Related papers: Compressed Indexing for Consecutive Occurrences

The problem of storing a set of strings --- a string dictionary --- in compact form appears naturally in many cases. While classically it has represented a small part of the whole data to be processed (e.g., for Natural Language processing…

Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…

Perfect sorting by reversals, a problem originating in computational genomics, is the process of sorting a signed permutation to either the identity or to the reversed identity permutation, by a sequence of reversals that do not break any…

An index for a finite automaton is a powerful data structure that supports locating paths labeled with a query pattern, thus solving pattern matching on the underlying regular language. In this paper, we solve the long-standing problem of…

We consider subsequences with gap constraints, i.e., length-k subsequences p that can be embedded into a string w such that the induced gaps (i.e., the factors of w between the positions to which p is mapped to) satisfy given gap…

An increasing number of scientific applications are making use of irregular data access patterns. An important class of such patterns involve subscripted-subscripts, wherein an array value appears in the index expression of another array.…

This article presents the use of Answer Set Programming (ASP) to mine sequential patterns. ASP is a high-level declarative logic programming paradigm for high level encoding combinatorial and optimization problem solving as well as…

We describe a substring search problem that arises in group presentation simplification processes. We suggest a two-level searching model: skip and match levels. We give two timestamp algorithms which skip searching parts of the text where…

A consecutive pattern in a permutation $\pi$ is another permutation $\sigma$ determined by the relative order of a subsequence of contiguous entries of $\pi$. Traditional notions such as descents, runs and peaks can be viewed as particular…

Sparse coding is a crucial subroutine in algorithms for various signal processing, deep learning, and other machine learning applications. The central goal is to learn an overcomplete dictionary that can sparsely represent a given input…

An approximate textual retrieval algorithm for searching sources with high levels of defects is presented. It considers splitting the words in a query into two overlapping segments and subsequently building composite regular expressions…

We present a new algorithm for subsequence matching in grammar compressed strings. Given a grammar of size $n$ compressing a string of size $N$ and a pattern string of size $m$ over an alphabet of size $\sigma$, our algorithm uses…

Jumbled indexing is the problem of indexing a text $T$ for queries that ask whether there is a substring of $T$ matching a pattern represented as a Parikh vector, i.e., the vector of frequency counts for each character. Jumbled indexing has…

Two strings are considered to have parameterized matching when there exists a bijection of the parameterized alphabet onto itself such that it transforms one string to another. Parameterized matching has application in software duplication…

Graphs are extremely versatile and ubiquitous mathematical structures with potential to model a wide range of domains. For this reason, graph problems have been of interest since the early days of computer science. Some of these problems…

Clustering is a well-known unsupervised machine learning approach capable of automatically grouping discrete sets of instances with similar characteristics. Constrained clustering is a semi-supervised extension to this process that can be…

Composite likelihood has shown promise in settings where the number of parameters $p$ is large due to its ability to break down complex models into simpler components, thus enabling inference even when the full likelihood is not tractable.…

Motivated by computing duplication patterns in sequences, a new fundamental problem called the longest subsequence-repeated subsequence (LSRS) is proposed. Given a sequence $S$ of length $n$, a letter-repeated subsequence is a subsequence…

The problem of finding a longest common subsequence of two main sequences with some constraint that must be a substring of the result (STR-IC-LCS) was formulated recently. It is a variant of the constrained longest common subsequence…

Let us call a sequence of numbers heapable if they can be sequentially inserted to form a binary tree with the heap property, where each insertion subsequent to the first occurs at a leaf of the tree, i.e. below a previously placed number.…