Related papers: Relative Suffix Trees
Prediction suffix trees (PST) provide an effective tool for sequence modelling and prediction. Current prediction techniques for PSTs rely on exact matching between the suffix of the current sequence and the previously observed sequence. We…
Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In this paper we consider the basic variant where the pattern is…
Dealing with datasets of very high dimension is a major challenge in machine learning. In this paper, we consider the problem of feature selection in applications where the memory is not large enough to contain all features. In this…
We introduce a dynamic data structure for the compact representation of binary relations $\mathcal{R} \subseteq A \times B$. The data structure is a dynamic variant of the k$^2$-tree, a static compact representation that takes advantage of…
Many common sequential data sources, such as source code and natural language, have a natural tree-structured representation. These trees can be generated by fitting a sequence to a grammar, yielding a hierarchical ordering of the tokens in…
Suffix trees have recently become very successful data structures in handling large data sequences such as DNA or Protein sequences. Consequently parallel architectures have become ubiquitous. We present a novel alphabet-dependent parallel…
We describe a data structure that stores a string $S$ in space similar to that of its Lempel-Ziv encoding and efficiently supports access, rank and select queries. These queries are fundamental for implementing succinct and compressed data…
Relational queries, and in particular join queries, often generate large output results when executed over a huge dataset. In such cases, it is often infeasible to store the whole materialized output if we plan to reuse it further down a…
Suffix tree construction algorithms based on suffix links are popular because they are simple to implement, can operate online in linear time, and because the suffix links are often convenient for pattern matching. We present an approach…
We introduce a new algorithm for constructing the generalized suffix array of a collection of highly similar strings. As a first step, we construct a compressed representation of the matching statistics of the collection with respect to a…
The size of the \textit{smallest suffixient set} of positions of a string recently emerged as a new measure of string \textit{repetitiveness} -- a measure reflecting how much of repetitive content the string contains. We study how to…
Highly-repetitive collections of strings are increasingly being amassed by genome sequencing and genetic variation experiments, as well as by storing all versions of human-generated files, like webpages and source code. Existing indexes for…
For a text given in advance, the substring minimal suffix queries ask to determine the lexicographically minimal non-empty suffix of a substring specified by the location of its occurrence in the text. We develop a data structure answering…
Dependency trees help relation extraction models capture long-range relations between words. However, existing dependency-based models either neglect crucial information (e.g., negation) by pruning the dependency trees too aggressively, or…
In this paper we study the structure of suffix trees. Given an unlabeled tree $\tau$ on $n$ nodes and suffix links of its internal nodes, we ask the question "Is $\tau$ a suffix tree?", i.e., is there a string $S$ whose suffix tree has the…
We prove that longest common prefix (LCP) information can be stored in much less space than previously known. More precisely, we show that in the presence of the text and the suffix array, o(n) additional bits are sufficient to answer…
Given two positions $i$ and $j$ in a string $T$ of length $N$, a longest common extension (LCE) query asks for the length of the longest common prefix between suffixes beginning at $i$ and $j$. A compressed LCE data structure is a data…
In this paper, we present a new data structure called the packed compact trie (packed c-trie) which stores a set $S$ of $k$ strings of total length $n$ in $n \log\sigma + O(k \log n)$ bits of space and supports fast pattern matching queries…
Linguists have long held that a key aspect of natural language syntax is the recursive organization of language units into constituent structures, and research has suggested that current state-of-the-art language models lack an inherent…
Because of their superior ability to preserve sequence information over time, Long Short-Term Memory (LSTM) networks, a type of recurrent neural network with a more complex computational unit, have obtained strong results on a variety of…