相关论文: Detecting gene innovations for phenotypic diversit…
We consider a Moran-type model of cultural evolution, which describes how traits emerge, are transmitted, and get lost in populations. Our analysis focuses on the underlying cultural genealogies; they were first described by Aguilar and…
In this paper we present a novel tool to evaluate problem solving systems. Instead of using a system to solve a problem, we suggest using the problem to evaluate the system. By finding a numerical representation of a problem's complexity,…
One of the main motivations for the use of competitive coevolution systems is their ability to capitalise on arms races between competing species to evolve increasingly sophisticated solutions. Such arms races can, however, be hard to…
How to compare whole genome sequences at large scale has not been achieved via conventional methods based on pair-wisely base-to-base comparison; nevertheless, no attention was paid to handle in-one-sitting a number of genomes crossing…
Social insect colonies and ensemble machine learning methods represent two of the most successful examples of decentralized information processing in nature and computation respectively. Here we develop a rigorous mathematical framework…
The genotype-phenotype gap is a persistent barrier to complex trait genetic dissection, worsened by the explosive growth of genomic data (1.5 billion variants identified in the UK Biobank WGS study) alongside persistently scarce and…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
Given a set of species whose evolution is represented by a species tree, a gene family is a group of genes having evolved from a single ancestral gene. A gene family evolves along the branches of a species tree through various mechanisms,…
Much of the natural variation for a complex trait can be explained by variation in DNA sequence levels. As part of sequence variation, gene-gene interaction has been ubiquitously observed in nature, where its role in shaping the development…
This issue includes six articles that develop and apply statistical methods for the analysis of gene sequencing data of different types. The methods are tailored to the different data types and, in each case, lead to biological insights not…
Exploiting the mathematical curiosity of intransitive dice, we present a simple theoretical model for co-evolution that captures scales ranging from the genome of the individual to the system-wide emergence of species diversity. We study a…
Robust generalization to new concepts has long remained a distinctive feature of human intelligence. However, recent progress in deep generative models has now led to neural architectures capable of synthesizing novel instances of unknown…
Over the past decade, advances in generative modeling, such as generative adversarial networks, masked autoencoders, and diffusion models, have significantly transformed biological research and discovery, enabling breakthroughs in molecule…
The paper surveys the evolution of main algorithmic techniques to compare and search biological sequences. We highlight key algorithmic ideas emerged in response to several interconnected factors: shifts of biological analytical paradigm,…
Since the advent of modern bioinformatics, the challenging, multifaceted problem of reconstructing phylogenetic history from biological sequences has hatched perennial statistical and algorithmic innovation. Studies of the phylogenetic…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
The combination of multiple classifiers using ensemble methods is increasingly important for making progress in a variety of difficult prediction problems. We present a comparative analysis of several ensemble methods through two case…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…
The overall aim of the software industry is to ensure delivery of high quality software to the end user. To ensure high quality software, it is required to test software. Testing ensures that software meets user specifications and…