Exact median-tree inference for unrooted reconciliation costs

Background Solving median tree problems under tree reconciliation costs is a classic and well-studied approach for inferring species trees from collections of discordant gene trees. These problems are NP-hard, and therefore are, in practice, typically addressed by local search heuristics. So far, however, such heuristics lack any provable correctness or precision. Further, even for small phylogenetic studies, it has been demonstrated that local search heuristics may only provide sub-optimal solutions. Obviating such heuristic uncertainties are exact dynamic programming solutions that allow solving tree reconciliation problems for smaller phylogenetic studies. Despite these promises, such exact solutions are only suitable for credibly rooted input gene trees, which constitute only a tiny fraction of the readily available gene trees. Standard gene tree inference approaches provide only unrooted gene trees and accurately rooting such trees is often difficult, if not impossible. Results Here, we describe complex dynamic programming solutions that represent the first nonnaïve exact solutions for solving the tree reconciliation problems for unrooted input gene trees. Further, we show that the asymptotic runtime of the proposed solutions does not increase when compared to the most time-efficient dynamic programming solutions for rooted input trees. Conclusions In an experimental evaluation, we demonstrate that the described solutions for unrooted gene trees are, like the solutions for rooted input gene trees, suitable for smaller phylogenetic studies. Finally, for the first time, we study the accuracy of classic local search heuristics for unrooted tree reconciliation problems.

Simple Hyper-Heuristics Control the Neighbourhood Size of Randomised Local Search Optimally for LeadingOnes

Selection hyper-heuristics (HHs) are randomised search methodologies which choose and execute heuristics during the optimisation process from a set of low-level heuristics. A machine learning mechanism is generally used to decide which low-level heuristic should be applied in each decision step. In this article, we analyse whether sophisticated learning mechanisms are always necessary for HHs to perform well. To this end we consider the most simple HHs from the literature and rigorously analyse their performance for the LeadingOnes benchmark function. Our analysis shows that the standard Simple Random, Permutation, Greedy, and Random Gradient HHs show no signs of learning. While the former HHs do not attempt to learn from the past performance of low-level heuristics, the idea behind the Random Gradient HH is to continue to exploit the currently selected heuristic as long as it is successful. Hence, it is embedded with a reinforcement learning mechanism with the shortest possible memory. However, the probability that a promising heuristic is successful in the next step is relatively low when perturbing a reasonable solution to a combinatorial optimisation problem. We generalise the “simple” Random Gradient HH so success can be measured over a fixed period of time [Formula: see text], instead of a single iteration. For LeadingOnes we prove that the Generalised Random Gradient (GRG) HH can learn to adapt the neighbourhood size of Randomised Local Search to optimality during the run. As a result, we prove it has the best possible performance achievable with the low-level heuristics (Randomised Local Search with different neighbourhood sizes), up to lower-order terms. We also prove that the performance of the HH improves as the number of low-level local search heuristics to choose from increases. In particular, with access to [Formula: see text] low-level local search heuristics, it outperforms the best-possible algorithm using any subset of the [Formula: see text] heuristics. Finally, we show that the advantages of GRG over Randomised Local Search and Evolutionary Algorithms using standard bit mutation increase if the anytime performance is considered (i.e., the performance gap is larger if approximate solutions are sought rather than exact ones). Experimental analyses confirm these results for different problem sizes (up to [Formula: see text]) and shed some light on the best choices for the parameter [Formula: see text] in various situations.