Search Results - "Yoshida, Ruriko"

Imputing Phylogenetic Trees Using Tropical Polytopes over the Space of Phylogenetic Trees by Yoshida, Ruriko

“…When we apply comparative phylogenetic analyses to genome data, it poses a significant problem and challenge that some of the given species (or taxa) often…”
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Tropical Balls and Its Applications to K Nearest Neighbor over the Space of Phylogenetic Trees by Yoshida, Ruriko

“…A tropical ball is a ball defined by the tropical metric over the tropical projective torus. In this paper we show several properties of tropical balls over…”
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Tropical principal component analysis on the space of phylogenetic trees by Page, Robert, Yoshida, Ruriko, Zhang, Leon

“…Abstract Motivation Due to new technology for efficiently generating genome data, machine learning methods are urgently needed to analyze large sets of gene…”
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Efficiencies of the NJp, Maximum Likelihood, and Bayesian Methods of Phylogenetic Construction for Compositional and Noncompositional Genes by Yoshida, Ruriko, Nei, Masatoshi

“…At the present time it is often stated that the maximum likelihood or the Bayesian method of phylogenetic construction is more accurate than the neighbor…”
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Tree Topologies along a Tropical Line Segment by Yoshida, Ruriko, Cox, Shelby

“…Tropical geometry with the max-plus algebra has been applied to statistical learning models over tree spaces because geometry with the tropical metric over…”
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Tropical Logistic Regression Model on Space of Phylogenetic Trees by Aliatimis, Georgios, Yoshida, Ruriko, Boyacı, Burak, Grant, James A.

“…Classification of gene trees is an important task both in the analysis of multi-locus phylogenetic data, and assessment of the convergence of Markov Chain…”
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Plücker coordinates of the best-fit Stiefel tropical linear space to a mixture of Gaussian distributions by Miura, Keiji, Yoshida, Ruriko

“…In this research, we investigate a tropical principal component analysis (PCA) as a best-fit Stiefel tropical linear space to a given sample over the tropical…”
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Clustering Methods over the Tropical Projective Torus by Barnhill, David, Yoshida, Ruriko

“…In this paper, we propose clustering methods for use on data described as tropically convex. Our approach is similar to clustering methods used in the…”
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Solving Reward-Collecting Problems with UAVs: A Comparison of Online Optimization and Q-Learning by Liu, Yixuan, Vogiatzis, Chrysafis, Yoshida, Ruriko, Morman, Erich

“…Uncrewed autonomous vehicles (UAVs) have made significant contributions to reconnaissance and surveillance missions in past US military campaigns. As the…”
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Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci by Schardl, Christopher L, Young, Carolyn A, Hesse, Uljana, Amyotte, Stefan G, Andreeva, Kalina, Calie, Patrick J, Fleetwood, Damien J, Haws, David C, Moore, Neil, Oeser, Birgitt, Panaccione, Daniel G, Schweri, Kathryn K, Voisey, Christine R, Farman, Mark L, Jaromczyk, Jerzy W, Roe, Bruce A, O'Sullivan, Donal M, Scott, Barry, Tudzynski, Paul, An, Zhiqiang, Arnaoudova, Elissaveta G, Bullock, Charles T, Charlton, Nikki D, Chen, Li, Cox, Murray, Dinkins, Randy D, Florea, Simona, Glenn, Anthony E, Gordon, Anna, Güldener, Ulrich, Harris, Daniel R, Hollin, Walter, Jaromczyk, Jolanta, Johnson, Richard D, Khan, Anar K, Leistner, Eckhard, Leuchtmann, Adrian, Li, Chunjie, Liu, JinGe, Liu, Jinze, Liu, Miao, Mace, Wade, Machado, Caroline, Nagabhyru, Padmaja, Pan, Juan, Schmid, Jan, Sugawara, Koya, Steiner, Ulrike, Takach, Johanna E, Tanaka, Eiji, Webb, Jennifer S, Wilson, Ella V, Wiseman, Jennifer L, Yoshida, Ruriko, Zeng, Zheng

“…The fungal family Clavicipitaceae includes plant symbionts and parasites that produce several psychoactive and bioprotective alkaloids. The family includes…”
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Stochastic Safety Radius on UPGMA by Yoshida, Ruriko, Paul, Lillian, Nesbitt, Peter

“…Unweighted Pair Group Method with Arithmetic Mean (UPGMA) is one of the most popular distance-based methods to reconstruct an equidistant phylogenetic tree…”
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Tropical Principal Component Analysis and Its Application to Phylogenetics by Yoshida, Ruriko, Zhang, Leon, Zhang, Xu

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kdetrees: Non-parametric estimation of phylogenetic tree distributions by Weyenberg, Grady, Huggins, Peter M, Schardl, Christopher L, Howe, Daniel K, Yoshida, Ruriko

“…Although the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is…”
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Principal component analysis and the locus of the Fréchet mean in the space of phylogenetic trees by NYE, TOM M. W., TANG, XIAOXIAN, WEYENBERG, GRADY, YOSHIDA, RURIKO

“…Evolutionary relationships are represented by phylogenetic trees, and a phylogenetic analysis of gene sequences typically produces a collection of these trees,…”
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Approximate Techniques in Solving Optimal Camera Placement Problems by Haws, David, Cheung, Sen-ching Samson, Yoshida, Ruriko, Zhao, Jian

“…While the theoretical foundation of the optimal camera placement problem has been studied for decades, its practical implementation has recently attracted…”
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A support vector machine based test for incongruence between sets of trees in tree space by Haws, David C, Huggins, Peter, O'Neill, Eric M, Weisrock, David W, Yoshida, Ruriko

“…The increased use of multi-locus data sets for phylogenetic reconstruction has increased the need to determine whether a set of gene trees significantly…”
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Effective lattice point counting in rational convex polytopes by De Loera, Jesús A., Hemmecke, Raymond, Tauzer, Jeremiah, Yoshida, Ruriko

“…This paper discusses algorithms and software for the enumeration of all lattice points inside a rational convex polytope: we describe LattE, a computer package…”
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On the optimality of the neighbor-joining algorithm by Eickmeyer, Kord, Huggins, Peter, Pachter, Lior, Yoshida, Ruriko

“…The popular neighbor-joining (NJ) algorithm used in phylogenetics is a greedy algorithm for finding the balanced minimum evolution (BME) tree associated to a…”
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Estimating the number of zero-one multi-way tables via sequential importance sampling by Xi, Jing, Yoshida, Ruriko, Haws, David

“…In 2005, Chen et al. introduced a sequential importance sampling (SIS) procedure to analyze zero-one two-way tables with given fixed marginal sums (row and…”
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A Markov basis for conditional test of common diagonal effect in quasi-independence model for square contingency tables by Hara, Hisayuki, Takemura, Akimichi, Yoshida, Ruriko

“…In two-way contingency tables we sometimes find that frequencies along the diagonal cells are relatively larger (or smaller) compared to off-diagonal cells,…”
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