PT  - JOURNAL ARTICLE
AU  - Ling-Hong Hung
AU  - Kaiyuan Shi
AU  - Migao Wu
AU  - William Chad Young
AU  - Adrian E. Raftery
AU  - Ka Yee Yeung
TI  - fastBMA: Scalable Network Inference and Transitive Reduction
AID  - 10.1101/099036
DP  - 2017 Jan 01
TA  - bioRxiv
PG  - 099036
4099  - http://biorxiv.org/content/early/2017/01/06/099036.short
4100  - http://biorxiv.org/content/early/2017/01/06/099036.full
AB  - BACKGROUND: Inferring genetic networks from genome-wide expression data is extremely demanding computationally. We have developed fastBMA, a distributed, parallel and scalable implementation of Bayesian model averaging (BMA) for this purpose. fastBMA also includes a novel and computationally efficient method for eliminating redundant indirect edges in the network.FINDINGS: We evaluated the performance of fastBMA on synthetic data and experimental genome-wide yeast and human datasets. When using a single CPU core, fastBMA is up to 100 times faster than the next fastest method, LASSO, with increased accuracy. It is a memory efficient, parallel and distributed application that scales to human genome wide expression data. A 10,000-gene regulation network can be obtained in a matter of hours using a 32-core cloud cluster.CONCLUSIONS: fastBMA is a significant improvement over its predecessor ScanBMA. It is orders of magnitude faster and more accurate than other fast network inference methods such as LASSO. The improved scalability allows it to calculate networks from genome scale data in a reasonable timeframe. The transitive reduction method can improve accuracy in denser networks. fastBMA is available as code (M.I.T. license) from GitHub (https://github.com/lhhunghimself/fastBMA), as part of the updated networkBMA Bioconductor package (https://www.bioconductor.org/packages/release/bioc/html/networkBMA.html) and as ready-to-deploy Docker images (https://hub.docker.com/r/biodepot/fastbma/).AUCarea under the curveAUROCarea under receiver operator curveAUPRarea under precision recallBMABayesian model averagingiBMAiterative Bayesian model averagingBICBayesian information criterionEMEstimation Maximization