Distributed, Numerically Stable Distance and Covariance Computation with MPI for Extremely Large Datasets

Abstract

The current explosion of data, which is impacting many different areas, is especially noticeable in biomedical research thanks to the development of new technologies that are able to capture high-dimensional and high-resolution data at the single-cell scale. Processing such data in an interpretable way often requires the computation of pairwise dissimilarity measures between the multiple features of the data, a task that can be very difficult to tackle when the dataset is large enough, and which is prone to numerical instability. In this paper we propose a distributed framework to efficiently compute dissimilarity matrices in arbitrarily large datasets in a numerically robust way. It implements a combination of the pairwise and two-pass algorithms for computing the variance, in order to maintain the numerical robustness of the former while reducing its overhead. The proposal is parallelizable both across multiple computers and multiple cores, maximizing the performance while maintaining the benefits of memory locality. The proposal is tested on a real use case: a dataset generated from high-content screening images composed by a billion individual cells and 786 features. The results showed linear scalability with respect to the size of the dataset and close to linear speedup.