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Relational Dose-Response Modeling for Cancer Drug Studies (arxiv.org)
3 points by sel1 on Oct 15, 2019 | hide | past | pdf | discuss on HN

In plain words: A model that borrows information across similar drugs and cancer cell lines to draw each dose-response curve, smooth but able to jump when the data demand it. It fit the curves better than the standard biology approach and flagged new markers of drug sensitivity.

Abstract · A Bayesian Model of Dose-Response for Cancer Drug Studies

Exploratory cancer drug studies test multiple tumor cell lines against multiple candidate drugs. The goal in each paired (cell line, drug) experiment is to map out the dose-response curve of the cell line as the dose level of the drug increases. We propose Bayesian Tensor Filtering (BTF), a hierarchical Bayesian model for dose-response modeling in multi-sample, multi-treatment cancer drug studies. BTF uses low-dimensional embeddings to share statistical strength between similar drugs and similar cell lines. Structured shrinkage priors in BTF encourage smoothness in the dose-response curves while remaining adaptive to sharp jumps when the data call for it. We focus on a pair of cancer drug studies exhibiting a particular pathology in their experimental design, leading us to a non-conjugate monotone mixture-of-Gammas likelihood. To perform posterior inference, we develop a variant of the elliptical slice sampling algorithm for sampling from linearly-constrained multivariate normal priors with non-conjugate likelihoods. In benchmarks, BTF outperforms state-of-the-art methods for covariance regression and dynamic Poisson matrix factorization. On the two cancer drug studies, BTF outperforms the current standard approach in biology and reveals potential new biomarkers of drug sensitivity in cancer. Code is available at https://github.com/tansey/functionalmf.

Wesley Tansey, Christopher Tosh, David M. Blei
arXiv:1906.04072 · stat.ML, cs.LG, stat.ME · submitted Jun 10, 2019 · updated Mar 22, 2021
abstract · pdf · html · Extended to handle covariates; additional benchmarks comparing to related work

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