Related papers: FM-Indexing Grammars Induced by Suffix Sorting for…

In this paper, we consider the problem of compressing a trie while supporting the powerful \emph{locate} queries: to return the pre-order identifiers of all nodes reached by a path labeled with a given query pattern. Our result builds on…

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…

Indexing very large collections of strings, such as those produced by the widespread next generation sequencing technologies, heavily relies on multistring generalization of the Burrows-Wheeler Transform (BWT): large requirements of…

The Burrows-Wheeler-Transform (BWT) is an invertible permutation of a text known to be highly compressible but also useful for sequence analysis, what makes the BWT highly attractive for lossless data compression. In this paper, we present…

The Burrows-Wheeler-Transform (BWT), a reversible string transformation, is one of the fundamental components of many current data structures in string processing. It is central in data compression, as well as in efficient query algorithms…

Cartesian tree matching is a form of generalized pattern matching where a substring of the text matches with the pattern if they share the same Cartesian tree. This form of matching finds application for time series of stock prices and can…

We characterize those strings whose suffix arrays are based on arithmetic progressions, in particular, arithmetically progressed permutations where all pairs of successive entries of the permutation have the same difference modulo the…

The move structure represents permutations with long contiguously permuted intervals in compressed space with optimal query time. They have become an important feature of compressed text indexes using space proportional to the number of…

When building Burrows-Wheeler Transforms (BWTs) of truly huge datasets, prefix-free parsing (PFP) can use an unreasonable amount of memory. In this paper we show how if a dataset can be broken down into small datasets that are not very…

Retrieval-augmented language models (LMs) have received much attention recently. However, typically the retriever is not trained jointly as a native component of the LM, but added post-hoc to an already-pretrained LM, which limits the…

In recent years, pangenomes received increasing attention from the scientific community for their ability to incorporate population variation information and alleviate reference genome bias. Maximal Exact Matches (MEMs) and Maximal Unique…

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…

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…

Detecting all the strings that occur in a text more frequently or less frequently than expected according to an IID or a Markov model is a basic problem in string mining, yet current algorithms are based on data structures that are either…

The Burrows-Wheeler Transform (BWT) is an important technique both in data compression and in the design of compact indexing data structures. It has been generalized from single strings to collections of strings and some classes of labeled…

The longest common prefix array is a very advantageous data structure that, combined with the suffix array and the Burrows-Wheeler transform, allows to efficiently compute some combinatorial properties of a string useful in several…

Recently, Cenzato et al.\ proposed a new text index, called the \emph{suffixient array}, which is a subset of the suffix array and supports locating a single pattern occurrence or finding its maximal exact matches (MEMs), assuming random…

The rise of repetitive datasets has lately generated a lot of interest in compressed self-indexes based on dictionary compression, a rich and heterogeneous family that exploits text repetitions in different ways. For each such compression…

In this paper, we describe a new type of match between a pattern and a text that aren't necessarily maximal in the query, but still contain useful matching information: locally maximal exact matches (LEMs). There are usually a large amount…

Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…