Takashi Horiyama

Hokkaido University

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Trends

Author Order

Document Type

Co-Authors

Ryuhei Uehara

Japan Advanced Institute of Science and Technology

Takeaki Uno

National Institute of Informatics

Katsuhisa Yamanaka

Iwate University

Jun Kawahara

Kyoto University

Toshiki Saitoh

Kyushu Institute of Technology

Yota Otachi

Nagoya University

Shin-ichi Minato

Kyoto University

Toshihide Ibaraki

Kyoto College of Graduate Studies for Informatics

K. Seto

Hokkaido University

Kazuo Iwama

National Tsing Hua University

Cooperative Institutions

Kyoto University

Hokkaido University

The University of Tokyo

Japan Science and Technology Agency

Tohoku University

Kyushu University

Japan Advanced Institute of Science and Technology

Waseda University

Nara Institute of Science and Technology

Kyoto College of Graduate Studies for Informatics

Author Statistics

Papers

Citation

H-Index

i-10 index

Research Field

Deciphering Time Scale Hierarchy in Reaction Networks

The Journal of Physical Chemistry B (2015)

Yutaka Nagahata Satoshi Maeda Hiroshi Teramoto Takashi Horiyama Tetsuya Taketsugu

Markovian dynamics on complex reaction networks are one of the most intriguing subjects in a wide range of research fields including chemical reactions, biological physics, and ecology. To represent the global kinetics from one node (corresponding to a basin on an energy landscape) to another requires information on multiple pathways that directly or indirectly connect these two nodes through the entire network. In this paper we present a scheme to extract a hierarchical set of global transition states (TSs) over a discrete-time Markov chain derived from first-order rate equations. The TSs can naturally take into account the multiple pathways connecting any pair of nodes. We also propose a new type of disconnectivity graph (DG) to capture the hierarchical organization of different time scales of reactions that can capture changes in the network due to changes in the time scale of observation. The crux is the introduction of the minimum conductance cut (MCC) in graph clustering, corresponding to the dividing surface across the network having the "smallest" transition probability between two disjoint subnetworks (superbasins on the energy landscape) in the network. We present a new combinatorial search algorithm for finding this MCC. We apply our method to a reaction network of Claisen rearrangement of allyl vinyl ether that consists of 23 nodes and 66 links (saddles on the energy landscape) connecting them. We compare the kinetic properties of our DG to those of the transition matrix of the rate equations and show that our graph can properly reveal the hierarchical organization of time scales in a network.

Energy landscape

Stochastic matrix

Clustering coefficient

Transition rate matrix

10.1021/acs.jpcb.5b09941

Cite

Citations (17)

Internal Longest Palindrome Queries in Optimal Time

Lecture notes in computer science (2023)

Kazuki Mitani Takuya Mieno K. Seto Takashi Horiyama

Substring

10.1007/978-3-031-27051-2_12

Cite

Citations (1)

Enumerating All Spanning Shortest Path Forests with Distance and Capacity Constraints

IEICE Transactions on Fundamentals of Electronics Communications and Computer Sciences (2018)

Yu Nakahata Jun Kawahara Takashi Horiyama Shoji Kasahara

This paper studies a variant of the graph partitioning problem, called the evacuation planning problem, which asks us to partition a target area, represented by a graph, into several regions so that each region contains exactly one shelter. Each region must be convex to reduce intersections of evacuation routes, the distance between each point to a shelter must be bounded so that inhabitants can quickly evacuate from a disaster, and the number of inhabitants assigned to each shelter must not exceed the capacity of the shelter. This paper formulates the convexity of connected components as a spanning shortest path forest for general graphs, and proposes a novel algorithm to tackle this multi-objective optimization problem. The algorithm not only obtains a single partition but also enumerates all partitions simultaneously satisfying the above complex constraints, which is difficult to be treated by existing algorithms, using zero-suppressed binary decision diagrams (ZDDs) as a compressed expression. The efficiency of the proposed algorithm is confirmed by the experiments using real-world map data. The results of the experiments show that the proposed algorithm can obtain hundreds of millions of partitions satisfying all the constraints for input graphs with a hundred of edges in a few minutes.

Convexity

10.1587/transfun.e101.a.1363

Cite

Citations (1)

Look Up Table Compaction Based on Folding of Logic Functions

Shinji Kimura Atsushi Ishii Takashi Horiyama Masaki Nakanishi Hirotsugu Kajihara

Table (database)

Folding (DSP implementation)

Cite

Citations (0)

Base Location Problems for Base-Monotone Regions

Lecture notes in computer science (2013)

Jinhee Chun Takashi Horiyama Takehiro Ito Natsuda Kaothanthong Hirotaka Ono

Disjoint sets

Base (topology)

10.1007/978-3-642-36065-7_7

Cite

Citations (1)

Continuous Flattening of Regular Dodecahedron and Regular Icosahedron

Takashi Horiyama 堀山貴史 Jin-ichi Itoh 伊藤仁一 Naoki Katoh

Dodecahedron

Flattening

Source

Cite

Citations (0)

Enumerating Polyominoes of p4 Tiling by the Reverse Search (Theoretical Computer Science and Its Applications)

数理解析研究所講究録 (2009)

Takashi Horiyama Masato Samejima

Polyomino

Source

Cite

Citations (0)

Sankaku-tori: An Old Western-Japanese Game Played on a Point Set

Journal of Information Processing (2017)

Takashi Horiyama Takashi Iizuka Masashi Kiyomi Yoshio Okamoto Ryuhei Uehara

We study a combinatorial game named "sankaku-tori" in Japanese, which means "triangle-taking" in English.It is an old pencil-and-paper game for two players played in Western Japan.The game is played on points on the plane in general position.In each turn, a player adds a line segment to join two points, and the game ends when a triangulation of the point set is completed.The player who completes more triangles than the other wins.In this paper, we formalize this game and investigate three restricted variants of this game.We first investigate a solitaire variant; for a given set of points and line segments with two integers t and k, the problem asks if you can obtain t triangles after k moves.We show that this variant is NP-complete in general.The second variant is the standard two player version, but the points are in convex position.In this case, the first player has a nontrivial winning strategy.The last variant is a natural extension of the second one; we have the points in convex position but one point inside.Then, it turns out that the first player has no winning strategy.

10.2197/ipsjjip.25.708

Cite

Citations (1)

Design and Implementation of LSI for Speech Recognition with Learning Mechanism Using C Language

Technical report of IEICE. VLD (2000)

Kazuhiro Nakamura Qiang Zhu Shinji Maruoka Takashi Horiyama Shinji Kimura

Source

Cite

Citations (0)

Accelerated enumeration of derivative structures using zero-suppressed binary decision diagram

Bulletin of the American Physical Society (2020)

Kohei Shinohara Atsuto Seko Takashi Horiyama Masakazu Ishihata Junya Honda