Extended Bayesian Information Criterion (EBIC) google
The ordinary Bayes information criterion is too liberal for model selection when the model space is large. In this article, we re-examine the Bayesian paradigm for model selection and propose an extended family of Bayes information criteria. The new criteria take into account both the number of unknown parameters and the complexity of the model space. Their consistency is established, in particular allowing the number of covariates to increase to in nity with the sample size. Their performance in various situations is evaluated by simulation studies. It is demonstrated that the extended Bayes information criteria incur a small loss in the positive selection rate but tightly control the false discovery rate, a desirable property in many applications. The extended Bayes information criteria are extremely useful for variable selection in problems with a moderate sample size but a huge number of covariates, especially in genome-wide association studies, which are now an active area in genetics research. Some keywords: Bayesian paradigm; Consistency; Genome-wide association study; Tour- nament approach; Variable selection. …

Deep Survival google
Previous research has shown that neural networks can model survival data in situations in which some patients’ death times are unknown, e.g. right-censored. However, neural networks have rarely been shown to outperform their linear counterparts such as the Cox proportional hazards model. In this paper, we run simulated experiments and use real survival data to build upon the risk-regression architecture proposed by Faraggi and Simon. We demonstrate that our model, DeepSurv, not only works as well as the standard linear Cox proportional hazards model but actually outperforms it in predictive ability on survival data with linear and nonlinear risk functions. We then show that the neural network can also serve as a recommender system by including a categorical variable representing a treatment group. This can be used to provide personalized treatment recommendations based on an individual’s calculated risk. We provide an open source Python module that implements these methods in order to advance research on deep learning and survival analysis. …

Regularized Optimal Scaling Regression (ROS Regression) google
In this paper we combine two important extensions of ordinary least squares regression: regularization and optimal scaling. Optimal scaling (sometimes also called optimal scoring) has originally been developed for categorical data, and the process finds quantifications for the categories that are optimal for the regression model in the sense that they maximize the multiple correlation. Although the optimal scaling method was developed initially for variables with a limited number of categories, optimal transformations of continuous variables are a special case. We will consider a variety of transformation types; typically we use step functions for categorical variables, and smooth (spline) functions for continuous variables. Both types of functions can be restricted to be monotonic, preserving the ordinal information in the data. In addition to optimal scaling, three regularization methods will be considered: Ridge regression, the Lasso, and the Elastic Net. The resulting method will be called ROS Regression (Regularized Optimal Scaling Regression. We will show that the basic OS algorithm provides straightforward and efficient estimation of the regularized regression coefficients, automatically gives the Group Lasso and Blockwise Sparse Regression, and extends them with monotonicity properties. We will show that Optimal Scaling linearizes nonlinear relationships between predictors and outcome, and improves upon the condition of the predictor correlation matrix, increasing (on average) the conditional independence of the predictors. Alternative options for regularization of either regression coefficients or category quantifications are mentioned. Extended examples are provided. Keywords: Categorical Data, Optimal Scaling, Conditional Independence, Step Functions, Splines, Monotonic Transformations, Regularization, Lasso, Elastic Net, Group Lasso, Blockwise Sparse Regression. …

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