-Kwan Ju, Ruriko Yoshida:
On the enumeration of certain weighted graphs. Discret. Appl. Math. 155(11): 1481-1496 (2007) - 2005
- [j3]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): 135-144 (2005) - 2004
- [j2]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): 959-973 (2004) - [j1]Jesús A. De Loera, Raymond Hemmecke, Jeremiah Tauzer, Ruriko Yoshida:
Effective lattice point counting in rational convex polytopes. J. Symb. Comput. 38(4): 1273-1302 (2004) - [c1]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: 244-255
Coauthor Index
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