Data released on August 07, 2017
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 av-eraging (BMA) for this purpose. fastBMA also includes a computationally efficient module for eliminat-ing redundant indirect edges in the network by mapping the transitive reduction to an easily solved shortest-path problem.
We evaluated the performance of fastBMA on synthetic data and experimental genome-wide time-series 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 (2 nodes of 16 cores).
fastBMA is a significant improvement over its predecessor ScanBMA. It is more accurate and orders of magnitude faster than other fast network inference methods such as one based on 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/).
Hung, L.-H., Shi, K., Wu, M., Young, W. C., Raftery, A. E., & Yeung, K. Y. (2017). fastBMA: scalable network inference and transitive reduction. GigaScience, 6(10), 1–10. doi:10.1093/gigascience/gix078
Network inference Bayesian models Time-series Distributed computing Gene regulation Cholesky decomposition Dijkstra’s algorithm Bloom filter Docker container Optimized software