Related papers: Cutting an alignment with Ockham's razor
Exact string matching has been a fundamental problem in computer science for decades because of many practical applications. Some are related to common procedures, such as searching in files and text editors, or, more recently, to more…
Genome rearrangements are events in which large blocks of DNA exchange pieces during evolution. The analysis of such events is a tool for understanding evolutionary genomics, based on finding the minimum number of rearrangements to…
In a graph, a (perfect) matching cut is an edge cut that is a (perfect) matching. Matching Cut (MC), respectively, Perfect Matching Cut (PMC), is the problem of deciding whether a given graph has a matching cut, respectively, a perfect…
Consider two or more strings $\mathbf{x}^1,\mathbf{x}^2,\ldots,$ that are concatenated to form $\mathbf{x}=\langle \mathbf{x}^1,\mathbf{x}^2,\ldots \rangle$. Suppose that up to $\delta$ deletions occur in each of the concatenated strings.…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
The problem of correcting deletions has received significant attention, partly because of the prevalence of these errors in DNA data storage. In this paper, we study the problem of correcting a consecutive burst of at most $t$ deletions in…
Artificial Neural Networks (ANN) comprise important symmetry properties, which can influence the performance of Monte Carlo methods in Neuroevolution. The problem of the symmetries is also known as the competing conventions problem or…
The binary perfect phylogeny model is too restrictive to model biological events such as back mutations. In this paper we consider a natural generalization of the model that allows a special type of back mutation. We investigate the problem…
This paper examines the use of a hierarchical coevolutionary genetic algorithm under different partnering strategies. Cascading clusters of sub-populations are built from the bottom up, with higher-level sub-populations optimising larger…
The problem of 1-bit compressive sampling is addressed in this paper. We introduce an optimization model for reconstruction of sparse signals from 1-bit measurements. The model targets a solution that has the least l0-norm among all signals…
Questions in computational molecular biology generate various discrete optimization problems, such as DNA sequence alignment and RNA secondary structure prediction. However, the optimal solutions are fundamentally dependent on the…
We revisit Hopcroft's problem and related fundamental problems about geometric range searching. Given $n$ points and $n$ lines in the plane, we show how to count the number of point-line incidence pairs or the number of point-above-line…
Reconstructing a complete object from its parts is a fundamental problem in many scientific domains. The purpose of this article is to provide a systematic survey on this topic. The reassembly problem requires understanding the attributes…
Research on the localization of the genetic basis associated with diseases or traits has been widely conducted in the last a few decades. Scan methods have been developed for region-based analysis in whole-genome association studies,…
We present a fast algorithm for linear least squares problems governed by hierarchically block separable (HBS) matrices. Such matrices are generally dense but data-sparse and can describe many important operators including those derived…
Recomi (REpeated COrrelation Matrix Inversion) is a polynomially fast algorithm for searching optimally stable solutions of the perceptron learning problem. For random unbiased and biased patterns it is shown that the algorithm is able to…
During the course of evolution, an organism's genome can undergo changes that affect the large-scale structure of the genome. These changes include gene gain, loss, duplication, chromosome fusion, fission, and rearrangement. When gene gain…
In this paper, we perform an experimental study of optimal recombination operator for makespan minimization problem on single machine with sequence-dependent setup times ($1|s_{vu}|C_{\max}$). The computational experiment on benchmark…
An NP-hard problem is considered of intersecting a given set of $n$ straight line segments on the plane with the smallest cardinality set of disks of fixed radii $r>0,$ where the set of segments forms a straight line drawing $G=(V,E)$ of a…
The problem of string reconstruction from substring information has found many applications due to its relevance in DNA- and polymer-based data storage. One practically important and challenging paradigm requires reconstructing mixtures of…