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Optimization and expansion of non-negative matrix factorization

  • Lin, Xihui1
  • Boutros, Paul C.1, 2, 3
  • 1 Informatics & Biocomputing, Ontario Institute for Cancer Research, Toronto, Canada , Toronto (Canada)
  • 2 Department of Human Genetics, University of California, Los Angeles, USA , Los Angeles (United States)
  • 3 Jonsson Comprehensive Cancer Center, University of California, Los Angeles, USA , Los Angeles (United States)
Published Article
BMC Bioinformatics
Springer (Biomed Central Ltd.)
Publication Date
Jan 06, 2020
DOI: 10.1186/s12859-019-3312-5
Springer Nature


BackgroundNon-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.ResultsWe 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.ConclusionsWe 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.

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