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Linked Matrix Factorization

In recent years, a number of methods have been developed for the dimension reduction and decomposition of multiple linked high-content data matrices. Typically these methods assume that just one dimension, rows or columns, is shared among the data sources. This shared dimension may represent common features that are measured for different sample sets (i.e., horizontal integration) or a common set of samples with measurements for different feature sets (i.e., vertical integration). In this article we introduce an approach for simultaneous horizontal and vertical integration, termed Linked Matrix Factorization (LMF), for the more general situation where some matrices share rows (e.g., features) and some share columns (e.g., samples). Our motivating application is a cytotoxicity study with accompanying genomic and molecular chemical attribute data. In this data set, the toxicity matrix (cell lines $\times$ chemicals) shares its sample set with a genotype matrix (cell lines $\times$ SNPs), and shares its feature set with a chemical molecular attribute matrix (chemicals $\times$ attributes). LMF gives a unified low-rank factorization of these three matrices, which allows for the decompo