Related papers: Cutting an alignment with Ockham's razor
We consider a class of pattern matching problems where a normalising transformation is applied at every alignment. Normalised pattern matching plays a key role in fields as diverse as image processing and musical information processing…
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 optimization-based image restoration models, the correct selection of hyperparameters is crucial for achieving superior performance. However, current research typically involves manual tuning of these hyperparameters, which is highly…
Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
The article describes the application of the Hough transform to a honeycomb block image. The problem of cutting a mold from a honeycomb block is described. A number of image transformations are considered to increase the efficiency of the…
The $k$-mismatch problem consists in computing the Hamming distance between a pattern $P$ of length $m$ and every length-$m$ substring of a text $T$ of length $n$, if this distance is no more than $k$. In many real-world applications, any…
We call change-point problem (CPP) the identification of changes in the probabilistic behavior of a sequence of observations. Solving the CPP involves detecting the number and position of such changes. In genetics the study of how and what…
A matching cut is a matching that is also an edge cut. In the problem Minimum Matching Cut, we ask for a matching cut with the minimum number of edges in the matching. We investigate the differences in complexity between Minimum Matching…
Cutting planes (cuts) are crucial for solving Mixed Integer Linear Programming (MILP) problems. Advanced MILP solvers typically rely on manually designed heuristic algorithms for cut selection, which require much expert experience and…
We tackle the image reassembly problem with wide space between the fragments, in such a way that the patterns and colors continuity is mostly unusable. The spacing emulates the erosion of which the archaeological fragments suffer. We…
A primary challenge in metagenomics is reconstructing individual microbial genomes from the mixture of short fragments created by sequencing. Recent work leverages the sparsity of the assembly graph to find $r$-dominating sets which enable…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…
A metro-line crossing minimization problem is to draw multiple lines on an underlying graph that models stations and rail tracks so that the number of crossings of lines becomes minimum. It has several variations by adding restrictions on…
Reconstructing ancestral gene orders in a given phylogeny is a classical problem in comparative genomics. Most existing methods compare conserved features in extant genomes in the phylogeny to define potential ancestral gene adjacencies,…
Changepoint detection identifies significant shifts in data sequences, making it important in areas like finance, genetics, and healthcare. The Optimal Partitioning algorithms efficiently detect these changes, using a penalty parameter to…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
Minimal Composite Higgs Models (MCHM) have long provided a solution to the hierarchy problem of the Standard Model, yet suffer from various sources of fine tuning that are becoming increasingly problematic with the lack of new physics…
Cohesive subgraph discovery in a network is one of the fundamental problems and investigated for several decades. In this paper, we propose the Overlapping Cohesive Subgraphs with Minimum degree (OCSM) problem which combines three key…
In many applications, we need algorithms which can align partially overlapping point sets and are invariant to the corresponding transformations. In this work, a method possessing such properties is realized by minimizing the objective of…
In this paper, we introduce the Maximum Matrix Contraction problem, where we aim to contract as much as possible a binary matrix in order to maximize its density. We study the complexity and the polynomial approximability of the problem.…