5 papers
Integrating opportunities and parametrized signatures for improved mutational processes estimation in extended sequence contexts
Ragnhild Laursen, Marta Pelizzola, Lasse Maretty +1
Mutational signatures describe the pattern of mutations over the different mutation types. Each mutation type is determined by a base substitution and the flanking nucleotides to t…
MM-algorithms for traditional and convex NMF with Tweedie and Negative Binomial cost functions and empirical evaluation
Elisabeth Sommer James, Asger Hobolth, Marta Pelizzola
Non-negative matrix factorisation (NMF) is a widely used tool for unsupervised learning and feature extraction, with applications ranging from genomics to text analysis and signal…
On the Relation Between Autoencoders and Non-negative Matrix Factorization, and Their Application for Mutational Signature Extraction
Ida Egendal, Rasmus Froberg Brøndum, Marta Pelizzola +2
The aim of this study is to provide a foundation to understand the relationship between non-negative matrix factorization (NMF) and non-negative autoencoders enabling proper interp…
Model selection and robust inference of mutational signatures using Negative Binomial non-negative matrix factorization
Marta Pelizzola, Ragnhild Laursen, Asger Hobolth
The spectrum of mutations in a collection of cancer genomes can be described by a mixture of a few mutational signatures. The mutational signatures can be found using non-negative…
Modifying the Chi-square and the CMH test for population genetic inference: adapting to over-dispersion
Kerstin Spitzer, Marta Pelizzola, Andreas Futschik
Evolve and resequence studies provide a popular approach to simulate evolution in the lab and explore its genetic basis. In this context, the chi-square test, Fishers exact test, a…