Parallel algorithms for masked sparse matrix-matrix products

Abstract

Computing the product of two sparse matrices (SpGEMM) is a fundamental operation in various combinatorial and graph algorithms as well as various bioinformatics and data analytics applications for computing inner-product similarities. For an important class of algorithms, only a subset of the output entries are needed, and the resulting operation is known as Masked SpGEMM since a subset of the output entries is considered to be "masked out". In this work, we investigate various novel algorithms and data structures for this rather challenging and important computation, and provide guidelines on how to design a fast Masked-SpGEMM for shared-memory architectures.