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Research Output 2001 2019

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Article
2019

Dynamic index and LZ factorization in compressed space

Nishimoto, T., Tomohiro, I., Inenaga, S., Bannai, H. & Takeda, M., Jan 1 2019, In : Discrete Applied Mathematics.

Research output: Contribution to journalArticle

Factorization
Deletion
Insertion
Encoding
Signature

Efficient dynamic dictionary matching with DAWGs and AC-automata

Hendrian, D., Inenaga, S., Yoshinaka, R. & Shinohara, A., Nov 5 2019, In : Theoretical Computer Science. 792, p. 161-172 12 p.

Research output: Contribution to journalArticle

Glossaries
Automata
Insertion
Pattern matching
Pattern Matching

On the size of the smallest alphabet for Lyndon trees

Nakashima, Y., Takagi, T., Inenaga, S., Bannai, H. & Takeda, M., Nov 5 2019, In : Theoretical Computer Science. 792, p. 131-143 13 p.

Research output: Contribution to journalArticle

Binary trees
Ordered Trees
Strings
Binary Tree
Leaves
2018
4 Citations (Scopus)

A hardness result and new algorithm for the longest common palindromic subsequence problem

Inenaga, S. & Hyyrö, H., Jan 2018, In : Information Processing Letters. 129, p. 11-15 5 p.

Research output: Contribution to journalArticle

Longest Common Subsequence
Hardness
Denote
Strings
Distinct
1 Citation (Scopus)

Algorithms and combinatorial properties on shortest unique palindromic substrings

Inoue, H., Nakashima, Y., Mieno, T., Inenaga, S., Bannai, H. & Takeda, M., Sep 1 2018, In : Journal of Discrete Algorithms. 52-53, p. 122-132 11 p.

Research output: Contribution to journalArticle

Strings
Interval
Query
Palindrome
Optimal Solution
1 Citation (Scopus)

Diverse Palindromic Factorization is NP-Complete

Bannai, H., Gagie, T., Inenaga, S., Kärkkäinen, J., Kempa, D., Piakowski, M. & Sugimoto, S., Feb 1 2018, In : International Journal of Foundations of Computer Science. 29, 2, p. 143-163 21 p.

Research output: Contribution to journalArticle

Factorization

Dynamic RLE-Compressed Edit Distance Tables under General Weighted Cost Functions

Hyyrö, H. & Inenaga, S., Jun 1 2018, In : International Journal of Foundations of Computer Science. 29, 4, p. 623-645 23 p.

Research output: Contribution to journalArticle

Cost functions
Costs
9 Citations (Scopus)
Palindrome
Optimal Algorithm
Integer
Upper bound
2017
1 Citation (Scopus)

Efficient Computation of Substring Equivalence Classes with Suffix Arrays

Narisawa, K., Hiratsuka, H., Inenaga, S., Bannai, H. & Takeda, M., Oct 1 2017, In : Algorithmica. 79, 2, p. 291-318 28 p.

Research output: Contribution to journalArticle

Suffix Array
Equivalence classes
Equivalence class
Strings
Text Indexing
1 Citation (Scopus)

Inferring strings from Lyndon factorization

Nakashima, Y., Okabe, T., I, T., Inenaga, S., Bannai, H. & Takeda, M., Aug 15 2017, In : Theoretical Computer Science. 689, p. 147-156 10 p.

Research output: Contribution to journalArticle

Factorization
Strings
p.m.
Lyndon Words
Unique factorisation
1 Citation (Scopus)

Packed compact tries: A fast and efficient data structure for online string processing

Takagi, T., Inenaga, S., Sadakane, K. & Arimura, H., Sep 1 2017, In : IEICE Transactions on Fundamentals of Electronics, Communications and Computer Sciences. E100A, 9, p. 1785-1793 9 p.

Research output: Contribution to journalArticle

Pattern matching
Data structures
Data Structures
Strings
Pattern Matching
20 Citations (Scopus)

The "runs" theorem

Bannai, H., I, T., Inenaga, S., Nakashima, Y., Takeda, M. & Tsuruta, K., Jan 1 2017, In : SIAM Journal on Computing. 46, 5, p. 1501-1514 14 p.

Research output: Contribution to journalArticle

Strings
Theorem
Linear-time Algorithm
Lyndon Words
Factorization
2016
5 Citations (Scopus)

Closed factorization

Badkobeh, G., Bannai, H., Goto, K., I, T., Iliopoulos, C. S., Inenaga, S., Puglisi, S. J. & Sugimoto, S., Oct 30 2016, In : Discrete Applied Mathematics. 212, p. 23-29 7 p.

Research output: Contribution to journalArticle

Factorization
Strings
Closed
Sturmian Words
Factorise
9 Citations (Scopus)

Faster Lyndon factorization algorithms for SLP and LZ78 compressed text

I, T., Nakashima, Y., Inenaga, S., Bannai, H. & Takeda, M., Dec 20 2016, In : Theoretical Computer Science. 656, p. 215-224 10 p.

Research output: Contribution to journalArticle

Straight-line Programs
Factorization
Data structures
Preprocessing
Data Structures
4 Citations (Scopus)

Generalized pattern matching and periodicity under substring consistent equivalence relations

Matsuoka, Y., Aoki, T., Inenaga, S., Bannai, H. & Takeda, M., Dec 20 2016, In : Theoretical Computer Science. 656, p. 225-233 9 p.

Research output: Contribution to journalArticle

Pattern matching
Pattern Matching
Equivalence relation
Periodicity
Strings
2015
5 Citations (Scopus)

Compressed automata for dictionary matching

I, T., Nishimoto, T., Inenaga, S., Bannai, H. & Takeda, M., May 1 2015, In : Theoretical Computer Science. 578, p. 30-41 12 p.

Research output: Contribution to journalArticle

Glossaries
Automata
Straight-line Programs
Matching Problem
Dictionary
5 Citations (Scopus)

Constructing LZ78 tries and position heaps in linear time for large alphabets

Nakashima, Y., I, T., Inenaga, S., Bannai, H. & Takeda, M., Sep 1 2015, In : Information Processing Letters. 115, 9, p. 655-659 5 p.

Research output: Contribution to journalArticle

Heap
Linear Time
Strings
Factorization
Suffix Tree
7 Citations (Scopus)

Detecting regularities on grammar-compressed strings

I, T., Matsubara, W., Shimohira, K., Inenaga, S., Bannai, H., Takeda, M., Narisawa, K. & Shinohara, A., Feb 1 2015, In : Information and Computation. 240, p. 74-89 16 p.

Research output: Contribution to journalArticle

Straight-line Programs
Grammar
Strings
Regularity
Context free grammars
3 Citations (Scopus)

Dynamic edit distance table under a general weighted cost function

Hyyrö, H., Narisawa, K. & Inenaga, S., Sep 1 2015, In : Journal of Discrete Algorithms. 34, p. 2-17 16 p.

Research output: Contribution to journalArticle

Edit Distance
Cost functions
Cost Function
Table
Strings
2014
9 Citations (Scopus)

Inferring strings from suffix trees and links on a binary alphabet

I, T., Inenaga, S., Bannai, H. & Takeda, M., Jan 30 2014, In : Discrete Applied Mathematics. 163, PART 3, p. 316-325 10 p.

Research output: Contribution to journalArticle

Suffix Tree
Reverse engineering
Strings
Binary
Information retrieval
2013
11 Citations (Scopus)

Fast q-gram mining on SLP compressed strings

Goto, K., Bannai, H., Inenaga, S. & Takeda, M., Jan 1 2013, In : Journal of Discrete Algorithms. 18, p. 89-99 11 p.

Research output: Contribution to journalArticle

Straight-line Programs
Mining
Strings
Data Classification
Computational Experiments
6 Citations (Scopus)

Palindrome pattern matching

I, T., Inenaga, S. & Takeda, M., Apr 29 2013, In : Theoretical Computer Science. 483, p. 162-170 9 p.

Research output: Contribution to journalArticle

Palindrome
Pattern matching
Pattern Matching
Strings
Matching Problem
2012
4 Citations (Scopus)

An efficient algorithm to test square-freeness of strings compressed by straight-line programs

Bannai, H., Gagie, T., I, T., Inenaga, S., Landau, G. M. & Lewenstein, M., Oct 15 2012, In : Information Processing Letters. 112, 19, p. 711-714 4 p.

Research output: Contribution to journalArticle

Straight-line Programs
Efficient Algorithms
Strings
Square free
Arbitrary
3 Citations (Scopus)

Finding characteristic substrings from compressed texts

Inenaga, S. & Bannai, H., Feb 1 2012, In : International Journal of Foundations of Computer Science. 23, 2, p. 261-280 20 p.

Research output: Contribution to journalArticle

Equivalence classes
Computer science
Polynomials
2011

Missing pattern discovery

Angelov, S., Inenaga, S., Kivioja, T. & Mäkinen, V., Jun 1 2011, In : Journal of Discrete Algorithms. 9, 2, p. 153-165 13 p.

Research output: Contribution to journalArticle

Pattern Discovery
Genes
Experiments
Genome
Experiment

Password based anonymous authentication with private information retrieval

Nakamura, T., Inenaga, S., Ikeda, D., Baba, K. & Yasuura, H., Apr 1 2011, In : Journal of Digital Information Management. 9, 2, p. 72-78 7 p.

Research output: Contribution to journalArticle

Information retrieval
information retrieval
Authentication
service provider
Private information
11 Citations (Scopus)

Verifying and enumerating parameterized border arrays

I, T., Inenaga, S., Bannai, H. & Takeda, M., Nov 25 2011, In : Theoretical Computer Science. 412, 50, p. 6959-6981 23 p.

Research output: Contribution to journalArticle

Pattern matching
Pattern Matching
Matching Problem
Linear-time Algorithm
Binary
2009
47 Citations (Scopus)

Efficient algorithms to compute compressed longest common substrings and compressed palindromes

Matsubara, W., Inenaga, S., Ishino, A., Shinohara, A., Nakamura, T. & Hashimoto, K., Mar 1 2009, In : Theoretical Computer Science. 410, 8-10, p. 900-913 14 p.

Research output: Contribution to journalArticle

Straight-line Programs
Palindrome
Efficient Algorithms
Strings
Polynomials
9 Citations (Scopus)

Linear-Time text compression by longest-first substitution

Nakamura, R., Inenaga, S., Bannai, H., Funamoto, T., Takeda, M. & Shinohara, A., Dec 1 2009, In : Algorithms. 2, 4, p. 1429-1448 20 p.

Research output: Contribution to journalArticle

Text Compression
Substitution
Linear Time
Substitution reactions
Linear-time Algorithm
2008

Reachability on suffix tree graphs

Higa, Y., Bannai, H., Inenaga, S. & Takeda, M., Feb 1 2008, In : International Journal of Foundations of Computer Science. 19, 1, p. 147-162 16 p.

Research output: Contribution to journalArticle

Merging
Labeling
2005
1 Citation (Scopus)

A fully compressed pattern matching algorithm for simple collage systems

Inenaga, S., Shinohara, A. & Takeda, M., Dec 1 2005, In : International Journal of Foundations of Computer Science. 16, 6, p. 1155-1166 12 p.

Research output: Contribution to journalArticle

Pattern matching
Glossaries
30 Citations (Scopus)

On-line construction of compact directed acyclic word graphs

Inenaga, S., Hoshino, H., Shinohara, A., Takeda, M., Arikawa, S., Mauri, G. & Pavesi, G., Mar 1 2005, In : Discrete Applied Mathematics. 146, 2, p. 156-179 24 p.

Research output: Contribution to journalArticle

Suffix Tree
Graph in graph theory
Linear Space
Linear Time
Strings
2004
4 Citations (Scopus)
Context free grammars
Context-free Grammar
Pattern matching
Pattern Matching
Matching Algorithm
7 Citations (Scopus)

Compact directed acyclic word graphs for a sliding window

Inenaga, S., Shinohara, A., Takeda, M. & Arikawa, S., Jan 1 2004, In : Journal of Discrete Algorithms. 2, 1 SPEC. ISS., p. 33-51 19 p.

Research output: Contribution to journalArticle

Suffix Tree
Sliding Window
Data structures
Data Structures
Data compression
19 Citations (Scopus)

Efficiently finding regulatory elements using correlation with gene expression

Bannai, H., Inenaga, S., Shinohara, A., Takeda, M. & Miyano, S., Jun 1 2004, In : Journal of bioinformatics and computational biology. 2, 2, p. 273-288 16 p.

Research output: Contribution to journalArticle

Gene expression
Gene Expression
Microarrays
Genes
DNA sequences
10 Citations (Scopus)
Strings
Efficient Algorithms
Denote
Form
Class
3 Citations (Scopus)

Ternary directed acyclic word graphs

Miyamoto, S., Inenaga, S., Takeda, M. & Shinohara, A., Nov 29 2004, In : Theoretical Computer Science. 328, 1-2, p. 97-111 15 p.

Research output: Contribution to journalArticle

Pattern matching
Ternary
Data structures
Graph in graph theory
Experiments
2003
14 Citations (Scopus)
Pattern matching
Strings
Pattern Matching
Pruning
Class
39 Citations (Scopus)
Strings
Graph in graph theory
Suffix Array
Subsequence
benzoylprop-ethyl
6 Citations (Scopus)
Text Compression
Substitution
Linear Time
Substitution reactions
Line
2 Citations (Scopus)
Pattern matching
Ternary
Data structures
Binary search
Graph in graph theory
2002
17 Citations (Scopus)
Introns
Zebrafish
Diptera
Gene Expression
Datasets