相关论文: Weighted genomic distance can hardly impose a boun…

2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper,…

The paper introduces the weighted convolution, a novel approach to the convolution for signals defined on regular grids (e.g., 2D images) through the application of an optimal density function to scale the contribution of neighbouring…

Structured pruning methods designed for Large Language Models (LLMs) generally focus on identifying and removing the least important components to optimize model size. However, in this work, we question this prevalent approach by instead…

A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…

In this work we study reverse complementary genomic word pairs in the human DNA, by comparing both the distance distribution and the frequency of a word to those of its reverse complement. Several measures of dissimilarity between distance…

Transposable elements are DNA sequences that can move around to different positions in the genome. During this process, they can cause mutations, and lead to an increase in genome size. Despite representing a large genomic fraction,…

Metabolism and evolution are closely connected: if a mutation incurs extra energetic costs for an organism, there is a baseline selective disadvantage that may or may not be compensated for by other adaptive effects. A long-standing, but to…

The genome-wide recombination rate ($RR$) of a species is often described by one parameter, the ratio between total genetic map length ($G$) and physical map length ($P$), measured in centiMorgans per Megabase (cM/Mb). The value of this…

Kernel approximation with exponentials is useful in many problems with convolution quadrature and particle interactions such as integral-differential equations, molecular dynamics and machine learning. This paper proposes a weighted…

Understanding the linear or nonlinear relationship between load and deformation in structural materials or structural frames is a key to a proper and a well-represented simulation. This research is dedicated to model a cyclic…

A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the…

How a nano-searcher finds its nano-target is a general problem in non-equilibrium statistical physics. It becomes vital when the searcher is a damaged DNA fragment trying to find its counterpart on the intact homologous chromosome. If the…

Dendrograms are a way to represent evolutionary relationships between organisms. Nowadays, these are inferred based on the comparison of genes or protein sequences by taking into account their differences and similarities. The genetic…

Homologous gene shuffling between DNA promotes genetic diversity and is an important pathway for DNA repair. For this to occur, homologous genes need to find and recognize each other. However, despite its central role in homologous…

Scoring DNA sequences against Position Weight Matrices (PWMs) is a widely adopted method to identify putative transcription factor binding sites. While common bioinformatics tools produce scores that can reflect the binding strength between…

The statistics and machine learning communities have recently seen a growing interest in classification-based approaches to two-sample testing. The outcome of a classification-based two-sample test remains a rejection decision, which is not…

Searching for similar genomic sequences is an essential and fundamental step in biomedical research and an overwhelming majority of genomic analyses. State-of-the-art computational methods performing such comparisons fail to cope with the…

In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…

Purpose: A major barrier to the implementation of artificial intelligence for medical applications is the lack of explainability and high confidence for incorrect decisions, specifically with out-of-domain samples. We propose a…

A common goal in observational research is to estimate marginal causal effects in the presence of confounding variables. One solution to this problem is to use the covariate distribution to weight the outcomes such that the data appear…