Pattern detection in bipartite networks: a review of terminology, applications and methods
Two dimensional matrices with binary (0/1) entries are a common data structure in many research fields. Examples include ecology, economics, mathematics, physics, psychometrics and others. Because the columns and rows of these matrices represent distinct entities, they can equivalently be expressed as a pair of bipartite networks that are linked by projection. A variety of diversity statistics and network metrics can then be used to quantify patterns in these matrices and networks. But what should these patterns be compared to? In all of these disciplines, researchers have recognized the necessity of comparing an empirical matrix to a benchmark set of "null" matrices created by randomizing certain elements of the original data. This common need has nevertheless promoted the independent development of methodologies by researchers who come from different backgrounds and use different terminology. Here, we provide a multidisciplinary review of randomization techniques for matrices representing binary, bipartite networks. We aim to translate the concepts from different technical domains into a common language that is accessible to a broad scientific audience. Specifically, after briefly reviewing examples of binary matrix structures across different fields, we introduce the major approaches and common strategies for randomizing these matrices. We then explore the details of and performance of specific techniques, and discuss their limitations and computational challenges. In particular, we focus on the conceptual importance and implementation of structural constraints on the randomization, such as preserving row or columns sums of the original matrix in each of the randomized matrices. Our review serves both as a guide for empiricists in different disciplines, as well as a reference point for researchers working on theoretical and methodological developments in matrix randomization methods.