Related papers: Constructing Suffixient Arrays Revisited
In this work, we focus on a lightweight convolutional architecture that creates fixed-size vector embeddings of sentences. Such representations are useful for building NLP systems, including conversational agents. Our work derives from a…
Prefix parsing asks whether an input prefix can be extended to a complete string generated by a given grammar. In the weighted setting, it also provides prefix probabilities, which are central to context-free language modeling,…
Pattern matching is the most central task for text indices. Most recent indices leverage compression techniques to make pattern matching feasible for massive but highly-compressible datasets. Within this kind of indices, we propose a new…
We propose a B tree representation storing $n$ keys, each of $k$ bits, in either (a) $nk + O(nk / \lg n)$ bits or (b) $nk + O(nk \lg \lg n/ \lg n)$ bits of space supporting all B tree operations in either (a) $O(\lg n )$ time or (b) $O(\lg…
Recently, Holt and McMillan [Bionformatics 2014, ACM-BCB 2014] have proposed a simple and elegant algorithm to merge the Burrows-Wheeler transforms of a family of strings. In this paper we show that the H&M algorithm can be improved so…
Dominant sequence models like the Transformer represent structure implicitly through dense attention weights, incurring quadratic complexity. We propose RewriteNets, a novel neural architecture built on an alternative paradigm: explicit,…
A prefix normal word is a binary word with the property that no substring has more 1s than the prefix of the same length. This class of words is important in the context of binary jumbled pattern matching. In this paper we present an…
Nishimoto and Tabei [CPM, 2021] proposed r-enum, an algorithm to enumerate various characteristic substrings, including maximal repeats, in a string $T$ of length $n$ in $O(r)$ words of compressed working space, where $r \le n$ is the…
Modern genomic analyses increasingly rely on pangenomes, that is, representations of the genome of entire populations. The simplest representation of a pangenome is a set of individual genome sequences. Compared to e.g. sequence graphs,…
We describe a compression-aware method to compute all-vs-all maximal exact matches (MEM) among strings of a repetitive collection $\mathcal{T}$. The key concept in our work is the construction of a fully-balanced grammar $\mathcal{G}$ from…
Set intersection is a fundamental operation in information retrieval and database systems. This paper introduces linear space data structures to represent sets such that their intersection can be computed in a worst-case efficient way. In…
String matching is the problem of finding all the occurrences of a pattern in a text. It has been intensively studied and the Boyer-Moore string matching algorithm is probably one of the most famous solution to this problem. This algorithm…
Parameterized strings are a generalization of strings in that their characters are drawn from two different alphabets, where one is considered to be the alphabet of static characters and the other to be the alphabet of parameter characters.…
Top-down parsing has received much attention recently. Parsing expression grammars (PEG) allows construction of linear time parsers using packrat algorithm. These techniques however suffer from problem of prefix hiding. We use alternative…
For the first time we provide a succinct pattern matching index for arbitrary graphs that can be built in polynomial time, which requires less space and answers queries more efficiently than the one in [SODA 2021]. We show that, given an…
The Burrows-Wheeler Transform (BWT) is an invertible text transformation that permutes symbols of a text according to the lexicographical order of its suffixes. BWT is the main component of popular lossless compression programs (such as…
The problem of Text Indexing is a fundamental algorithmic problem in which one wishes to preprocess a text in order to quickly locate pattern queries within the text. In the ever evolving world of dynamic and on-line data, there is also a…
Due to the exponential growth of genomic data, constructing dedicated data structures has become the principal bottleneck in common bioinformatics applications. In particular, the Burrows-Wheeler Transform (BWT) is the basis of some of 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…
In this paper a sublinear time algorithm is presented for the reconstruction of functions that can be represented by just few out of a potentially large candidate set of Fourier basis functions in high spatial dimensions, a so-called…