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Phylodynamic Model Adequacy Using Posterior Predictive Simulations.

ABSTRACT: Rapidly evolving pathogens, such as viruses and bacteria, accumulate genetic change at a similar timescale over which their epidemiological processes occur, such that, it is possible to make inferences about their infectious spread using phylogenetic time-trees. For this purpose it is necessary to choose a phylodynamic model. However, the resulting inferences are contingent on whether the model adequately describes key features of the data. Model adequacy methods allow formal rejection of a model if it cannot generate the main features of the data. We present TreeModelAdequacy, a package for the popular BEAST2 software that allows assessing the adequacy of phylodynamic models. We illustrate its utility by analyzing phylogenetic trees from two viral outbreaks of Ebola and H1N1 influenza. The main features of the Ebola data were adequately described by the coalescent exponential-growth model, whereas the H1N1 influenza data were best described by the birth-death susceptible-infected-recovered model.

SUBMITTER: Duchene S

PROVIDER: S-EPMC6368481 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Phylodynamic Model Adequacy Using Posterior Predictive Simulations.

Duchene Sebastian S Bouckaert Remco R Duchene David A DA Stadler Tanja T Drummond Alexei J AJ

Systematic biology 20190301 2

Rapidly evolving pathogens, such as viruses and bacteria, accumulate genetic change at a similar timescale over which their epidemiological processes occur, such that, it is possible to make inferences about their infectious spread using phylogenetic time-trees. For this purpose it is necessary to choose a phylodynamic model. However, the resulting inferences are contingent on whether the model adequately describes key features of the data. Model adequacy methods allow formal rejection of a mode ...[more]

PMID: 29945220

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Project description:In order to have confidence in model-based phylogenetic methods, such as maximum likelihood (ML) and Bayesian analyses, one must use an appropriate model of molecular evolution identified using statistically rigorous criteria. Although model selection methods such as the likelihood ratio test and Akaike information criterion are widely used in the phylogenetic literature, model selection methods lack the ability to reject all models if they provide an inadequate fit to the data. There are two methods, however, that assess absolute model adequacy, the frequentist Goldman-Cox (GC) test and Bayesian posterior predictive simulations (PPSs), which are commonly used in conjunction with the multinomial log likelihood test statistic. In this study, we use empirical and simulated data to evaluate the adequacy of common substitution models using both frequentist and Bayesian methods and compare the results with those obtained with model selection methods. In addition, we investigate the relationship between model adequacy and performance in ML and Bayesian analyses in terms of topology, branch lengths, and bipartition support. We show that tests of model adequacy based on the multinomial likelihood often fail to reject simple substitution models, especially when the models incorporate among-site rate variation (ASRV), and normally fail to reject less complex models than those chosen by model selection methods. In addition, we find that PPSs often fail to reject simpler models than the GC test. Use of the simplest substitution models not rejected based on fit normally results in similar but divergent estimates of tree topology and branch lengths. In addition, use of the simplest adequate substitution models can affect estimates of bipartition support, although these differences are often small with the largest differences confined to poorly supported nodes. We also find that alternative assumptions about ASRV can affect tree topology, tree length, and bipartition support. Our results suggest that using the simplest substitution models not rejected based on fit may be a valid alternative to implementing more complex models identified by model selection methods. However, all common substitution models may fail to recover the correct topology and assign appropriate bipartition support if the true tree shape is difficult to estimate regardless of model adequacy.

Project description:Background: Accurate estimation of perioperative blood transfusion risk in lumbar posterior interbody fusion is essential to reduce the number, cost, and complications associated with blood transfusions. Machine learning algorithms have the potential to outperform traditional prediction methods in predicting perioperative blood transfusion. This study aimed to construct a machine learning-based perioperative transfusion risk prediction model for lumbar posterior interbody fusion in order to improve the efficacy of surgical decision-making. Methods: We retrospectively collected clinical data on 1905 patients who underwent lumbar posterior interbody fusion surgery at the Second Hospital of Shanxi Medical University between January 2021 and March 2023. All the data was randomly divided into a training set and a validation set, and the "feature_importances" method provided by eXtreme Gradient Boosting (XGBoost) algorithm was applied to select statistically significant features on the training set to establish five machine learning prediction models. The optimal model was identified by utilizing the area under the curve (AUC) and the probability calibration curve on the validation set. Shapley additive explanations (SHAP) and local interpretable model-agnostic explanations (LIME) were employed for interpretable analysis of the optimal model. Results: In the postoperative outcomes of patients, the number of hospital days in the transfusion group was longer than that in the non-transfusion group. Additionally, the transfusion group experienced higher total hospital costs, 90-day readmission rates, and complication rates within 90 days after surgery than the non-transfusion group. A total of 9 features were selected for the models. The XGBoost model performed best with an AUC value of 0.958. The SHAP values showed that intraoperative blood loss, intraoperative fluid infusion, and number of fused segments were the top 3 most important features affecting perioperative blood transfusion in lumbar posterior interbody fusion. The LIME algorithm was used to interpret the individualized prediction. Conclusion: Surgery, ASA class, levels fused, total intraoperative blood loss, operative time, and preoperative Hb are viable predictors of perioperative blood transfusion in lumbar posterior interbody fusion. The XGBoost model has demonstrated superior predictive efficacy compared to the traditional logistic regression model, making it a more effective decision-making tool for perioperative blood transfusion.

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Phylodynamic Model Adequacy Using Posterior Predictive Simulations.

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Phylodynamic Model Adequacy Using Posterior Predictive Simulations.

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