Related papers: Identification of repeats in DNA sequences using n…
A new numerical characterization of symbolic sequences is proposed. The partition of sequence based on Ke and Tong algorithm is a starting point. Algorithm decomposes original sequence into set of distinct subsequences - a patterns. The set…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
We introduce a method to estimate the complexity function of symbolic dynamical systems from a finite sequence of symbols. We test such complexity estimator on several symbolic dynamical systems whose complexity functions are known exactly.…
This study proposes a data condensation method for multivariate kernel density estimation by genetic algorithm. First, our proposed algorithm generates multiple subsamples of a given size with replacement from the original sample. The…
Genotype networks are a method used in systems biology to study the "innovability" of a set of genotypes having the same phenotype. In the past they have been applied to determine the genetic heterogeneity, and stability to mutations, of…
By using the Jensen-Shannon divergence, genomic DNA can be divided into compositionally distinct domains through a standard recursive segmentation procedure. Each domain, while significantly different from its neighbours, may however share…
We introduce a complexity measure for symbolic sequences. Starting from a segmentation procedure of the sequence, we define its complexity as the entropy of the distribution of lengths of the domains of relatively uniform composition in…
A fundamental property of DNA is that the reverse complement (RC) of a sequence often carries identical biological meaning. However, state-of-the-art DNA language models frequently fail to capture this symmetry, producing inconsistent…
The identification of anomalies in temporal data is a core component of numerous research areas such as intrusion detection, fault prevention, genomics and fraud detection. This article provides an experimental comparison of the novelty…
The article presents the theoretical foundations of the algorithm for calculating the number of different genomes in the medium under study and of two algorithms for determining the presence of a particular (known) genome in this medium.…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…
A DNA palindrome is a segment of double-stranded DNA sequence with inver- sion symmetry which may form secondary structures conferring significant biolog- ical functions ranging from RNA transcription to DNA replication. To test if the…
The modeling of genomic sequences presents unique challenges due to their length and structural complexity. Traditional sequence models struggle to capture long-range dependencies and biological features inherent in DNA. In this work, we…
Gene annotation has traditionally required direct comparison of DNA sequences between an unknown gene and a database of known ones using string comparison methods. However, these methods do not provide useful information when a gene does…
The purpose of this research is to describe an efficient iterative method suitable for obtaining high accuracy solutions to high frequency time-harmonic scattering problems. The method allows for both refinement of local polynomial degree…
Frequent pattern mining is a relevant method to analyse structured data, like sequences, trees or graphs. It consists in identifying characteristic substructures of a dataset. This paper deals with a new type of patterns for tree data:…
Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…
A new version of DNA walks, where nucleotides are regarded unequal in their contribution to a walk is introduced, which allows us to study thoroughly the "fine structure" of nucleotide sequences. The approach is based on the assumption that…
Finding repeated patterns or motifs in a time series is an important unsupervised task that has still a number of open issues, starting by the definition of motif. In this paper, we revise the notion of motif support, characterizing it as…
In this paper we describe a new method for detecting and counting a repeating object in an image. While the method relies on a fairly sophisticated deformable part model, unlike existing techniques it estimates the model parameters in an…