Tropical Fréchet means: a polyhedral approach to exact optimization.

Ruriko Yoshida https://orcid.org/0000-0003-0995-2553 https://www.wikidata.org/entity/Q89943705

Kamillo Ferry Bo Lin 0008 Carlos Améndola Anthea Monod Ruriko Yoshida Tropical Fréchet means: a polyhedral approach to exact optimization. 2026 102572 137 J. Symb. Comput. https://doi.org/10.1016/j.jsc.2026.102572 db/journals/jsc/jsc137.html#FerryLAMY26 streams/journals/jsc

Kurt Pasque Christopher Teska Ruriko Yoshida Keiji Miura Jefferson Huang Adversarially robust neural network decision boundaries via tropical geometry. 2026 108624 199 Neural Networks https://doi.org/10.1016/j.neunet.2026.108624 db/journals/nn/nn199.html#PasqueTYMH26 streams/journals/nn

David Barnhill Ruriko Yoshida Keiji Miura Maximum inscribed and minimum enclosing tropical balls of tropical polytopes and applications to volume estimation and uniform sampling. 102163 2025 128 Comput. Geom. https://doi.org/10.1016/j.comgeo.2025.102163 db/journals/comgeo/comgeo128.html#BarnhillYM25 streams/journals/comgeo

Bo Lin 0008 Kamillo Ferry Carlos Améndola Anthea Monod Ruriko Yoshida Tropical Fréchet Means. 240-248 2025 ISSAC https://doi.org/10.1145/3747199.3747567 conf/issac/2025 db/conf/issac/issac2025.html#0008FAMY25

Gillian Grindstaff Julia Lindberg Daniela Schkoda Miruna-Stefana Sorea Ruriko Yoshida Tropical Bisectors and Carlini-Wagner Attacks. 2025 March abs/2503.22653 CoRR https://doi.org/10.48550/arXiv.2503.22653 db/journals/corr/corr2503.html#abs-2503-22653 streams/journals/corr

Mark Adams Kamillo Ferry Ruriko Yoshida Inference for max-linear Bayesian networks with noise. 2025 May abs/2505.00229 CoRR https://doi.org/10.48550/arXiv.2505.00229 db/journals/corr/corr2505.html#abs-2505-00229 streams/journals/corr

Baran Hashemi Kurt Pasque Christopher Teska Ruriko Yoshida Tropical Attention: Neural Algorithmic Reasoning for Combinatorial Algorithms. 2025 May abs/2505.17190 CoRR https://doi.org/10.48550/arXiv.2505.17190 db/journals/corr/corr2505.html#abs-2505-17190 streams/journals/corr

Ruriko Yoshida David Barnhill Keiji Miura Daniel K. Howe Tropical Density Estimation of Phylogenetic Trees. 1855-1863 2024 November - December 21 IEEE ACM Trans. Comput. Biol. Bioinform. 6 https://doi.org/10.1109/TCBB.2024.3420815 db/journals/tcbb/tcbb21.html#YoshidaBMH24 streams/journals/tcbb

Ruriko Yoshida Georgios Aliatimis Keiji Miura Tropical Neural Networks and Its Applications to Classifying Phylogenetic Trees. 1-9 2024 IJCNN https://doi.org/10.1109/IJCNN60899.2024.10650971 conf/ijcnn/2024 db/conf/ijcnn/ijcnn2024.html#YoshidaAM24 streams/conf/ijcnn

Kurt Pasque Christopher Teska Ruriko Yoshida Keiji Miura Jefferson Huang Tropical Decision Boundaries for Neural Networks Are Robust Against Adversarial Attacks. 2024 abs/2402.00576 CoRR https://doi.org/10.48550/arXiv.2402.00576 db/journals/corr/corr2402.html#abs-2402-00576

Ruriko Yoshida Misaki Takamori Hideyuki Matsumoto Keiji Miura Tropical support vector machines: Evaluations and extension to function spaces. 77-89 2023 157 Neural Networks https://doi.org/10.1016/j.neunet.2022.10.002 db/journals/nn/nn157.html#YoshidaTMM23

David Barnhill Ruriko Yoshida Georgios Aliatimis Keiji Miura Tropical Geometric Tools for Machine Learning: the TML package. 2023 abs/2309.01082 CoRR https://doi.org/10.48550/arXiv.2309.01082 db/journals/corr/corr2309.html#abs-2309-01082

Ruriko Yoshida Georgios Aliatimis Keiji Miura Tropical neural networks and its applications to classifying phylogenetic trees. 2023 abs/2309.13410 CoRR https://doi.org/10.48550/arXiv.2309.13410 db/journals/corr/corr2309.html#abs-2309-13410

Ruriko Yoshida Lillian Paul Peter Nesbitt Stochastic Safety Radius on UPGMA. 483 2022 15 Algorithms 12 https://doi.org/10.3390/a15120483 db/journals/algorithms/algorithms15.html#YoshidaPN22

Bo Lin 0008 Anthea Monod Ruriko Yoshida Tropical Geometric Variation of Tree Shapes. 817-849 2022 68 Discret. Comput. Geom. 3 https://doi.org/10.1007/s00454-022-00410-y https://www.wikidata.org/entity/Q114229295 db/journals/dcg/dcg68.html#LinMY22

Yixuan Liu Chrysafis Vogiatzis Ruriko Yoshida Erich Morman Solving Reward-Collecting Problems with UAVs: A Comparison of Online Optimization and Q-Learning. 35 2022 104 J. Intell. Robotic Syst. 2 https://doi.org/10.1007/s10846-021-01548-2 db/journals/jirs/jirs104.html#LiuVYM22

Patrick Urrutia David Wren Chrysafis Vogiatzis Ruriko Yoshida SARS-CoV-2 Dissemination Using a Network of the US Counties. 2022 3 Oper. Res. Forum 2 https://doi.org/10.1007/s43069-022-00139-7 db/journals/orf/orf3.html#UrrutiaWVY22

Ruriko Yoshida Carolyne Vu Network Classification with Missing Information. 166-183 2021 IntelliSys (2) https://doi.org/10.1007/978-3-030-82196-8_13 conf/intellisys/2021-2 db/conf/intellisys/intellisys2021-2.html#YoshidaV21 Ruriko Yoshida Tropical Data Science over the Space of Phylogenetic Trees. 340-361 2021 IntelliSys (2) https://doi.org/10.1007/978-3-030-82196-8_26 conf/intellisys/2021-2 db/conf/intellisys/intellisys2021-2.html#Yoshida21

Ruriko Yoshida Misaki Takamori Hideyuki Matsumoto Keiji Miura Tropical Support Vector Machines: Evaluations and Extension to Function Spaces. 2021 abs/2101.11531 CoRR https://arxiv.org/abs/2101.11531 db/journals/corr/corr2101.html#abs-2101-11531

Patrick Urrutia David Wren Chrysafis Vogiatzis Ruriko Yoshida SARS-CoV-2 Dissemination using a Network of the United States Counties. 2021 abs/2111.13723 CoRR https://arxiv.org/abs/2111.13723 db/journals/corr/corr2111.html#abs-2111-13723

Yixuan Liu Chrysafis Vogiatzis Ruriko Yoshida Erich Morman Solving reward-collecting problems with UAVs: a comparison of online optimization and Q-learning. 2021 abs/2112.00141 CoRR https://arxiv.org/abs/2112.00141 db/journals/corr/corr2112.html#abs-2112-00141

Robert Page Ruriko Yoshida Leon Zhang Tropical principal component analysis on the space of phylogenetic trees. 4590-4598 2020 36 Bioinform. 17 https://doi.org/10.1093/bioinformatics/btaa564 https://www.wikidata.org/entity/Q96223958 db/journals/bioinformatics/bioinformatics36.html#PageYZ20

Qiwen Kang Neil Moore Christopher L. Schardl Ruriko Yoshida CURatio: Genome-Wide Phylogenomic Analysis Method Using Ratios of Total Branch Lengths. 981-989 2020 17 IEEE ACM Trans. Comput. Biol. Bioinform. 3 https://doi.org/10.1109/TCBB.2018.2878564 https://www.wikidata.org/entity/Q58592045 db/journals/tcbb/tcbb17.html#KangMSY20

Niko Yasui Chrysafis Vogiatzis Ruriko Yoshida Kenji Fukumizu imPhy: Imputing Phylogenetic Trees with Missing Information Using Mathematical Programming. 1222-1230 2020 17 IEEE ACM Trans. Comput. Biol. Bioinform. 4 https://doi.org/10.1109/TCBB.2018.2884459 https://www.wikidata.org/entity/Q90210851 db/journals/tcbb/tcbb17.html#YasuiVYF20

Ruriko Yoshida Tropical Data Science. 2020 abs/2005.06586 CoRR https://arxiv.org/abs/2005.06586 db/journals/corr/corr2005.html#abs-2005-06586

Ruriko Yoshida Kenji Fukumizu Chrysafis Vogiatzis Multilocus phylogenetic analysis with gene tree clustering. 293-313 2019 276 Ann. Oper. Res. 1-2 https://doi.org/10.1007/s10479-017-2456-9 db/journals/anor/anor276.html#YoshidaFV19

Bo Lin 0006 Ruriko Yoshida Tropical Fermat-Weber Points. 1229-1245 2018 32 SIAM J. Discret. Math. 2 https://doi.org/10.1137/16M1071122 db/journals/siamdm/siamdm32.html#LinY18

Ralucca Gera Ruriko Yoshida Network Similarity Using Distribution of Distance Matrices. 1176-1183 2018 ASONAM https://doi.org/10.1109/ASONAM.2018.8508321 https://doi.ieeecomputersociety.org/10.1109/ASONAM.2018.8508321 conf/asunam/2018 db/conf/asunam/asonam2018.html#GeraY18 Qiwen Kang Ruriko Yoshida Estimating Tropical Principal Components Using Metropolis Hasting Algorithm. 272-279 2018 ICMS https://doi.org/10.1007/978-3-319-96418-8_32 conf/icms/2018 db/conf/icms/icms2018.html#KangY18

Bo Lin 0006 Bernd Sturmfels Xiaoxian Tang Ruriko Yoshida Convexity in Tree Spaces. 2015-2038 2017 31 SIAM J. Discret. Math. 3 https://doi.org/10.1137/16M1079841 db/journals/siamdm/siamdm31.html#LinSTY17

Grady Weyenberg Ruriko Yoshida Daniel K. Howe Normalizing Kernels in the Billera-Holmes-Vogtmann Treespace. 1359-1365 2017 14 IEEE ACM Trans. Comput. Biol. Bioinform. 6 https://doi.org/10.1109/TCBB.2016.2565475 https://doi.ieeecomputersociety.org/10.1109/TCBB.2016.2565475 https://dl.acm.org/doi/10.1109/TCBB.2016.2565475 https://www.wikidata.org/entity/Q48000016 db/journals/tcbb/tcbb14.html#WeyenbergYH17

Jing Xi Ruriko Yoshida The Characteristic Imset Polytope of Bayesian Networks with Ordered Nodes. 697-715 2015 29 SIAM J. Discret. Math. 2 https://doi.org/10.1137/130933848 https://www.wikidata.org/entity/Q57439593 db/journals/siamdm/siamdm29.html#XiY15

Bo Lin 0006 Bernd Sturmfels Xiaoxian Tang Ruriko Yoshida Convexity in Tree Spaces. 2015 abs/1510.08797 CoRR http://arxiv.org/abs/1510.08797 db/journals/corr/corr1510.html#LinSTY15

Grady Weyenberg Peter Huggins Christopher L. Schardl Daniel K. Howe Ruriko Yoshida kdetrees: non-parametric estimation of phylogenetic tree distributions. 2280-2287 2014 30 Bioinform. 16 https://doi.org/10.1093/bioinformatics/btu258 https://www.wikidata.org/entity/Q41839141 db/journals/bioinformatics/bioinformatics30.html#WeyenbergHSHY14

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. A18 2013 14 BMC Bioinform. S-17 https://doi.org/10.1186/1471-2105-14-S17-A18 https://www.wikidata.org/entity/Q55399090 db/journals/bmcbi/bmcbi14S.html#ParkeFFFJJMSYC13

Jian Zhao 0003 Ruriko Yoshida Sen-ching Samson Cheung David Haws Approximate Techniques in Solving Optimal Camera Placement Problems. 2013 9 Int. J. Distributed Sens. Networks https://doi.org/10.1155/2013/241913 db/journals/ijdsn/ijdsn9.html#ZhaoYCH13

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. 210 2012 13 BMC Bioinform. https://doi.org/10.1186/1471-2105-13-210 https://www.wikidata.org/entity/Q34386856 db/journals/bmcbi/bmcbi13.html#HawsHOWY12

Jian Zhao 0003 David Haws Ruriko Yoshida Sen-ching Samson Cheung Approximate techniques in solving optimal camera placement problems. 1705-1712 2011 ICCV Workshops https://doi.org/10.1109/ICCVW.2011.6130455 https://doi.ieeecomputersociety.org/10.1109/ICCVW.2011.6130455 conf/iccvw/2011 db/conf/iccvw/iccvw2011.html#ZhaoHYC11

Elissaveta G. Arnaoudova Jerzy W. Jaromczyk Neil Moore Christopher L. Schardl Ruriko Yoshida <i>Phylotree</i> - a toolkit for computing experiments with distance-based methods for genome coevolution. P6 2010 11 BMC Bioinform. S-4 https://doi.org/10.1186/1471-2105-11-S4-P6 https://www.wikidata.org/entity/Q46782741 db/journals/bmcbi/bmcbi11S.html#ArnaoudovaJMSY10

Hisayuki Hara Akimichi Takemura Ruriko Yoshida On connectivity of fibers with positive marginals in multiple logistic regression. 909-925 2010 101 J. Multivar. Anal. 4 https://doi.org/10.1016/j.jmva.2009.12.014 db/journals/ma/ma101.html#HaraTY10

Raymond Hemmecke Akimichi Takemura Ruriko Yoshida Computing holes in semi-groups and its applications to transportation problems. 2009 4 Contributions Discret. Math. 1 https://doi.org/10.11575/cdm.v4i1.62036 db/journals/cdm/cdm4.html#HemmeckeTY09

Hisayuki Hara Akimichi Takemura Ruriko Yoshida A Markov basis for conditional test of common diagonal effect in quasi-independence model for square contingency tables. 1006-1014 2009 53 Comput. Stat. Data Anal. 4 https://doi.org/10.1016/j.csda.2008.11.030 db/journals/csda/csda53.html#HaraTY09

Peter Huggins Wenbin Li David Haws Thomas Friedrich 0004 Jinze Liu Ruriko Yoshida Bayes estimators for phylogenetic reconstruction http://arxiv.org/abs/0911.0645 2009 CoRR abs/0911.0645 db/journals/corr/corr0911.html#abs-0911-0645

Kord Eickmeyer Peter Huggins Lior Pachter Ruriko Yoshida On the optimality of the neighbor-joining algorithm. 2008 3 Algorithms Mol. Biol. https://doi.org/10.1186/1748-7188-3-5 https://www.wikidata.org/entity/Q39244848 db/journals/almob/almob3.html#EickmeyerHPY08

Akimichi Takemura Ruriko Yoshida A generalization of the integer linear infeasibility problem. 36-52 2008 5 Discret. Optim. 1 https://doi.org/10.1016/j.disopt.2007.10.004 db/journals/disopt/disopt5.html#TakemuraY08

Satoshi Aoki Akimichi Takemura Ruriko Yoshida Indispensable monomials of toric ideals and Markov bases. 490-507 2008 43 J. Symb. Comput. 6-7 https://doi.org/10.1016/j.jsc.2007.07.012 db/journals/jsc/jsc43.html#AokiTY08

Kord Eickmeyer Ruriko Yoshida The Geometry of the Neighbor-Joining Algorithm for Small Trees. 81-95 2008 AB https://doi.org/10.1007/978-3-540-85101-1_7 conf/ab/2008 db/conf/ab/ab2008.html#EickmeyerY08 Akimichi Takemura Patrick Thomas Ruriko Yoshida Holes in Semigroups and Their Applications to the Two-way Common Diagonal Effect Model. 67-72 2008 ITSL conf/itsl/2008 db/conf/itsl/itsl2008.html#TakemuraTY08

Miklós Bóna Hyeong-Kwan Ju Ruriko Yoshida On the enumeration of certain weighted graphs. 1481-1496 2007 155 Discret. Appl. Math. 11 https://doi.org/10.1016/j.dam.2007.04.001 db/journals/dam/dam155.html#BonaJY07

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. 135-144 2005 2 Discret. Optim. 2 https://doi.org/10.1016/j.disopt.2005.04.001 db/journals/disopt/disopt2.html#LoeraHHHY05

Jesús A. De Loera David Haws Raymond Hemmecke Peter Huggins Bernd Sturmfels Ruriko Yoshida Short rational functions for toric algebra and applications. 959-973 2004 38 J. Symb. Comput. 2 https://doi.org/10.1016/j.jsc.2004.02.001 db/journals/jsc/jsc38.html#LoeraHHHSY04

Jesús A. De Loera Raymond Hemmecke Jeremiah Tauzer Ruriko Yoshida Effective lattice point counting in rational convex polytopes. 1273-1302 2004 38 J. Symb. Comput. 4 https://doi.org/10.1016/j.jsc.2003.04.003 db/journals/jsc/jsc38.html#LoeraHTY04

Jesús A. De Loera David Haws Raymond Hemmecke Peter Huggins Ruriko Yoshida Three Kinds of Integer Programming Algorithms Based on Barvinok's Rational Functions. 244-255 https://doi.org/10.1007/978-3-540-25960-2_19 2004 conf/ipco/2004 IPCO db/conf/ipco/ipco2004.html#LoeraHHHY04 Mark Adams Georgios Aliatimis Carlos Améndola Satoshi Aoki Elissaveta G. Arnaoudova David Barnhill Miklós Bóna Patrick Calie Sen-Ching S. CheungSen-ching Samson Cheung Kord Eickmeyer Mark L. Farman Elizabeth Farnsworth Kamillo Ferry Derek Fox Kenji Fukumizu Ralucca Gera Gillian Grindstaff Hisayuki Hara Baran Hashemi David HawsDavid C. Haws Raymond Hemmecke Daniel K. Howe Jefferson Huang Peter Huggins Jerzy W. Jaromczyk Jolanta Jaromczyk Hyeong-Kwan Ju Qiwen Kang Wenbin Li Bo Lin 0006 Bo Lin 0008 Julia Lindberg Jinze Liu Yixuan Liu Jesús A. De Loera Hideyuki Matsumoto Keiji Miura Thomas W. D. MöbiusThomas Friedrich 0004 Anthea Monod Neil Moore Erich Morman Peter Nesbitt Eric M. O'Neill Lior Pachter Robert Page Tyler Parke Kurt Pasque Lillian Paul Christopher L. Schardl Daniela Schkoda Miruna-Stefana Sorea Bernd Sturmfels Misaki Takamori Akimichi Takemura Xiaoxian Tang Jeremiah Tauzer Christopher Teska Patrick Thomas Patrick Urrutia Chrysafis Vogiatzis Carolyne Vu David W. Weisrock Grady Weyenberg David Wren Jing Xi Niko Yasui Leon Zhang Jian Zhao 0003