Nested sampling for Bayesian model comparison in the context of Salmonella disease dynamics.
Nested sampling for Bayesian model comparison in the context of Salmonella disease dynamics.
复制标题
DOI：
10.1371/journal.pone.0082317
复制
发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Restif O
中科院分区：
文献类型：
--
作者：
Dybowski R;McKinley TJ;Mastroeni P;Restif O
理解复杂生物系统的观测动态的机制需要对多个替代模型进行统计评估和比较。虽然这在传统上是使用基于最大似然的方法，如Akaike的信息准则（AIC），贝叶斯方法已经获得了普及，因为它们提供了更多的信息输出的形式后验概率分布。然而，在贝叶斯框架中的多个模型之间的比较是困难的计算成本的数值积分在大的参数空间。最近提出了一种计算后验概率的新的有效方法，并将其应用于物理科学的复杂问题。在这里，我们演示了如何嵌套抽样可以用于生物科学中的推理和模型比较。我们提出了一个重新分析的数据，从实验感染小鼠肠道沙门氏菌显示肝细胞中的细菌分布。除了确认依赖于AIC的原始分析的主要发现外，我们的方法还提供：（a）跨参数空间的积分，（B）后验参数分布的估计（参数相关性的可视化），以及（c）模型拟合优度评估的后验预测分布的估计。拟合优度的结果表明，替代机械模型和放松的准静态假设应被考虑。
Understanding the mechanisms underlying the observed dynamics of complex biological systems requires the statistical assessment and comparison of multiple alternative models. Although this has traditionally been done using maximum likelihood-based methods such as Akaike's Information Criterion (AIC), Bayesian methods have gained in popularity because they provide more informative output in the form of posterior probability distributions. However, comparison between multiple models in a Bayesian framework is made difficult by the computational cost of numerical integration over large parameter spaces. A new, efficient method for the computation of posterior probabilities has recently been proposed and applied to complex problems from the physical sciences. Here we demonstrate how nested sampling can be used for inference and model comparison in biological sciences. We present a reanalysis of data from experimental infection of mice with Salmonella enterica showing the distribution of bacteria in liver cells. In addition to confirming the main finding of the original analysis, which relied on AIC, our approach provides: (a) integration across the parameter space, (b) estimation of the posterior parameter distributions (with visualisations of parameter correlations), and (c) estimation of the posterior predictive distributions for goodness-of-fit assessments of the models. The goodness-of-fit results suggest that alternative mechanistic models and a relaxation of the quasi-stationary assumption should be considered.
登录
查看更多内容
DOI：
10.1126/science.1199884
发表时间：
2011-05-06
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Charleston B;Bankowski BM;Gubbins S;Chase-Topping ME;Schley D;Howey R;Barnett PV;Gibson D;Juleff ND;Woolhouse ME
通讯作者：
Woolhouse ME
影响因子：
2.7
作者：
Chopin, Nicolas;Robert, Christian P.
通讯作者：
Robert, Christian P.
DOI：
10.1111/j.1365-2966.2007.12353.x
发表时间：
2008-02-21
影响因子：
4.8
作者：
Feroz, F.;Hobson, M. P.
通讯作者：
Hobson, M. P.
DOI：
10.1086/649541
发表时间：
2010-01-15
期刊：
Clinical infectious diseases : an official publication of the Infectious Diseases Society of America
影响因子：
--
作者：
Crump JA;Mintz ED
通讯作者：
Mintz ED
影响因子：
6.4
作者：
Grant, Andrew J.;Sheppard, Mark;Mastroeni, Pietro
通讯作者：
Mastroeni, Pietro