Related papers: Self-Organizing Approach for Finding Borders of DN…
Analyzing large datasets to select optimal features is one of the most important research areas in machine learning and data mining. This feature selection procedure involves dimensionality reduction which is crucial in enhancing the…
We employ an evolutionary algorithm to automatically optimize different stages of a cold atom experiment without human intervention. This approach closes the loop between computer based experimental control systems and automatic real time…
Finite element codes typically use data structures that represent unstructured meshes as collections of cells, faces, and edges, each of which require associated coordinate systems. One then needs to store how the coordinate system of each…
Self-organisation is the spontaneous emergence of spatio-temporal structures and patterns from the interaction of smaller individual units. Examples are found across many scales in very different systems and scientific disciplines, from…
Systems biology studies the structure and behavior of complex gene regulatory networks. One of its aims is to develop a quantitative understanding of the modular components that constitute such networks. The self-regulating gene is a type…
In this paper, we adopt a probability distribution estimation perspective to explore the optimization mechanisms of supervised classification using deep neural networks. We demonstrate that, when employing the Fenchel-Young loss, despite…
The bioinformatical methods to detect lateral gene transfer events are mainly based on functional coding DNA characteristics. In this paper, we propose the use of DNA traits not depending on protein coding requirements. We introduce several…
Several modern genomic technologies, such as DNA-Methylation arrays, measure spatially registered probes that number in the hundreds of thousands across multiplechromosomes. The measured probes are by themselves less interesting…
This methods paper presents computational protocols for the identification of non-coding RNA genes or RNA motifs within genomic sequences. An application to bacterial small RNA is proposed.
In this paper, we consider the problem of designing DNA sequences (codewords) for DNA storage systems and DNA computing that are unlikely to fold back onto themselves to form undesirable secondary structures. The paper addresses both the…
This paper presents an algorithm for an automatic transformation (=routing) of time ordered topologies of Goldstone diagrams (i.e. Wick contractions) into graphical representations of these topologies. Since there is no hard criterion for…
Several computer vision and artificial intelligence projects are nowadays exploiting the manifold data distribution using, e.g., the diffusion process. This approach has produced dramatic improvements on the final performance thanks to the…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
The identification of low-energy conformers for a given molecule is a fundamental problem in computational chemistry and cheminformatics. We assess here a conformer search that employs a genetic algorithm for sampling the low-energy segment…
Document segmentation is a method of rending the document into distinct regions. A document is an assortment of information and a standard mode of conveying information to others. Pursuance of data from documents involves ton of human…
The folding structure of the DNA molecule combined with helper molecules, also referred to as the chromatin, is highly relevant for the functional properties of DNA. The chromatin structure is largely determined by the underlying primary…
Recognition and binding of specific sites on DNA by proteins is central for many cellular functions such as transcription, replication, and recombination. In the process of recognition, a protein rapidly searches for its specific site on a…
RNA design aims to identify RNA sequences that fold into a target secondary structure. This task is challenging in terms of computational efficiency. Most existing methods focus on either minimum free energy (MFE)-based or ensemble-based…
Self-assembly is a phenomenon observed in nature at all scales where autonomous entities build complex structures, without external influences nor centralised master plan. Modelling such entities and programming correct interactions among…
The nucleotide sequence representation of DNA can be inadequate for resolving protein-DNA binding sites and regulatory substrates, such as those involved in gene expression and horizontal gene transfer. Considering that sequence-like…