Related papers: Relative Suffix Trees
The Block Tree (BT) is a novel compact data structure designed to compress sequence collections. It obtains compression ratios close to Lempel-Ziv and supports efficient direct access to any substring. The BT divides the text recursively…
Sampling (evenly) the suffixes from the suffix array is an old idea trading the pattern search time for reduced index space. A few years ago Claude et al. showed an alphabet sampling scheme allowing for more efficient pattern searches…
In many modern applications, including analysis of gene expression and text documents, the data are noisy, high-dimensional, and unordered--with no particular meaning to the given order of the variables. Yet, successful learning is often…
In this paper, we propose a new indexing structure for parameterized strings which we call PLSTs, by generalizing linear-size suffix tries for ordinary strings. Two parameterized strings are said to match if there is a bijection on the…
Given a string $T$, it is known that its suffix tree can be represented using the compact directed acyclic word graph (CDAWG) with $e_T$ arcs, taking overall $O(e_T+e_{{\overline{T}}})$ words of space, where ${\overline{T}}$ is the reverse…
The suffix array is the key to efficient solutions for myriads of string processing problems in different applications domains, like data compression, data mining, or Bioinformatics. With the rapid growth of available data, suffix array…
We show how to build several data structures of central importance to string processing, taking as input the Burrows-Wheeler transform (BWT) and using small extra working space. Let $n$ be the text length and $\sigma$ be the alphabet size.…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Relative Lempel-Ziv (RLZ) parsing is a dictionary compression method in which a string $S$ is compressed relative to a second string $R$ (called the reference) by parsing $S$ into a sequence of substrings that occur in $R$. RLZ is…
Data augmentation is an effective approach to tackle over-fitting. Many previous works have proposed different data augmentations strategies for NLP, such as noise injection, word replacement, back-translation etc. Though effective, they…
The problem of selecting small groups of itemsets that represent the data well has recently gained a lot of attention. We approach the problem by searching for the itemsets that compress the data efficiently. As a compression technique we…
We introduce top trees as a design of a new simpler interface for data structures maintaining information in a fully-dynamic forest. We demonstrate how easy and versatile they are to use on a host of different applications. For example, we…
We consider a sliding window $W$ over a stream of characters from some alphabet of constant size. The user wants to perform deterministic substring matching on the current sliding window content and obtain positions of the matches. We…
Highly-concurrent system models with vast state spaces like Chemical Reaction Networks (CRNs) that model biological and chemical systems pose a formidable challenge to cutting-edge formal analysis tools. Although many symbolic approaches…
In this paper, a new and novel data structure is proposed to dynamically insert and delete segments. Unlike the standard segment trees[3], the proposed data structure permits insertion of a segment with interval range beyond the interval…
Wavelet trees are widely used in the representation of sequences, permutations, text collections, binary relations, discrete points, and other succinct data structures. We show, however, that this still falls short of exploiting all of the…
Data augmentation is widely used for training a neural network given little labeled data. A common practice of augmentation training is applying a composition of multiple transformations sequentially to the data. Existing augmentation…
A Concept Tree is a structure for storing knowledge where the trees are stored in a database called a Concept Base. It sits between the highly distributed neural architectures and the distributed information systems, with the intention of…
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…
In this paper, we consider a tree-structured data model used in many commercial databases like Dremel, F1, JSON stores. We define identity and referential constraints within each tree-structured record. The query language is a variant of…