Related papers: Evolution of biosequence search algorithms: a brie…
The alignment of biological sequences such as DNA, RNA, and proteins, is one of the basic tools that allow to detect evolutionary patterns, as well as functional/structural characterizations between homologous sequences in different…
Massively parallel sequencing techniques have revolutionized biological and medical sciences by providing unprecedented insight into the genomes of humans, animals, and microbes. Modern sequencing platforms generate enormous amounts of…
The rapid development of high-throughput sequencing technologies has led to an explosive increase in biological sequence data, making sequence clustering a fundamental task in large-scale bioinformatics analyses. Unlike traditional…
Genetic algorithms, computer programs that simulate natural evolution, are increasingly applied across many disciplines. They have been used to solve various optimisation problems from neural network architecture search to strategic games,…
Evolutionary algorithm research and applications began over 50 years ago. Like other artificial intelligence techniques, evolutionary algorithms will likely see increased use and development due to the increased availability of computation,…
Identifying similar documents within extensive volumes of data poses a significant challenge. To tackle this issue, researchers have developed a variety of effective distributed computing techniques. With the advancement of computing power…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
This paper reviews recent advances in big data optimization, providing the state-of-art of this emerging field. The main focus in this review are optimization techniques being applied in big data analysis environments. Integer linear…
Evolutionary algorithms have been frequently applied to constrained continuous optimisation problems. We carry out feature based comparisons of different types of evolutionary algorithms such as evolution strategies, differential evolution…
We present an efficient phylogenetic reconstruction algorithm allowing insertions and deletions which provably achieves a sequence-length requirement (or sample complexity) growing polynomially in the number of taxa. Our algorithm is…
Context: Evolutionary algorithms typically require a large number of evaluations (of solutions) to converge - which can be very slow and expensive to evaluate.Objective: To solve search-based software engineering (SE) problems, using fewer…
Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used for comparative analysis of biological genomes. However, the…
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…
Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these…
This paper presents a new approach to statistical similarity assessment based on sequence alignment. The algorithm performs mutual matching of two random sequences by successively searching for common elements and by applying sequence…
Graph comparison is fundamentally important for many applications such as the analysis of social networks and biological data and has been a significant research area in the pattern recognition and pattern analysis domains. Nowadays, the…
In the last decade the broad scope of complex networks has led to a rapid progress. In this area a particular interest has the study of community structures. The analysis of this type of structure requires the formalization of the intuitive…
Genome and metagenome comparisons based on large amounts of next-generation sequencing (NGS) data pose significant challenges for alignment-based approaches due to the huge data size and the relatively short length of the reads.…
A key aspect of the design of evolutionary and swarm intelligence algorithms is studying their performance. Statistical comparisons are also a crucial part which allows for reliable conclusions to be drawn. In the present paper we gather…
This paper surveys foundation models for AI-enabled biological design, focusing on recent developments in applying large-scale, self-supervised models to tasks such as protein engineering, small molecule design, and genomic sequence design.…