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Binary jumbled pattern matching asks to preprocess a binary string $S$ in order to answer queries $(i,j)$ which ask for a substring of $S$ that is of length $i$ and has exactly $j$ 1-bits. This problem naturally generalizes to…
We present a systematic, algebraically based, design methodology for efficient implementation of computer programs optimized over multiple levels of the processor/memory and network hierarchy. Using a common formalism to describe the…
This paper focuses on pattern matching in the DNA sequence. It was inspired by a previously reported method that proposes encoding both pattern and sequence using prime numbers. Although fast, the method is limited to rather small pattern…
The classic algorithm of Viterbi computes the most likely path in a Hidden Markov Model (HMM) that results in a given sequence of observations. It runs in time $O(Tn^2)$ given a sequence of $T$ observations from a HMM with $n$ states.…
This paper presents theoretical and practical results for the bin packing problem with scenarios, a generalization of the classical bin packing problem which considers the presence of uncertain scenarios, of which only one is realized. For…
Efficient optimal prefix coding has long been accomplished via the Huffman algorithm. However, there is still room for improvement and exploration regarding variants of the Huffman problem. Length-limited Huffman coding, useful for many…
Finding approximate occurrences of a pattern in a text using a full-text index is a central problem in bioinformatics and has been extensively researched. Bidirectional indices have opened new possibilities in this regard allowing the…
Graph rewriting is a popular tool for the optimisation and modification of graph expressions in domains such as compilers, machine learning and quantum computing. The underlying data structures are often port graphs - graphs with labels at…
Material Fingerprinting is a lookup table-based strategy to discover material models from experimental measurements, which completely avoids the need to solve an optimization problem. In an offline phase, a comprehensive database of…
This paper discusses the computational resolution and presents numerical results for solving affine combinations of Heaviside composite optimization problems (abbreviated as A-HSCOPs) by a progressive integer programming (abbreviated as…
Given an approximation algorithm $A$, we want to find the input with the worst approximation ratio, i.e., the input for which $A$'s output's objective value is the worst possible compared to the optimal solution's objective value. Such hard…
Graph pattern matching, which aims to discover structural patterns in graphs, is considered one of the most fundamental graph mining problems in many real applications. Despite previous efforts, existing systems face two main challenges.…
We study distributed algorithms for string matching problem in presence of wildcard characters. Given a string T (a text), we look for all occurrences of another string P (a pattern) as a substring of string T . Each wildcard character in…
The paper considers the problem of finding a given substring in a text. It is known that the complexity of a classical search query in an unordered database is linear in the length of the text and a given substring. At the same time,…
A hypergraph is a generalization of a graph, in which a hyperedge can connect multiple vertices, modeling complex relationships involving multiple vertices simultaneously. Hypergraph pattern matching, which is to find all isomorphic…
Computing string or sequence alignments is a classical method of comparing strings and has applications in many areas of computing, such as signal processing and bioinformatics. Semi-local string alignment is a recent generalisation of this…
In this article, we provide a new algorithm for solving constraint satisfaction problems over templates with few subpowers, by reducing the problem to the combination of solvability of a polynomial number of systems of linear equations over…
The (axis-parallel) stabbing number of a given set of line segments is the maximum number of segments that can be intersected by any one (axis-parallel) line. This paper deals with finding perfect matchings, spanning trees, or…
In this paper we propose and study a new complexity model for approximation algorithms. The main motivation are practical problems over large data sets that need to be solved many times for different scenarios, e.g., many multicast trees…
String barcoding is a recently introduced technique for genomic-based identification of microorganisms. In this paper we describe the engineering of highly scalable algorithms for robust string barcoding. Our methods enable distinguisher…