Accelerating key bioinformatics tasks 100-fold by improving memory access

Abstract: Most experimental sciences now rely on computing, and biological sciences are no exception. As datasets get bigger, so do the computing costs, making proper optimization of the codes used by scientists increasingly important. Many of the codes developed in recent years are based on the Python-based NumPy, due to its ease of use and good performance characteristics. The composable nature of NumPy, however, does not generally play well with the multi-tier nature of modern CPUs, making any non-trivial multi-step algorithm limited by the external memory access speeds, which are hundreds of times slower than the CPU's compute capabilities. In order to fully utilize the CPU compute capabilities, one must keep the working memory footprint small enough to fit in the CPU caches, which requires splitting the problem into smaller portions and fusing together as many steps as possible. In this paper, we present changes based on these principles to two important functions in the scikit-bio library, principal coordinates analysis and the Mantel test, that resulted in over 100x speed improvement in these widely used, general-purpose tools.