Inferring phylogenetic networks from multifurcating trees via cherry picking and machine learning

The Hybridization problem asks to reconcile a set of conflicting phylogenetic trees into a single phylogenetic network with the smallest possible number of reticulation nodes. This problem is computationally hard and previous solutions are limited to small and/or severely restricted data sets, for example, a set of binary trees with the same taxon set or only two non-binary trees with non-equal taxon sets. Building on our previous work on binary trees, we present FHyNCH, the first algorithmic framework to heuristically solve the Hybridization problem for large sets of multifurcating trees whose sets of taxa may differ. Our heuristics combine the cherrypicking technique, recently proposed to solve the same problem for binary trees, with two carefully designed machine-learning models. We demonstrate that our methods are practical and produce qualitatively good solutions through experiments on both synthetic and real data sets.