Fast Numerical Optimization for Genome Sequencing Data in Population Biobanks

Preprint posted on bioRxiv, 2021

In this project led by Ruilin Li, we improved the efficiency of the R snpnet package by taking advantage of the sparsity-aware compact on-memory representation of the genotype data matrix.

Please also check our snpnet/BASIL paper and its extension to survival models.

snpnet v2 fig 2

Citation: R. Li, C. Chang, Y. Tanigawa, B. Narasimhan, T. Hastie, R. Tibshirani, M. A. Rivas, Fast Numerical Optimization for Genome Sequencing Data in Population Biobanks. bioRxiv, 2021.02.14.431030 (2021). https://doi.org/10.1101/2021.02.14.431030