One of the Grand Challenges in Science is the construction of the Tree of Life, an evolutionary tree containing several million species, spanning all life on earth. However, the construction of the Tree of Life is enormously computationally challenging, as all the current most accurate methods are either heuristics for NP-hard optimization problems or Bayesian MCMC methods that sample from tree space. One of the most promising approaches for improving scalability and accuracy for phylogeny estimation uses divide-and-conquer: a set of species is divided into overlapping subsets, trees are constructed on the subsets, and then merged together using a "supertree method". Here, we present Exact-RFS-2, the first polynomial-time algorithm to find an optimal supertree of two trees, using the Robinson-Foulds Supertree (RFS) criterion (a major approach in supertree estimation that is related to maximum likelihood supertrees), and we prove that finding the RFS of three input trees is NP-hard. We also present GreedyRFS (a greedy heuristic that operates by repeatedly using Exact-RFS-2 on pairs of trees, until all the trees are merged into a single supertree). We evaluate Exact-RFS-2 and GreedyRFS, and show that they have better accuracy than the current leading heuristic for RFS.

In the hypergraph k-cut problem, the input is a hypergraph, and the goal is to find a smallest subset of hyperedges whose removal ensures that the remaining hypergraph has at least k connected components. This problem is known to be at least as hard as the densest k-subgraph problem when k is part of the input (Chekuri-Li, 2015). We present a randomized polynomial time algorithm to solve the hypergraph k-cut problem for constant k. Our algorithm solves the more general hedge k-cut problem when the subgraph induced by every hedge has a constant number of connected components. In the hedge k-cut problem, the input is a hedgegraph specified by a vertex set and a disjoint set of hedges, where each hedge is a subset of edges defined over the vertices. The goal is to find a smallest subset of hedges whose removal ensures that the number of connected components in the remaining underlying (multi-)graph is at least k. Our algorithm is based on random contractions akin to Karger's min cut algorithm. Our main technical contribution is a distribution over the hedges (hyperedges) so that random contraction of hedges (hyperedges) chosen from the distribution succeeds in returning an optimum solution with large probability.