Cliff, A.; Romero, J.; Kainer, D.; Walker, A.; Furches, A.; Jacobson, D. A High-Performance Computing Implementation of Iterative Random Forest for the Creation of Predictive Expression Networks. Genes2019, 10, 996.
Cliff, A.; Romero, J.; Kainer, D.; Walker, A.; Furches, A.; Jacobson, D. A High-Performance Computing Implementation of Iterative Random Forest for the Creation of Predictive Expression Networks. Genes 2019, 10, 996.
Cliff, A.; Romero, J.; Kainer, D.; Walker, A.; Furches, A.; Jacobson, D. A High-Performance Computing Implementation of Iterative Random Forest for the Creation of Predictive Expression Networks. Genes2019, 10, 996.
Cliff, A.; Romero, J.; Kainer, D.; Walker, A.; Furches, A.; Jacobson, D. A High-Performance Computing Implementation of Iterative Random Forest for the Creation of Predictive Expression Networks. Genes 2019, 10, 996.
Abstract
As time progresses and technology improves, biological data sets are continuously increasing in size. New methods and new implementations of existing methods are needed to keep pace with this increase. In this paper, we present a high performance computing(HPC)-capable implementation of Iterative Random Forest (iRF). This new implementation enables the explainable-AI eQTL analysis of SNP sets with over a million SNPs. Using this implementation we also present a new method, iRF Leave One Out Prediction (iRF-LOOP), for the creation of Predictive Expression Networks on the order of 40,000 genes or more. We compare the new implementation of iRF with the previous R version and analyze its time to completion on two of the world's fastest supercomputers Summit and Titan. We also show iRF-LOOP's ability to capture biologically significant results when creating Predictive Expression Networks. This new implementation of iRF will enable the analysis of biological data sets at scales that were previously not possible.
Keywords
Random Forest; Iterative Random Forest; gene expression networks; high performance computing; X-AI-based eQTL
Subject
Computer Science and Mathematics, Mathematical and Computational Biology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
