Finding a most parsimonious or likely tree in a network with respect to an alignment

Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant phylogenetic signals that were not present in the input. Here we show that, given a multiple alignment A for a set...

Contrastive Pessimistic Likelihood Estimation for Semi-Supervised Classification

Improvement guarantees for semi-supervised classifiers can currently only be given under restrictive conditions on the data. We propose a general way to perform semi-supervised parameter estimation for likelihood-based classifiers for which, on the full training set, the estimates are never worse than the supervised solution in terms of the log...