Comparison of signatures predicted by four signature discovery methods on real tumor sequencing data.

Sparsity is measured as the fraction of cells in the signature matrix with value < 10−4. Cross-signature similarity is measured as the mean cosine similarity between all pairs of predicted signatures. Background contamination is measured as the mean cosine similarity between the background signature and all non-background predicted signatures. Median per-patient correlation is measured as the median Pearson’s correlation coefficient between the observed mutation spectrum and the predicted mutation spectrum for each patient, indicating how well each method fits the observed mutations in individual patients.