Algorithm-Engineered Compressed Indexes

项目来源

日本学术振兴会基金(JSPS)

项目主持人

Koeppl Dominik

项目受资助机构

山梨大学

项目编号

25K21150

立项年度

2025

立项时间

未公开

项目级别

国家级

研究期限

未知 / 未知

受资助金额

4680000.00日元

学科

情報学基礎論関連

学科代码

未公开

基金类别

若手研究

关键词

Matrix Compression ; Pattern Matching ; Algorithm Engineering ; Substring Compression ; Generalized Pattern

参与者

未公开

参与机构

山梨大学,大学院総合研究部

项目标书摘要:Outline of Research at the Start:The primary goal of this research is to develop efficient,practical construction methods for compressed data structures,which are often limited to theoretical advancements without adequate real-world applications.While many data structures exist,their practical utility is hampered by inefficiencies in their construction and capabilities(e.g.,the types of supported queries).This project will focus on improving the speed and efficiency of constructing these structures,particularly for tasks such as graph traversal,generalized pattern matching,and substring compression。

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  • 1.Efficient Solutions toVariants ofInversion Problems ofRange Minimum Queries

    • 关键词:
    • Query processing;Consistent sequence;Constant delays;Enumeration algorithms;Inversion problems;Minimum value;Range minimum queries;Survey analysis;Unified analysis;Value-based
    • Kobayashi, Souta;Köppl, Dominik;Yoshinaka, Ryo;Shinohara, Ayumi
    • 《51st International Conference on Current Trends in Theory and Practice of Computer Science, SOFSEM 2026》
    • 2026年
    • February 9, 2026 - February 13, 2026
    • Krakow, Poland
    • 会议

    Given a set of results from range minimum queries (RMQs), our task is to construct a sequence that is consistent with the results of the queries. We study two types of RMQs: a value-based RMQ returns the minimum value and an index-based RMQ returns the index of the minimum. While the value-based version has been discussed informally in the context of competitive programming, the index-based version appears to be unexplored. In this paper, we provide a survey and unified analysis of the value-based version, and we propose efficient algorithms for the index-based version. These include algorithms for computing the lexicographically smallest consistent sequence and permutation, as well as an enumeration algorithm that outputs all consistent permutations with constant delay. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2026.

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  • 2.Counting Distinct (Non-)crossing Substrings

    • 关键词:
    • Rhenium compounds;All positions;Constant sizes;Distinct substring;LPF array;Ordered alphabets;Run;String algorithms;Sub-strings
    • Umezaki, Haruki;Shibata, Hiroki;Köppl, Dominik;Nakashima, Yuto;Inenaga, Shunsuke;Bannai, Hideo
    • 《32nd International Symposium on String Processing and Information Retrieval, SPIRE 2025》
    • 2026年
    • September 8, 2025 - September 11, 2025
    • London, United kingdom
    • 会议

    Let w be a string of length n. The problem of counting factors crossing a position - Problem 64 fromthe textbook "125 Problems in Text Algorithms" [Crochemore, Leqroc, and Rytter, 2021], asks to count the number C(w,k) (resp. N(w,k)) of distinct substrings in w that have occurrences containing (resp. not containing) a position k in w. The solutions provided in their textbook compute C(w,k) and N(w,k) in O(n) time for a single positionk in w, and thus a direct application would require O(n2) time for all positionsk=1,…,n in w. Their solution is designed for constant-size alphabets. In this paper, we present new algorithms which compute C(w,k) in O(n) total time for general ordered alphabets, and N(w,k) in O(n) total time for linearly sortable alphabets, for all positions k=1,…,n in w. © The Author(s), under exclusive license to Springer Nature Switzerland AG 2026.

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  • 3.A Survey of the Bijective Burrows-Wheeler Transform

    • 关键词:
    • Backward wave tubes;Compaction;Indexing (of information);Soft computing;Bijective string transformation;Burrows-Wheeler Transform;Compression;Construction algorithms;Index construction;Index construction algorithm;Lyndon words;Repetitiveness measure;String transformation;Text-indexing
    • Bannai, Hideo;Köppl, Dominik;Lipták, Zsuzsanna
    • 《Expanding World of Compressed Data: A Festschrift for Giovanni Manzini's 60th Birthday》
    • 2025年
    • July 25, 2025
    • Venice, Italy
    • 会议

    The Bijective BWT (BBWT), conceived by Scott in 2007, later summarized in a preprint by Gil and Scott in 2009 (arXiv 2012), is a variant of the Burrows-Wheeler Transform which is bijective: every string is the BBWT of some string. Indeed, the BBWT of a string is the extended BWT [Mantaci et al., 2007] of the factors of its Lyndon factorization. The BBWT has been receiving increasing interest in recent years. In this paper, we survey existing research on the BBWT, starting with its history and motivation. We then present algorithmic topics including construction algorithms with various complexities and an index on top of the BBWT for pattern matching. We subsequently address some properties of the BBWT as a compressor, discussing robustness to operations such as reversal, edits, rotation, as well as compression power. We close with listing other bijective variants of the BWT and open problems concerning the BBWT. © Hideo Bannai, Dominik Köppl, and Zsuzsanna Lipták.

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  • 4.Enumeration of Ordered Trees with Leaf Restrictions

    • 关键词:
    • Forestry;Time delay;Timing circuits;Trees (mathematics);Constant time delays;Enumeration algorithms;Nonnegative integers;Ordered tree;Rooted trees
    • Kobayashi, Yasuaki;Köppl, Dominik;Matsui, Yasuko;Ono, Hirotaka;Saitoh, Toshiki;Uno, Yushi
    • 《From Strings to Graphs, and Back Again: A Festschrift for Roberto Grossi's 60th Birthday 2025》
    • 2025年
    • July 25, 2025
    • Venice, Italy
    • 会议

    An α-ary tree for a constant α ≥ 2 is a rooted tree in which each node has at most α children. A node having no children is called a leaf. For a given rooted tree and a node v, the number of edges from the root to v is called the depth of v. We call a vector w = (w1, w2, . . ., wd) of nonnegative integers an (α-ary) distribution if there is an α-ary tree T such that the number of leaves at each depth i ∈ [1..d] in T is wi. Although not every vector of nonnegative integers is a distribution, a distribution can be associated with many α-ary trees. In this paper, we present an algorithm to enumerate all α-ary trees for a given distribution. Our algorithm reports the first tree in O(d + ∑di=1 wi) time, and then each subsequent α-ary tree in O(maxdi=1 wi) time by representing each tree as the difference from the previous one. The algorithm can be restricted to computing all trees that are full, i.e., trees whose nodes have exactly α or no children. © Yasuaki Kobayashi, Dominik Köppl, Yasuko Matsui, Hirotaka Ono, Toshiki Saitoh, and Yushi Uno;

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