Related papers: Composite repetition-aware data structures
A suffix tree is a data structure used mainly for pattern matching. It is known that the space complexity of simple suffix trees is quadratic in the length of the string. By a slight modification of the simple suffix trees one gets the…
Advances in DNA sequencing mean databases of thousands of human genomes will soon be commonplace. In this paper we introduce a simple technique for reducing the size of conventional indexes on such highly repetitive texts. Given upper…
An indexed sequence of strings is a data structure for storing a string sequence that supports random access, searching, range counting and analytics operations, both for exact matches and prefix search. String sequences lie at the core of…
Words in some natural languages can have a composite structure. Elements of this structure include the root (that could also be composite), prefixes and suffixes with which various nuances and relations to other words can be expressed.…
In many real-world database systems, a large fraction of the data is represented by strings: sequences of letters over some alphabet. This is because strings can easily encode data arising from different sources. It is often crucial to…
Boolean networks have been widely used in many areas of science and engineering to represent various dynamical behaviour. In systems biology, they became useful tools to study the dynamical characteristics of large-scale biomolecular…
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…
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…
Complex information needs may involve set-compositional queries using conjunction, disjunction, and exclusion, yet it remains unclear whether current retrieval paradigms genuinely satisfy such constraints or exploit `semantic shortcuts'. We…
Ordinals can help prove termination for dependently typed programs. Brouwer trees are a particular ordinal notation that make it very easy to assign sizes to higher order data structures. They extend natural numbers with a limit…
We consider strategies to organize easily updatable associative arrays in external memory. These arrays are used for full-text search. We study indexes with different keys: single word form, two word forms, and sequences of word forms. The…
Data duplication during pretraining can degrade generalization and lead to memorization, motivating aggressive deduplication pipelines. However, at web scale, it is unclear what constitutes a ``duplicate'': beyond surface-form matches,…
Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their…
The task of accumulating a portion of a list of values, whose values may be updated at any time, is widely used throughout various applications in computer science. While it is trivial to accomplish this task without any constraints,…
Most existing recursive neural network (RvNN) architectures utilize only the structure of parse trees, ignoring syntactic tags which are provided as by-products of parsing. We present a novel RvNN architecture that can provide dynamic…
We study the asymptotics and fine-scale behavior of quantitative combinatorial measures of infinite words and related dynamical and algebraic structures. We construct infinite recurrent words $w$ whose complexity functions $p_w(n)$ are…
Many different classification tasks need to manage structured data, which are usually modeled as graphs. Moreover, these graphs can be dynamic, meaning that the vertices/edges of each graph may change during time. Our goal is to jointly…
Given a random text over a finite alphabet, we study the frequencies at which fixed-length words occur as subsequences. As the data size grows, the joint distribution of word counts exhibits a rich asymptotic structure. We investigate all…
Data generated from a system of interest typically consists of measurements from an ensemble of subjects across multiple response and covariate features, and is naturally represented by one response-matrix against one covariate-matrix.…
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…