Yasuo Tabei

Takaaki Nishimoto, Yasuo Tabei

A compressed self-index stores a string in compressed form while supporting locate queries without decompression. For highly repetitive strings (arising in web crawls, versioned documents, and genomic collections), static self-indexes can match the $δ$-optimal lower bound of $Ω(δ\log(n \log σ/ (δ\log n)) \log n)$ bits up to constant factors, where $n$ is the string length, $σ$ is the alphabet size, and $δ$ is the substring complexity. Their dynamic counterparts, however, remain scarce: every existing dynamic self-index either fails to attain $δ$-optimal space, pays at least $Θ(\log n)$ time per reported occurrence during locate, or exposes the longest common prefix (LCP) of the text inside its update time. We present the dynamic RR-index, a dynamic grammar-compressed self-index built on the restricted recompression run-length straight-line program (RLSLP). To our knowledge, it is the first dynamic self-index to attain $δ$-optimal space. The index occupies expected $O(δ\log(n \log σ/ (δ\log n)) \log n)$ bits, answers locate queries in expected $O(m + \log m \log^{2} n + \mathit{occ} (\log n / \log \log n))$ time (where $m$ is the pattern length and $\mathit{occ}$ is the number of occurrences), and supports insertions and deletions of a length-$m'$ substring in expected amortized $O(m' \log^{2} n + \log^{3} n)$ time, with no dependence on the LCP. On eleven highly repetitive corpora, including a $37$ GB Wikipedia dump and a $59$ GB human-chromosome collection, the dynamic RR-index is up to $77\times$ faster than the dynamic r-index on updates and up to $11\times$ faster than other dynamic indexes on locate.

Shunsuke Kanda, Yasuo Tabei

Similarity-preserving hashing is a core technique for fast similarity searches, and it randomly maps data points in a metric space to strings of discrete symbols (i.e., sketches) in the Hamming space. While traditional hashing techniques produce binary sketches, recent ones produce integer sketches for preserving various similarity measures. However, most similarity search methods are designed for binary sketches and inefficient for integer sketches. Moreover, most methods are either inapplicable or inefficient for dynamic datasets, although modern real-world datasets are updated over time. We propose dynamic filter trie (DyFT), a dynamic similarity search method for both binary and integer sketches. An extensive experimental analysis using large real-world datasets shows that DyFT performs superiorly with respect to scalability, time performance, and memory efficiency. For example, on a huge dataset of 216 million data points, DyFT performs a similarity search 6,000 times faster than a state-of-the-art method while reducing to one-thirteenth in memory.

Shunsuke Kanda, Koh Takeuchi, Keisuke Fujii et al.

Massive datasets of spatial trajectories representing the mobility of a diversity of moving objects are ubiquitous in research and industry. Similarity search of a large collection of trajectories is indispensable for turning these datasets into knowledge. Locality sensitive hashing (LSH) is a powerful technique for fast similarity searches. Recent methods employ LSH and attempt to realize an efficient similarity search of trajectories; however, those methods are inefficient in terms of search time and memory when applied to massive datasets. To address this problem, we present the trajectory-indexing succinct trit-array trie (tSTAT), which is a scalable method leveraging LSH for trajectory similarity searches. tSTAT quickly performs the search on a tree data structure called trie. We also present two novel techniques that enable to dramatically enhance the memory efficiency of tSTAT. One is a node reduction technique that substantially omits redundant trie nodes while maintaining the time performance. The other is a space-efficient representation that leverages the idea behind succinct data structures (i.e., a compressed data structure supporting fast data operations). We experimentally test tSTAT on its ability to retrieve similar trajectories for a query from large collections of trajectories and show that tSTAT performs superiorly in comparison to state-of-the-art similarity search methods.

Shunsuke Kanda, Yasuo Tabei

Recently, randomly mapping vectorial data to strings of discrete symbols (i.e., sketches) for fast and space-efficient similarity searches has become popular. Such random mapping is called similarity-preserving hashing and approximates a similarity metric by using the Hamming distance. Although many efficient similarity searches have been proposed, most of them are designed for binary sketches. Similarity searches on integer sketches are in their infancy. In this paper, we present a novel space-efficient trie named $b$-bit sketch trie on integer sketches for scalable similarity searches by leveraging the idea behind succinct data structures (i.e., space-efficient data structures while supporting various data operations in the compressed format) and a favorable property of integer sketches as fixed-length strings. Our experimental results obtained using real-world datasets show that a trie-based index is built from integer sketches and efficiently performs similarity searches on the index by pruning useless portions of the search space, which greatly improves the search time and space-efficiency of the similarity search. The experimental results show that our similarity search is at most one order of magnitude faster than state-of-the-art similarity searches. Besides, our method needs only 10 GiB of memory on a billion-scale database, while state-of-the-art similarity searches need 29 GiB of memory.

Shunsuke Kanda, Dominik Köppl, Yasuo Tabei et al.

A keyword dictionary is an associative array whose keys are strings. Recent applications handling massive keyword dictionaries in main memory have a need for a space-efficient implementation. When limited to static applications, there are a number of highly-compressed keyword dictionaries based on the advancements of practical succinct data structures. However, as most succinct data structures are only efficient in the static case, it is still difficult to implement a keyword dictionary that is space efficient and dynamic. In this article, we propose such a keyword dictionary. Our main idea is to embrace the path decomposition technique, which was proposed for constructing cache-friendly tries. To store the path-decomposed trie in small memory, we design data structures based on recent compact hash trie representations. Experiments on real-world datasets reveal that our dynamic keyword dictionary needs up to 68% less space than the existing smallest ones, while achieving a relevant space-time tradeoff.

Vo Nguyen Le Duy, Takuto Sakuma, Taiju Ishiyama et al.

We study the problem of discriminative sub-trajectory mining. Given two groups of trajectories, the goal of this problem is to extract moving patterns in the form of sub-trajectories which are more similar to sub-trajectories of one group and less similar to those of the other. We propose a new method called Statistically Discriminative Sub-trajectory Mining (SDSM) for this problem. An advantage of the SDSM method is that the statistical significance of the extracted sub-trajectories are properly controlled in the sense that the probability of finding a false positive sub-trajectory is smaller than a specified significance threshold alpha (e.g., 0.05), which is indispensable when the method is used in scientific or social studies under noisy environment. Finding such statistically discriminative sub-trajectories from massive trajectory dataset is both computationally and statistically challenging. In the SDSM method, we resolve the difficulties by introducing a tree representation among sub-trajectories and running an efficient permutation-based statistical inference method on the tree. To the best of our knowledge, SDSM is the first method that can efficiently extract statistically discriminative sub-trajectories from massive trajectory dataset. We illustrate the effectiveness and scalability of the SDSM method by applying it to a real-world dataset with 1,000,000 trajectories which contains 16,723,602,505 sub-trajectories.

Yasuo Tabei, Yoshihiro Yamanishi, Rasmus Pagh

String kernels are attractive data analysis tools for analyzing string data. Among them, alignment kernels are known for their high prediction accuracies in string classifications when tested in combination with SVM in various applications. However, alignment kernels have a crucial drawback in that they scale poorly due to their quadratic computation complexity in the number of input strings, which limits large-scale applications in practice. We address this need by presenting the first approximation for string alignment kernels, which we call space-efficient feature maps for edit distance with moves (SFMEDM), by leveraging a metric embedding named edit sensitive parsing (ESP) and feature maps (FMs) of random Fourier features (RFFs) for large-scale string analyses. The original FMs for RFFs consume a huge amount of memory proportional to the dimension d of input vectors and the dimension D of output vectors, which prohibits its large-scale applications. We present novel space-efficient feature maps (SFMs) of RFFs for a space reduction from O(dD) of the original FMs to O(d) of SFMs with a theoretical guarantee with respect to concentration bounds. We experimentally test SFMEDM on its ability to learn SVM for large-scale string classifications with various massive string data, and we demonstrate the superior performance of SFMEDM with respect to prediction accuracy, scalability and computation efficiency.