4 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…
Markov embedding of ranked unlabelled evolutionary trees and its applications
Lasse Thorup Fallesen, Simon Pauli, Elisabeth Sommer James +2
Rooted bifurcating trees are mathematical objects used to model evolutionary relationships and arise naturally in both coalescent theory and phylogenetics. Recent numerical represe…
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…
Advanced posterior analyses of hidden Markov models: finite Markov chain imbedding and hybrid decoding
Zenia Elise Damgaard Bæk, Moisès Coll MaciÃ, Laurits Skov +1
Two major tasks in applications of hidden Markov models are to (i) compute distributions of summary statistics of the hidden state sequence, and (ii) decode the hidden state sequen…