FastCPH: Efficient Survival Analysis for Neural Networks

The Cox proportional hazards model is a canonical method in survival analysis for prediction of the life expectancy of a patient given clinical or genetic covariates -- it is a linear model in its original form. In recent years, several methods have been proposed to generalize the Cox model to neural networks, but none of these are both numerically correct and computationally efficient. We propose FastCPH, a new method that runs in linear time and supports both the standard Breslow and Efron methods for tied events. We also demonstrate the performance of FastCPH combined with LassoNet, a neural network that provides interpretability through feature sparsity, on survival datasets. The final procedure is efficient, selects useful covariates and outperforms existing CoxPH approaches.

Confidence intervals for the Cox model test error from cross-validation

Cross-validation (CV) is one of the most widely used techniques in statistical learning for estimating the test error of a model, but its behavior is not yet fully understood. It has been shown that standard confidence intervals for test error using estimates from CV may have coverage below nominal levels. This phenomenon occurs because each sample is used in both the training and testing procedures during CV and as a result, the CV estimates of the errors become correlated. Without accounting for this correlation, the estimate of the variance is smaller than it should be. One way to mitigate this issue is by estimating the mean squared error of the prediction error instead using nested CV. This approach has been shown to achieve superior coverage compared to intervals derived from standard CV. In this work, we generalize the nested CV idea to the Cox proportional hazards model and explore various choices of test error for this setting.

Cooperative learning for multi-view analysis

We propose a new method for supervised learning with multiple sets of features ("views"). Cooperative learning combines the usual squared error loss of predictions with an "agreement" penalty to encourage the predictions from different data views to agree. By varying the weight of the agreement penalty, we get a continuum of solutions that include the well-known early and late fusion approaches. Cooperative learning chooses the degree of agreement (or fusion) in an adaptive manner, using a validation set or cross-validation to estimate test set prediction error. One version of our fitting procedure is modular, where one can choose different fitting mechanisms (e.g. lasso, random forests, boosting, neural networks) appropriate for different data views. In the setting of cooperative regularized linear regression, the method combines the lasso penalty with the agreement penalty. The method can be especially powerful when the different data views share some underlying relationship in their signals that we aim to strengthen, while each view has its idiosyncratic noise that we aim to reduce. We illustrate the effectiveness of our proposed method on simulated and real data examples.

Cross-validation: what does it estimate and how well does it do it?

Cross-validation is a widely-used technique to estimate prediction error, but its behavior is complex and not fully understood. Ideally, one would like to think that cross-validation estimates the prediction error for the model at hand, fit to the training data. We prove that this is not the case for the linear model fit by ordinary least squares; rather it estimates the average prediction error of models fit on other unseen training sets drawn from the same population. We further show that this phenomenon occurs for most popular estimates of prediction error, including data splitting, bootstrapping, and Mallow's Cp. Next, the standard confidence intervals for prediction error derived from cross-validation may have coverage far below the desired level. Because each data point is used for both training and testing, there are correlations among the measured accuracies for each fold, and so the usual estimate of variance is too small. We introduce a nested cross-validation scheme to estimate this variance more accurately, and show empirically that this modification leads to intervals with approximately correct coverage in many examples where traditional cross-validation intervals fail. Lastly, our analysis also shows that when producing confidence intervals for prediction accuracy with simple data splitting, one should not re-fit the model on the combined data, since this invalidates the confidence intervals.

Feature-weighted elastic net: using "features of features" for better prediction

In some supervised learning settings, the practitioner might have additional information on the features used for prediction. We propose a new method which leverages this additional information for better prediction. The method, which we call the feature-weighted elastic net ("fwelnet"), uses these "features of features" to adapt the relative penalties on the feature coefficients in the elastic net penalty. In our simulations, fwelnet outperforms the lasso in terms of test mean squared error and usually gives an improvement in true positive rate or false positive rate for feature selection. We also apply this method to early prediction of preeclampsia, where fwelnet outperforms the lasso in terms of 10-fold cross-validated area under the curve (0.86 vs. 0.80). We also provide a connection between fwelnet and the group lasso and suggest how fwelnet might be used for multi-task learning.

Reluctant generalized additive modeling

Sparse generalized additive models (GAMs) are an extension of sparse generalized linear models which allow a model's prediction to vary non-linearly with an input variable. This enables the data analyst build more accurate models, especially when the linearity assumption is known to be a poor approximation of reality. Motivated by reluctant interaction modeling (Yu et al. 2019), we propose a multi-stage algorithm, called $\textit{reluctant generalized additive modeling (RGAM)}$, that can fit sparse generalized additive models at scale. It is guided by the principle that, if all else is equal, one should prefer a linear feature over a non-linear feature. Unlike existing methods for sparse GAMs, RGAM can be extended easily to binary, count and survival data. We demonstrate the method's effectiveness on real and simulated examples.

Reluctant additive modeling

Sparse generalized additive models (GAMs) are an extension of sparse generalized linear models which allow a model's prediction to vary non-linearly with an input variable. This enables the data analyst build more accurate models, especially when the linearity assumption is known to be a poor approximation of reality. Motivated by reluctant interaction modeling (Yu et al. 2019), we propose a multi-stage algorithm, called $\textit{reluctant additive modeling (RAM)}$, that can fit sparse generalized additive models at scale. It is guided by the principle that, if all else is equal, one should prefer a linear feature over a non-linear feature. Unlike existing methods for sparse GAMs, RAM can be extended easily to binary, count and survival data. We demonstrate the method's effectiveness on real and simulated examples.