Skip to main content
Open Access Publications from the University of California


UCLA Previously Published Works bannerUCLA

Optimization and expansion of non-negative matrix factorization

Published Web Location
No data is associated with this publication.

BACKGROUND:Non-negative matrix factorization (NMF) is a technique widely used in various fields, including artificial intelligence (AI), signal processing and bioinformatics. However existing algorithms and R packages cannot be applied to large matrices due to their slow convergence or to matrices with missing entries. Besides, most NMF research focuses only on blind decompositions: decomposition without utilizing prior knowledge. Finally, the lack of well-validated methodology for choosing the rank hyperparameters also raises concern on derived results. RESULTS:We adopt the idea of sequential coordinate-wise descent to NMF to increase the convergence rate. We demonstrate that NMF can handle missing values naturally and this property leads to a novel method to determine the rank hyperparameter. Further, we demonstrate some novel applications of NMF and show how to use masking to inject prior knowledge and desirable properties to achieve a more meaningful decomposition. CONCLUSIONS:We show through complexity analysis and experiments that our implementation converges faster than well-known methods. We also show that using NMF for tumour content deconvolution can achieve results similar to existing methods like ISOpure. Our proposed missing value imputation is more accurate than conventional methods like multiple imputation and comparable to missForest while achieving significantly better computational efficiency. Finally, we argue that the suggested rank tuning method based on missing value imputation is theoretically superior to existing methods. All algorithms are implemented in the R package NNLM, which is freely available on CRAN and Github.

Many UC-authored scholarly publications are freely available on this site because of the UC's open access policies. Let us know how this access is important for you.

Item not freely available? Link broken?
Report a problem accessing this item