A Framework for Regularized Non-Negative Matrix Factorization, with Application to the Analysis of Gene Expression Data

Non-negative matrix factorization (NMF) condenses high-dimensional data into lower-dimensional models subject to the requirement that data can only be added, never subtracted. However, the NMF problem does not have a unique solution, creating a need for additional constraints (regularization constraints) to promote informative solutions. Regularized NMF problems are more complicated than conventional NMF problems, creating a need for computational methods that incorporate the extra constraints in a reliable way. We developed novel methods for regularized NMF based on block-coordinate descent with proximal point modification and a fast optimization procedure over the alpha simplex. Our framework has important advantages in that it (a) accommodates for a wide range of regularization terms, including sparsity-inducing terms like the L1 penalty, (b) guarantees that the solutions satisfy necessary conditions for optimality, ensuring that the results have well-defined numerical meaning, (c) allows the scale of the solution to be controlled exactly, and (d) is computationally efficient. We illustrate the use of our approach on in the context of gene expression microarray data analysis. The improvements described remedy key limitations of previous proposals, strengthen the theoretical basis of regularized NMF, and facilitate the use of regularized NMF in applications.