Ryuhei Uehara

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98ranked-venue papers
15as first author
18since 2021 · last 2026
0000-0003-0895-3765ORCID · verified

Domains — the database's venue-derived domains; a paper can count in several

Theory of computation · 77 · 15 first-author · 11 since 2021Graphics, computer vision, multimedia, augmented reality and games · 12 · 6 since 2021Databases, data management, data science and information retrieval · 5 · 4 first-authorArtificial intelligence and machine learning · 4 · 1 since 2021Applied, interdisciplinary, general and emerging computing · 3 · 1 since 2021Computer networks · 1
YearPublicationVenuePosition
2026 Dudeney's Dissection Is Optimal
abstract
In 1907, Henry Ernest Dudeney posed a puzzle: "cut any equilateral triangle ... into as few pieces as possible that will fit together and form a perfect square" (without overlap, via translation and rotation). Four weeks later, Dudeney demonstrated a beautiful four-piece solution, which today remains perhaps the most famous example of dissection. In this paper (over a century later), we finally solve Dudeney’s puzzle, by proving that the equilateral triangle and square have no common dissection with three or fewer polygonal pieces. We reduce the problem to the analysis of discrete graph structures representing the correspondence between the edges and the vertices of the pieces forming each polygon.
Erik D. Demaine, Tonan Kamata, Ryuhei Uehara
ITCS3
2025 Multi-Objective Combinatorial Reconfiguration Considering Cost and Length by Answer Set Programming: Algorithms, Encodings, and Empirical Analysis
abstract
We introduce the Multi-Objective Combinatorial Reconfiguration Optimization Problem (MO-CROP), and propose an Answer Set Programming (ASP) based approach for its solution. MO-CROP involves finding the Pareto-optimal sequences (or Pareto front) of adjacent feasible solutions between two given feasible solutions of a combinatorial problem, considering both cost and length. Our algorithm is compactly implemented through multi-shot ASP solving, and its implementing solver optirecon provides an effective tool for solving MO-CROP. As a concrete example of MO-CROP, we present an ASP encoding for solving the multi-objective independent set reconfiguration optimization problem. Experimental results on the benchmark set from the recent CoRe Challenge demonstrate our approach’s ability to capture diverse optimal sequences that reveal trade-offs between cost and length, a capability often lacking in traditional combinatorial reconfiguration methods.
Kazuki Takada, Mutsunori Banbara, Takehiro Ito, Jun Kawahara, Shin-ichi Minato, Torsten Schaub, Ryuhei Uehara
ECAI7
2025 Constant time enumeration of weighted trees
abstract
This study specifically addresses the enumeration problem of the class of weighted trees. A weighted tree is a rooted unordered tree, and each vertex in a weighted tree is assigned an integer weight. The task is to enumerate the weighted trees. Given a tree and a weight , the objective is to enumerate all weighted trees that share the same tree structure as and have a total weight of . Note that the weight assigned to each vertex must be non-negative. The algorithm utilizes reverse search and enumerates each weighted tree in a constant amortized time. By combining our findings with the enumeration of the class of rooted trees, we can efficiently enumerate every weighted tree with a maximum of vertices and a total weight of for any given positive inputs and .
Mengze Qian, Ryuhei Uehara
Discret. Appl. Math.2
2025 Gathering on a circle with limited visibility by anonymous oblivious robots
Giuseppe Antonio Di Luna, Ryuhei Uehara, Giovanni Viglietta, Yukiko Yamauchi
Theor. Comput. Sci.2
2024 On the Computational Complexity of Generalized Common Shape Puzzles
Mutsunori Banbara, Shin-ichi Minato, Hirotaka Ono 0001, Ryuhei Uehara
SOFSEM4
2024 Efficient enumeration of non-isomorphic distance-hereditary graphs and related graphs
Kazuaki Yamazaki, Mengze Qian, Ryuhei Uehara
Discret. Appl. Math.3
2024 Computational complexity of jumping block puzzles
Masaaki Kanzaki, Yota Otachi, Giovanni Viglietta, Ryuhei Uehara
Theor. Comput. Sci.4
2023 Any platonic solid can transform to another by O(1) refoldings
Erik D. Demaine, Martin L. Demaine, Jenny Diomidova, Tonan Kamata, Ryuhei Uehara, Hanyu Alice Zhang
Comput. Geom.5
2023 Developing a tetramonohedron with minimum cut length
Erik D. Demaine, Martin L. Demaine, Ryuhei Uehara
Comput. Geom.3
2023 Efficient Folding Algorithms for Convex Polyhedra
Tonan Kamata, Akira Kadoguchi, Takashi Horiyama, Ryuhei Uehara
Discret. Comput. Geom.4
2023 Sorting balls and water: Equivalence and computational complexity
Takehiro Ito, Jun Kawahara, Shin-ichi Minato, Yota Otachi, Toshiki Saitoh, Akira Suzuki 0001, Ryuhei Uehara, Takeaki Uno, Katsuhisa Yamanaka, Ryo Yoshinaka
Theor. Comput. Sci.7
2023 Mathematical characterizations and computational complexity of anti-slide puzzles
abstract
For a given set of pieces and a frame, an anti-slide puzzle asks us to arrange the pieces so that none of the pieces can slide in the frame. Since the first anti-slide puzzle that consists of dozens of cuboid pieces in 3D was invented, tons of anti-slide puzzles using pentominoes have been proposed. Some of them are not in a frame, which we call that interlock puzzles. In this paper, we investigate computational complexity of anti-slide puzzles and interlock puzzles in 2D. In previous work in theoretical computer science, a few models have been proposed for dealing with the notion of anti-slide, however, there exist gaps between these models and real puzzles. We first give mathematical characterizations of anti-slide puzzles and show the relationship between the previous work. Using a mathematical characterization, we give a polynomial time algorithm for determining if a given arrangement of polyominoes is anti-slide or not in a model. Next, we prove that the decision problem whether a given set of polyominoes can be arranged to be anti-slide or not is strongly NP-complete even if every piece is x-monotone. On the other hand, a set of pieces cannot be arranged to be interlocked if all pieces are convex polygons.
Ko Minamisawa, Ryuhei Uehara, Masao Hara
Theor. Comput. Sci.2
2022 Ununfoldable polyhedra with 6 vertices or 6 faces
Hugo A. Akitaya, Erik D. Demaine, David Eppstein, Tomohiro Tachi, Ryuhei Uehara
Comput. Geom.5
2022 Efficient segment folding is hard
Takashi Horiyama, Fabian Klute, Matias Korman, Irene Parada, Ryuhei Uehara, Katsuhisa Yamanaka
Comput. Geom.5
2021 Computational Complexity of Jumping Block Puzzles
Masaaki Kanzaki, Yota Otachi, Ryuhei Uehara
COCOON3
2021 Token Shifting on Graphs
Win Hlaing Hlaing Myint, Ryuhei Uehara, Giovanni Viglietta
COCOON2
2021 Algorithmic enumeration of surrounding polygons
Katsuhisa Yamanaka, David Avis, Takashi Horiyama, Yoshio Okamoto, Ryuhei Uehara, Tanami Yamauchi
Discret. Appl. Math.5
2021 Shortest reconfiguration of sliding tokens on subclasses of interval graphs
Takeshi Yamada, Ryuhei Uehara
Theor. Comput. Sci.2
2020 Efficient Enumeration of Non-isomorphic Ptolemaic Graphs
Dat Hoang Tran, Ryuhei Uehara
WALCOM2
2020 Gathering on a Circle with Limited Visibility by Anonymous Oblivious Robots
abstract
A swarm of anonymous oblivious mobile robots, operating in deterministic Look-Compute-Move cycles, is confined within a circular track. All robots agree on the clockwise direction (chirality), they are activated by an adversarial semi-synchronous scheduler (SSYNCH), and an active robot always reaches the destination point it computes (rigidity). Robots have limited visibility: each robot can see only the points on the circle that have an angular distance strictly smaller than a constant $\vartheta$ from the robot's current location, where $0<\vartheta\leqπ$ (angles are expressed in radians). We study the Gathering problem for such a swarm of robots: that is, all robots are initially in distinct locations on the circle, and their task is to reach the same point on the circle in a finite number of turns, regardless of the way they are activated by the scheduler. Note that, due to the anonymity of the robots, this task is impossible if the initial configuration is rotationally symmetric; hence, we have to make the assumption that the initial configuration be rotationally asymmetric. We prove that, if $\vartheta=π$ (i.e., each robot can see the entire circle except its antipodal point), there is a distributed algorithm that solves the Gathering problem for swarms of any size. By contrast, we also prove that, if $\vartheta\leq π/2$, no distributed algorithm solves the Gathering problem, regardless of the size of the swarm, even under the assumption that the initial configuration is rotationally asymmetric and the visibility graph of the robots is connected. The latter impossibility result relies on a probabilistic technique based on random perturbations, which is novel in the context of anonymous mobile robots. Such a technique is of independent interest, and immediately applies to other Pattern-Formation problems.
Giuseppe Antonio Di Luna, Ryuhei Uehara, Giovanni Viglietta, Yukiko Yamauchi
DISC2
2020 Symmetric assembly puzzles are hard, beyond a few pieces
Erik D. Demaine, Matias Korman, Jason S. Ku, Joseph S. B. Mitchell, Yota Otachi, André van Renssen, Marcel Roeloffzen, Ryuhei Uehara, Yushi Uno
Comput. Geom.8
2020 Parameterized complexity of independent set reconfiguration problems
Takehiro Ito, Marcin Kaminski 0001, Hirotaka Ono 0001, Akira Suzuki 0001, Ryuhei Uehara, Katsuhisa Yamanaka
Discret. Appl. Math.5
2020 Enumeration of nonisomorphic interval graphs and nonisomorphic permutation graphs
Kazuaki Yamazaki, Toshiki Saitoh, Masashi Kiyomi, Ryuhei Uehara
Theor. Comput. Sci.4
2019 Shortest Reconfiguration Sequence for Sliding Tokens on Spiders
Duc A. Hoang 0001, Amanj Khorramian, Ryuhei Uehara
CIAC3
2019 Max-Min 3-Dispersion Problems
Takashi Horiyama, Shin-Ichi Nakano, Toshiki Saitoh, Koki Suetsugu, Akira Suzuki 0001, Ryuhei Uehara, Takeaki Uno, Kunihiro Wasa
COCOON6
2019 On the Complexity of Lattice Puzzles
Yasuaki Kobayashi, Koki Suetsugu, Hideki Tsuiki, Ryuhei Uehara
ISAAC4
2019 Reconfiguring Undirected Paths
Erik D. Demaine, David Eppstein, Adam Hesterberg, Kshitij Jain 0001, Anna Lubiw, Ryuhei Uehara, Yushi Uno
WADS6
2019 Efficient Algorithm for Box Folding
Koichi Mizunashi, Takashi Horiyama, Ryuhei Uehara
WALCOM3
2018 Computational Complexity of Robot Arm Simulation Problems
Tianfeng Feng, Takashi Horiyama, Yoshio Okamoto, Yota Otachi, Toshiki Saitoh, Takeaki Uno, Ryuhei Uehara
IWOCA7
2018 Complexity of the Maximum k-Path Vertex Cover Problem
Eiji Miyano, Toshiki Saitoh, Ryuhei Uehara, Tsuyoshi Yagita, Tom C. van der Zanden
WALCOM3
2018 Enumeration of Nonisomorphic Interval Graphs and Nonisomorphic Permutation Graphs
Kazuaki Yamazaki, Toshiki Saitoh, Masashi Kiyomi, Ryuhei Uehara
WALCOM4
2018 Bumpy pyramid folding
Zachary Abel, Erik D. Demaine, Martin L. Demaine, Hiro Ito, Jack Snoeyink, Ryuhei Uehara
Comput. Geom.6
2018 Swapping colored tokens on graphs
Katsuhisa Yamanaka, Takashi Horiyama, J. Mark Keil, David G. Kirkpatrick, Yota Otachi, Toshiki Saitoh, Ryuhei Uehara, Yushi Uno
Theor. Comput. Sci.7
2017 Common developments of three incongruent boxes of area 30
Takashi Horiyama, Toshihiro Shirakawa, Ryuhei Uehara
Comput. Geom.4
2017 Ferrers dimension of grid intersection graphs
Steven Chaplick, Pavol Hell, Yota Otachi, Toshiki Saitoh, Ryuhei Uehara
Discret. Appl. Math.5
2017 Complexity of Tiling a Polygon with Trominoes or Bars
Takashi Horiyama, Takehiro Ito, Keita Nakatsuka, Akira Suzuki 0001, Ryuhei Uehara
Discret. Comput. Geom.5
2016 Sliding Tokens on a Cactus
abstract
Given two independent sets I and J of a graph G, imagine that a token (coin) is placed on each vertex in I. Then, the Sliding Token problem asks if one could transforms I to J using a sequence of elementary steps, where each step requires sliding a token from one vertex to one of its neighbors, such that the resulting set of vertices where tokens are placed still remains independent. In this paper, we describe a polynomial-time algorithm for solving Sliding Token in case the graph G is a cactus. Our algorithm is designed based on two observations. First, all structures that forbid the existence of a sequence of token slidings between I and J, if exist, can be found in polynomial time. A no-instance may be easily deduced using this characterization. Second, without such forbidden structures, a sequence of token slidings between I and J does exist.
Duc A. Hoang 0001, Ryuhei Uehara
ISAAC2
2016 A polynomial-time approximation scheme for the geometric unique coverage problem on unit squares
Takehiro Ito, Shin-Ichi Nakano, Yoshio Okamoto, Yota Otachi, Ryuhei Uehara, Takeaki Uno, Yushi Uno
Comput. Geom.5
2016 Polynomial-time algorithms for Subgraph Isomorphism in small graph classes of perfect graphs
Matsuo Konagaya, Yota Otachi, Ryuhei Uehara
Discret. Appl. Math.3
2015 Sliding Token on Bipartite Permutation Graphs
Eli Fox-Epstein, Duc A. Hoang 0001, Yota Otachi, Ryuhei Uehara
ISAAC4
2015 Common Developments of Three Incongruent Boxes of Area 30
Takashi Horiyama, Toshihiro Shirakawa, Ryuhei Uehara
TAMC4
2015 Competitive Diffusion on Weighted Graphs
Takehiro Ito, Yota Otachi, Toshiki Saitoh, Hisayuki Satoh, Akira Suzuki 0001, Kei Uchizawa, Ryuhei Uehara, Katsuhisa Yamanaka, Xiao Zhou 0001
WADS7
2015 Swapping Colored Tokens on Graphs
Katsuhisa Yamanaka, Takashi Horiyama, David G. Kirkpatrick, Yota Otachi, Toshiki Saitoh, Ryuhei Uehara, Yushi Uno
WADS6
2015 Linear-time algorithm for sliding tokens on trees
Erik D. Demaine, Martin L. Demaine, Eli Fox-Epstein, Duc A. Hoang 0001, Takehiro Ito, Hirotaka Ono 0001, Yota Otachi, Ryuhei Uehara, Takeshi Yamada
Theor. Comput. Sci.8
2014 Flat Foldings of Plane Graphs with Prescribed Angles and Edge Lengths
Zachary Abel, Erik D. Demaine, Martin L. Demaine, David Eppstein, Anna Lubiw, Ryuhei Uehara
GD6
2014 Depth-First Search Using O(n) Bits
Tetsuo Asano, Taisuke Izumi, Masashi Kiyomi, Matsuo Konagaya, Hirotaka Ono 0001, Yota Otachi, Pascal Schweitzer, Jun Tarui, Ryuhei Uehara
ISAAC9
2014 Polynomial-Time Algorithm for Sliding Tokens on Trees
Erik D. Demaine, Martin L. Demaine, Eli Fox-Epstein, Duc A. Hoang 0001, Takehiro Ito, Hirotaka Ono 0001, Yota Otachi, Ryuhei Uehara, Takeshi Yamada
ISAAC8
2014 Intersection Dimension of Bipartite Graphs
Steven Chaplick, Pavol Hell, Yota Otachi, Toshiki Saitoh, Ryuhei Uehara
TAMC5
2014 On the Parameterized Complexity for Token Jumping on Graphs
Takehiro Ito, Marcin Kaminski 0001, Hirotaka Ono 0001, Akira Suzuki 0001, Ryuhei Uehara, Katsuhisa Yamanaka
TAMC5
2014 Polynomial-Time Algorithms for Subgraph Isomorphism in Small Graph Classes of Perfect Graphs
Matsuo Konagaya, Yota Otachi, Ryuhei Uehara
TAMC3
2014 Base-object location problems for base-monotone regions
Jinhee Chun, Takashi Horiyama, Takehiro Ito, Natsuda Kaothanthong, Hirotaka Ono 0001, Yota Otachi, Takeshi Tokuyama, Ryuhei Uehara, Takeaki Uno
Theor. Comput. Sci.8
2014 UNO is hard, even for a single player
Erik D. Demaine, Martin L. Demaine, Nicholas J. A. Harvey, Ryuhei Uehara, Takeaki Uno, Yushi Uno
Theor. Comput. Sci.4
2014 A 4.31-approximation for the geometric unique coverage problem on unit disks
Takehiro Ito, Shin-Ichi Nakano, Yoshio Okamoto, Yota Otachi, Ryuhei Uehara, Takeaki Uno, Yushi Uno
Theor. Comput. Sci.5
2013 Route-Enabling Graph Orientation Problems
Takehiro Ito, Yuichiro Miyamoto, Hirotaka Ono 0001, Hisao Tamaki, Ryuhei Uehara
Algorithmica5
2013 Efficient algorithms for a simple network design problem
abstract
Abstract We consider the following simple network design problem. The input consists of n weighted nodes, and the output is an edge‐weighted connected network such that the total weight of the edges incident to a node is at least the given weight of the node. We aim to design the cheapest connected network; that is, the reachability of the network should be guaranteed, and the network is better if its total weight is less. In this article, we first show an efficient algorithm that produces an optimal network with minimum weight. The algorithm runs in linear time, and the resulting network contains at most n edges, where n is the number of nodes. To construct a connected network, at least n ‐ 1 edges are required. However, the algorithm sometimes outputs n edges. Next, we aim to minimize not only the weight but also the number of edges. That is, for given n weighted nodes, we aim to design a cheapest tree. Then, the problem becomes \documentclass{article}\usepackage{mathrsfs, amsmath, amssymb}\pagestyle{empty}\begin{document}\begin{align*}\mathcal{N}\mathcal{P}\end{align*} \end{document} ‐complete. We also propose efficient approximation algorithms for constructing a cheapest tree. © 2013 Wiley Periodicals, Inc. NETWORKS, 2013
Shin-Ichi Nakano, Ryuhei Uehara, Takeaki Uno
Networks2
2013 The complexity of the stamp folding problem
Takuya Umesato, Toshiki Saitoh, Ryuhei Uehara, Hiro Ito, Yoshio Okamoto
Theor. Comput. Sci.3
2012 A 4.31-Approximation for the Geometric Unique Coverage Problem on Unit Disks
Takehiro Ito, Shin-Ichi Nakano, Yoshio Okamoto, Yota Otachi, Ryuhei Uehara, Takeaki Uno, Yushi Uno
ISAAC5
2012 Faster computation of the Robinson-Foulds distance between phylogenetic networks
Tetsuo Asano, Jesper Jansson 0001, Kunihiko Sadakane, Ryuhei Uehara, Gabriel Valiente
Inf. Sci.4
2011 Complexity of the Stamp Folding Problem
Takuya Umesato, Toshiki Saitoh, Ryuhei Uehara, Hiro Ito
COCOA3
2011 Hardness Results and an Exact Exponential Algorithm for the Spanning Tree Congestion Problem
Yoshio Okamoto, Yota Otachi, Ryuhei Uehara, Takeaki Uno
TAMC3
2011 On the complexity of reconfiguration problems
Takehiro Ito, Erik D. Demaine, Nicholas J. A. Harvey, Christos H. Papadimitriou, Martha Sideri, Ryuhei Uehara, Yushi Uno
Theor. Comput. Sci.6
2010 Coverage with k-Transmitters in the Presence of Obstacles
Brad Ballinger, Nadia M. Benbernou, Prosenjit Bose, Mirela Damian, Erik D. Demaine, Vida Dujmovic, Robin Y. Flatland, Ferran Hurtado, John Iacono, Anna Lubiw, Pat Morin, Vera Sacristán Adinolfi, Diane L. Souvaine, Ryuhei Uehara
COCOA (2)14
2010 Bipartite Permutation Graphs Are Reconstructible
Masashi Kiyomi, Toshiki Saitoh, Ryuhei Uehara
COCOA (2)3
2010 Faster Computation of the Robinson-Foulds Distance between Phylogenetic Networks
Tetsuo Asano, Jesper Jansson 0001, Kunihiko Sadakane, Ryuhei Uehara, Gabriel Valiente
CPM4
2010 Reconstruction of interval graphs
Masashi Kiyomi, Toshiki Saitoh, Ryuhei Uehara
Theor. Comput. Sci.3
2010 Enumeration of the perfect sequences of a chordal graph
Yasuko Matsui, Ryuhei Uehara, Takeaki Uno
Theor. Comput. Sci.2
2010 Efficient enumeration of all ladder lotteries and its application
Katsuhisa Yamanaka, Shin-Ichi Nakano, Yasuko Matsui, Ryuhei Uehara, Kento Nakada
Theor. Comput. Sci.4
2009 Reconstruction of Interval Graphs
Masashi Kiyomi, Toshiki Saitoh, Ryuhei Uehara
COCOON3
2009 Algorithmic Folding Complexity
Jean Cardinal, Erik D. Demaine, Martin L. Demaine, Shinji Imahori, Stefan Langerman, Ryuhei Uehara
ISAAC6
2009 Route-Enabling Graph Orientation Problems
Takehiro Ito, Yuichiro Miyamoto, Hirotaka Ono 0001, Hisao Tamaki, Ryuhei Uehara
ISAAC5
2009 Random Generation and Enumeration of Bipartite Permutation Graphs
Toshiki Saitoh, Yota Otachi, Katsuhisa Yamanaka, Ryuhei Uehara
ISAAC4
2009 Counting the Number of Matchings in Chordal and Chordal Bipartite Graph Classes
Yoshio Okamoto, Ryuhei Uehara, Takeaki Uno
WG2
2009 Laminar structure of ptolemaic graphs with applications
Ryuhei Uehara, Yushi Uno
Discret. Appl. Math.1
2009 A New Approach to Graph Recognition and Applications to Distance-Hereditary Graphs
Shin-Ichi Nakano, Ryuhei Uehara, Takeaki Uno
J. Comput. Sci. Technol.2
2009 Scale free interval graphs
Naoto Miyoshi, Takeya Shigezumi, Ryuhei Uehara, Osamu Watanabe 0001
Theor. Comput. Sci.3
2008 Scale Free Interval Graphs
Naoto Miyoshi, Takeya Shigezumi, Ryuhei Uehara, Osamu Watanabe 0001
AAIM3
2008 On the Complexity of Reconfiguration Problems
Takehiro Ito, Erik D. Demaine, Nicholas J. A. Harvey, Christos H. Papadimitriou, Martha Sideri, Ryuhei Uehara, Yushi Uno
ISAAC6
2008 Enumeration of Perfect Sequences of Chordal Graph
Yasuko Matsui, Ryuhei Uehara, Takeaki Uno
ISAAC2
2008 Bandwidth of Bipartite Permutation Graphs
Ryuhei Uehara
ISAAC1
2007 A New Approach to Graph Recognition and Applications to Distance-Hereditary Graphs
Shin-Ichi Nakano, Ryuhei Uehara, Takeaki Uno
TAMC2
2007 Efficient Algorithms for Airline Problem
Shin-Ichi Nakano, Ryuhei Uehara, Takeaki Uno
TAMC2
2007 Tree Spanners for Bipartite Graphs and Probe Interval Graphs
Andreas Brandstädt, Feodor F. Dragan, Hoàng-Oanh Le, Van Bang Le, Ryuhei Uehara
Algorithmica5
2007 Linear structure of bipartite permutation graphs and the longest path problem
Ryuhei Uehara, Gabriel Valiente
Inf. Process. Lett.1
2005 Laminar Structure of Ptolemaic Graphs and Its Applications
Ryuhei Uehara, Yushi Uno
ISAAC1
2005 Linear-Time Counting Algorithms for Independent Sets in Chordal Graphs
Yoshio Okamoto, Takeaki Uno, Ryuhei Uehara
WG3
2005 Graph isomorphism completeness for chordal bipartite graphs and strongly chordal graphs
Ryuhei Uehara, Seinosuke Toda, Takayuki Nagoya
Discret. Appl. Math.1
2004 Canonical Data Structure for Interval Probe Graphs
Ryuhei Uehara
ISAAC1
2004 Efficient Algorithms for the Longest Path Problem
Ryuhei Uehara, Yushi Uno
ISAAC1
2004 A double classification tree search algorithm for index SNP selection
abstract
BACKGROUND: In population-based studies, it is generally recognized that single nucleotide polymorphism (SNP) markers are not independent. Rather, they are carried by haplotypes, groups of SNPs that tend to be coinherited. It is thus possible to choose a much smaller number of SNPs to use as indices for identifying haplotypes or haplotype blocks in genetic association studies. We refer to these characteristic SNPs as index SNPs. In order to reduce costs and work, a minimum number of index SNPs that can distinguish all SNP and haplotype patterns should be chosen. Unfortunately, this is an NP-complete problem, requiring brute force algorithms that are not feasible for large data sets. RESULTS: We have developed a double classification tree search algorithm to generate index SNPs that can distinguish all SNP and haplotype patterns. This algorithm runs very rapidly and generates very good, though not necessarily minimum, sets of index SNPs, as is to be expected for such NP-complete problems. CONCLUSIONS: A new algorithm for index SNP selection has been developed. A webserver for index SNP selection is available at http://cognia.cu-genome.org/cgi-bin/genome/snpIndex.cgi/
Peisen Zhang, Huitao Sheng, Ryuhei Uehara
BMC Bioinform.3
2003 Tree Spanners for Bipartite Graphs and Probe Interval Graphs
Andreas Brandstädt, Feodor F. Dragan, Hoàng-Oanh Le, Van Bang Le, Ryuhei Uehara
WG5
2002 Linear Time Algorithms on Chordal Bipartite and Strongly Chordal Graphs
Ryuhei Uehara
ICALP1
2000 Parallel approximation algorithms for maximum weighted matching in general graphs
Ryuhei Uehara, Zhi-Zhong Chen
Inf. Process. Lett.1
2000 Identification of Partial Disjunction, Parity, and Threshold Functions
Ryuhei Uehara, Kensei Tsuchida, Ingo Wegener
Theor. Comput. Sci.1
1999 Fast RNC and NC Algorithms for Maximal Path Sets
Ryuhei Uehara, Zhi-Zhong Chen, Xin He 0005
Theor. Comput. Sci.1
1997 A Measure of Parallelization for the Lexicographically First Maximal Subgraph Problems
Ryuhei Uehara
WG1
1997 Collapse of PP with a Semi-Random Source to BPP
Ryuhei Uehara
Inf. Process. Lett.1
1996 Fast RNC and NC Algorithms for Finding a Maximal Set of Paths with an Application
Ryuhei Uehara, Zhi-Zhong Chen, Xin He 0005
COCOON1
1995 Efficient Simulations by a Biased Coin
Ryuhei Uehara
Inf. Process. Lett.1