登录 注册

An adaptive time-tree transition kernel for 贝叶斯 (Bayesian) phylogenetic inference
An adaptive time-tree transition kernel for Bayesian phylogenetic inference

🔗 访问原文
🔗 Access Paper

📝 摘要
Abstract

Bayesian phylogenetic and phylodynamic analyses can be very time-consuming, owing to the combination of complex models that are used to estimate key parameters from increasingly large genomic data sets and their associated metadata. The use of high-performance computer hardware can -- to a certain extent -- alleviate the computational burden and markedly decrease the time to results. Still, even converging to the posterior can be a lengthy endeavour, with the burn-in aspect of such analyses potentially taking days or even weeks for large data sets. One of the key aspects that hampers performance in Bayesian phylogenetic inference is the efficiency with which tree topology proposals explore tree space. We here propose a novel adaptive tree transition kernel, which we call `subTreeLeap' (STL), which involves modifying the phylogeny by walking along patristic distance paths in the tree according to an adaptable radius parameter. STL is a general proposal, which can be used with contemporaneous or time-calibrated sequence data, being particularly suited to the latter due to respecting temporal precedence constraints. We carefully assess its impact on convergence and statistical mixing of the exploration of posterior tree space, by comparison to replicate ``golden runs'' obtained from lengthy analyses of empirical data under standard tree transition kernels. We find that STL successfully explores the same posterior tree space as standard kernels, but often does so in a more efficient manner. We discuss limitations as well as future potential improvements to STL that could substantially increase the speed at which Bayesian phylogenetic inferences are obtained.

📊 文章统计
Article Statistics

基础数据
Basic Stats

64 浏览
Views
0 下载
Downloads
17 引用
Citations

引用趋势
Citation Trend

阅读国家分布
Country Distribution

阅读机构分布
Institution Distribution

月度浏览趋势
Monthly Views

相关关键词
Related Keywords

影响因子分析
Impact Analysis

4.40 综合评分
Overall Score
引用影响力
Citation Impact
浏览热度
View Popularity
下载频次
Download Frequency

📄 相关文章
Related Articles

海洋智能分析Ocean AI Analysis

正在分析中,请稍候…Analyzing, please wait…
海洋智能体 🌊
海洋智能体
AI科研助手 · 3420篇文献
我看到你正在阅读一篇文献,需要我帮你解读摘要、推荐相关论文,或者分析研究方法论吗?