相关论文: FM-index for dummies

A compressed full-text self-index occupies space close to that of the compressed text and simultaneously allows fast pattern matching and random access to the underlying text. Among the best compressed self-indexes, in theory and in…

Motivation: As a fundamental task in bioinformatics, searching for massive short patterns over a long text is widely accelerated by various compressed full-text indexes. These indexes are able to provide similar searching functionalities to…

The FM-index is a well-known compressed full-text index, based on the Burrows-Wheeler transform (BWT). During a pattern search, the BWT sequence is accessed at "random" locations, which is cache-unfriendly. In this paper, we are interested…

FM-indexes are a crucial data structure in DNA alignment, for example, but searching with them usually takes at least one random access per character in the query pattern. Ferragina and Fischer observed in 2007 that word-based indexes often…

Indexed pattern search in text has been studied for many decades. For small alphabets, the FM-Index provides unmatched performance, in terms of both space required and search speed. For large alphabets -- for example, when the tokens are…

In this work, we present a literature review for full-text and keyword indexes as well as our contributions (which are mostly practice-oriented). The first contribution is the FM-bloated index, which is a modification of the well-known…

It has been shown in the indexing literature that there is an essential difference between prefix/range searches on the one hand, and predecessor/rank searches on the other hand, in that the former provably allows faster query resolution.…

Text indexing is a fundamental and well-studied problem. Classic solutions either replace the original text with a compressed representation, e.g., the FM-index and its variants, or keep it uncompressed but attach some redundancy - an index…

Rank and select queries on bitmaps are essential building bricks of many compressed data structures, including text indexes, membership and range supporting spatial data structures, compressed graphs, and more. Theoretically considered yet…

Summary: We present a new method to incrementally construct the FM-index for both short and long sequence reads, up to the size of a genome. It is the first algorithm that can build the index while implicitly sorting the sequences in the…

Recently, a compressed index for similar strings, called the FM-index of alignment (FMA), has been proposed with the functionalities of pattern search and random access. The FMA is quite efficient in space requirement and pattern search…

In this paper, we present a compressed data structure for moving object trajectories in a road network, which are represented as sequences of road edges. Unlike existing compression methods for trajectories in a network, our method supports…

Factorization machines (FM) are a popular model class to learn pairwise interactions by a low-rank approximation. Different from existing FM-based approaches which use a fixed rank for all features, this paper proposes a Rank-Aware FM…

We consider the problem of representing, in a compressed format, a bit-vector $S$ of $m$ bits with $n$ 1s, supporting the following operations, where $b \in \{0, 1 \}$: $rank_b(S,i)$ returns the number of occurrences of bit $b$ in the…

Low-rank matrix factorization (MF) is an important technique in data science. The key idea of MF is that there exists latent structures in the data, by uncovering which we could obtain a compressed representation of the data. By factorizing…

Text retrieval using learned sparse representations of queries and documents has, over the years, evolved into a highly effective approach to search. It is thanks to recent advances in approximate nearest neighbor search-with the emergence…

An index on a finite-state automaton is a data structure able to locate specific patterns on the automaton's paths and consequently on the regular language accepted by the automaton itself. Cotumaccio and Prezza [SODA '21], introduced a…

The Fenwick tree is a classical implicit data structure that stores an array in such a way that modifying an element, accessing an element, computing a prefix sum and performing a predecessor search on prefix sums all take logarithmic time.…

The data structure at the core of large-scale search engines is the inverted index, which is essentially a collection of sorted integer sequences called inverted lists. Because of the many documents indexed by such engines and stringent…

The suffix array is an efficient data structure for in-memory pattern search. Suffix arrays can also be used for external-memory pattern search, via two-level structures that use an internal index to identify the correct block of suffix…