Extending models via gradient boosting: an application to Mendelian models

DOI10.1214/21-AOAS1482MaRDI QIDQ2247455zbMATHOpenAlexFDO

Authors Theodore Huang, Gregory Idos, Christine Hong, Stephen B. Gruber, Giovanni Parmigiani, Danielle Braun

Publication date 17 November 2021

Published in The Annals of Applied Statistics (Search for Journal in Brave)

Full work available at URL https://arxiv.org/abs/2105.06559

zbMATH Keywords

risk modelgradient boostingMendelian model

Mathematics Subject Classification ID

Applications of statistics to biology and medical sciences; meta analysis (62P10) Inference from stochastic processes and prediction (62M20)

Abstract: Improving existing widely-adopted prediction models is often a more efficient and robust way towards progress than training new models from scratch. Existing models may (a) incorporate complex mechanistic knowledge, (b) leverage proprietary information and, (c) have surmounted barriers to adoption. Compared to model training, model improvement and modification receive little attention. In this paper we propose a general approach to model improvement: we combine gradient boosting with any previously developed model to improve model performance while retaining important existing characteristics. To exemplify, we consider the context of Mendelian models, which estimate the probability of carrying genetic mutations that confer susceptibility to disease by using family pedigrees and health histories of family members. Via simulations we show that integration of gradient boosting with an existing Mendelian model can produce an improved model that outperforms both that model and the model built using gradient boosting alone. We illustrate the approach on genetic testing data from the USC-Stanford Cancer Genetics Hereditary Cancer Panel (HCP) study.

Recommendations

• Stochastic gradient boosting.
• Method for improving gradient boosting learning efficiency based on modified loss functions
• Boosting beyond the mean -- extending component-wise gradient boosting algorithms to multiple dimensions
• Model-based boosting 2.0
• Accelerated gradient boosting

Cites work

• Additive logistic regression: a statistical view of boosting. (With discussion and a rejoinder by the authors)
• An Empirical Distribution Function for Sampling with Incomplete Information
• Bagging predictors
• BayesMendel: an R Environment for Mendelian Risk Prediction
• Greedy function approximation: A gradient boosting machine.
• Maximum Likelihood Estimates of Monotone Parameters
• Stochastic gradient boosting.

Cited in

(1)

• Offset Boosting for Breeding Conditional Symmetry

Describes a project that uses

Uses Software

• BayesMendel
• ElemStatLearn
• DevCan
• XGBoost
• BOADICEA

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