Black Box FDR
Wesley Tansey, Yixin Wang, David Blei, Raul Rabadan
Abstract
Analyzing large-scale, multi-experiment studies requires scientists to test each experimental outcome for statistical significance and then assess the results as a whole. We present Black Box FDR (BB-FDR), an empirical-Bayes method for analyzing multi-experiment studies when many covariates are gathered per experiment. BB-FDR learns a series of black box predictive models to boost power and control the false discovery rate (FDR) at two stages of study analysis. In Stage 1, it uses a deep neural network prior to report which experiments yielded significant outcomes. In Stage 2, a separate black box model of each covariate is used to select features that have significant predictive power across all experiments. In benchmarks, BB-FDR outperforms competing state-of-the-art methods in both stages of analysis. We apply BB-FDR to two real studies on cancer drug efficacy. For both studies, BB-FDR increases the proportion of significant outcomes discovered and selects variables that reveal key genomic drivers of drug sensitivity and resistance in cancer.
BibTeX
@InProceedings{pmlr-v80-tansey18a,
title = {Black Box {FDR}},
author = {Tansey, Wesley and Wang, Yixin and Blei, David and Rabadan, Raul},
booktitle = {Proceedings of the 35th International Conference on Machine Learning},
pages = {4867--4876},
year = {2018},
editor = {Dy, Jennifer and Krause, Andreas},
volume = {80},
series = {Proceedings of Machine Learning Research},
month = {10--15 Jul},
publisher = {PMLR},
pdf = {http://proceedings.mlr.press/v80/tansey18a/tansey18a.pdf},
url = {https://proceedings.mlr.press/v80/tansey18a.html},
abstract = {Analyzing large-scale, multi-experiment studies requires scientists to test each experimental outcome for statistical significance and then assess the results as a whole. We present Black Box FDR (BB-FDR), an empirical-Bayes method for analyzing multi-experiment studies when many covariates are gathered per experiment. BB-FDR learns a series of black box predictive models to boost power and control the false discovery rate (FDR) at two stages of study analysis. In Stage 1, it uses a deep neural network prior to report which experiments yielded significant outcomes. In Stage 2, a separate black box model of each covariate is used to select features that have significant predictive power across all experiments. In benchmarks, BB-FDR outperforms competing state-of-the-art methods in both stages of analysis. We apply BB-FDR to two real studies on cancer drug efficacy. For both studies, BB-FDR increases the proportion of significant outcomes discovered and selects variables that reveal key genomic drivers of drug sensitivity and resistance in cancer.}
}