论文标题
使用多摩学数据的生存预测方法的大规模基准研究
Large-scale benchmark study of survival prediction methods using multi-omics data
论文作者
论文摘要
多矩数据,即包含不同类型的高维分子变量(通常是经典临床变量)的数据集,它越来越多地用于研究各种疾病。然而,关于多摩智数据在预测诸如生存时间之类的疾病结果的有用性仍然存在的问题。还不清楚哪些方法最适合得出此类预测模型。我们的目标是通过使用实际数据进行大规模的基准研究来对这些问题提供一些答案。来自机器学习和统计数据的不同预测方法在数据库“癌症基因组地图集”的18个多态癌症数据集上应用,其中包含35至1,000个观测值,从60,000到100,000个变量。考虑的结果是(审查)生存时间。比较了基于增强,惩罚回归和随机森林的十二种方法,包括这两种方法,这些方法都可以考虑到OMICS变量的组结构。仅使用临床变量的Kaplan-Meier估计和COX模型被用作参考方法。使用几种5倍交叉验证的重复比较了这些方法。 UNO的C-Index和集成的Brier-Score是性能指标。结果表明,尽管多摩学数据可以改善预测性能,但通常情况并非如此。只有方法阻止森林在所有数据集中平均表现出略高于COX模型。考虑到多词结构可以提高预测性能,并保护低维组(尤其是临床变量)的变量免受模型中未包括的变量。所有分析均使用免费可用的R代码重现。
Multi-omics data, that is, datasets containing different types of high-dimensional molecular variables (often in addition to classical clinical variables), are increasingly generated for the investigation of various diseases. Nevertheless, questions remain regarding the usefulness of multi-omics data for the prediction of disease outcomes such as survival time. It is also unclear which methods are most appropriate to derive such prediction models. We aim to give some answers to these questions by means of a large-scale benchmark study using real data. Different prediction methods from machine learning and statistics were applied on 18 multi-omics cancer datasets from the database "The Cancer Genome Atlas", containing from 35 to 1,000 observations and from 60,000 to 100,000 variables. The considered outcome was the (censored) survival time. Twelve methods based on boosting, penalized regression and random forest were compared, comprising both methods that do and that do not take the group structure of the omics variables into account. The Kaplan-Meier estimate and a Cox model using only clinical variables were used as reference methods. The methods were compared using several repetitions of 5-fold cross-validation. Uno's C-index and the integrated Brier-score served as performance metrics. The results show that, although multi-omics data can improve the prediction performance, this is not generally the case. Only the method block forest slightly outperformed the Cox model on average over all datasets. Taking into account the multi-omics structure improves the predictive performance and protects variables in low-dimensional groups - especially clinical variables - from not being included in the model. All analyses are reproducible using freely available R code.