A node-wise multinomial Potts model with sparse group Lasso and structural distance weights predicts mutation fitness better than EVmutation across 12 protein families, with new convergence rate guarantees.
$\ell_1$-penalized Multinomial Regression: Estimation, inference, and prediction, with an application to risk factor identification for different dementia subtypes
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abstract
High-dimensional multinomial regression models are very useful in practice but have received less research attention than logistic regression models, especially from the perspective of statistical inference. In this work, we analyze the estimation and prediction error of the contrast-based $\ell_1$-penalized multinomial regression model and extend the debiasing method to the multinomial case, providing a valid confidence interval for each coefficient and $p$-value of the individual hypothesis test. We also examine cases of model misspecification and non-identically distributed data to demonstrate the robustness of our method when some assumptions are violated. We apply the debiasing method to identify important predictors in the progression into dementia of different subtypes. Results from extensive simulations show the superiority of the debiasing method compared to other inference methods.
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Modeling and prediction of mutation fitness on protein functionality with structural information using high-dimensional Potts model
A node-wise multinomial Potts model with sparse group Lasso and structural distance weights predicts mutation fitness better than EVmutation across 12 protein families, with new convergence rate guarantees.