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The normalized edit distance is one of the distances derived from the edit distance. It is useful in some applications because it takes into account the lengths of the two strings compared. The normalized edit distance is not defined in…
DNA motif discovery is an important issue in gene research, which aims to identify transcription factor binding sites (i.e., motifs) in DNA sequences to reveal the mechanisms that regulate gene expression. However, the phenomenon of data…
In this work we seek clusters of genomic words in human DNA by studying their inter-word lag distributions. Due to the particularly spiked nature of these histograms, a clustering procedure is proposed that first decomposes each…
The present research work proposes advancement for Data Assimilation strategies using Convolutional Neural Networks (CNN). More precisely, multi-fidelity and multi-level algorithms for the Ensemble Kalman Filter are enhanced by CNN tools,…
In medical imaging, chromosome straightening plays a significant role in the pathological study of chromosomes and in the development of cytogenetic maps. Whereas different approaches exist for the straightening task, typically geometric…
Cluster deletion is an NP-hard graph clustering objective with applications in computational biology and social network analysis, where the goal is to delete a minimum number of edges to partition a graph into cliques. We first provide a…
In this paper we describe a variation of the classical permutation decoding algorithm that can be applied to any affine-invariant code with respect to certain type of information sets. In particular, we can apply it to the family of…
Genetic algorithms, which mimic evolutionary processes to solve optimization problems, can be enhanced by using powerful semi-local search algorithms as mutation operators. Here, we introduce reverse quantum annealing, a class of quantum…
We present a new algorithm to detect inter-cluster galaxy filaments based upon the assumption that the orientations of constituent galaxies along such filaments are non-isotropic. We apply the algorithm to the 2dF Galaxy Redshift Survey…
The integration of multi-omics data has emerged as a promising approach for gaining comprehensive insights into complex diseases such as cancer. This paper proposes a novel approach to identify cancer subtypes through the integration of…
In molecular phylogeny, relationships among organisms are reconstructed using DNA or protein sequences and are displayed as trees. A linear increase in the number of sequences results in an exponential increase of possible trees. Thus,…
When an external field is applied across a liquid-crystal cell, the twist and tilt distributions cannot be calculated analytically and must be extracted numerically. In the standard approach, the Euler-Lagrange equations are derived from…
In this paper we present novel algorithms for several multidimensional data processing problems. We consider problems related to the computation of restricted clusters and of the diameter of a set of points using a new distance function. We…
Genome rearrangement has been an active area of research in computational comparative genomics for the last three decades. While initially mostly an interesting algorithmic endeavor, now the practical application by applying rearrangement…
Circular RNAs (circRNAs) are important components of the non-coding RNA regulatory network. Previous circRNA identification primarily relies on high-throughput RNA sequencing (RNA-seq) data combined with alignment-based algorithms that…
We consider foliations given by deformations $dF+\epsilon\omega$ of exact forms $dF$ in $\mathbb{C}^2$ in a neighborhood of a family of cycles $\gamma(t)\subset F^{-1}(t)$. In 1996 Francoise gave an algorithm for calculating the first…
In this paper, we study systems of distributed entities that can actively modify their communication network. This gives rise to distributed algorithms that apart from communication can also exploit network reconfiguration in order to carry…
The Dynamical Graph Grammar (DGG) formalism can describe complex system dynamics with graphs that are mapped into a master equation. An exact stochastic simulation algorithm may be used, but it is slow for large systems. To overcome this…
This paper provides technical details regarding the application of the FLAME methodology to derive algorithms hand in hand with their proofs of correctness for the computation of the $ L T L^T $ decomposition (with and without pivoting) of…
Clearing is a niching method inspired by the principle of assigning the available resources among a niche to a single individual. The clearing procedure supplies these resources only to the best individual of each niche: the winner. So far,…