5 papers
Improved Phylogeny Comparisons: Non-Shared Edges Nearest Neighbor Interchanges, and Subtree Transfers
Wing-Kai Hon, Ming-Yang Kao, Tak-Wah Lam +2
The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approxim…
Predicting RNA Secondary Structures with Arbitrary Pseudoknots by Maximizing the Number of Stacking Pairs
Samuel Ieong, Ming-Yang Kao, Tak-Wah Lam +2
The paper investigates the computational problem of predicting RNA secondary structures. The general belief is that allowing pseudoknots makes the problem hard. Existing polynomial…
Cavity Matchings, Label Compressions, and Unrooted Evolutionary Trees
Ming-Yang Kao, Tak-Wah Lam, Wing-Kin Sung +1
We present an algorithm for computing a maximum agreement subtree of two unrooted evolutionary trees. It takes O(n^{1.5} log n) time for trees with unbounded degrees, matching the…
An Even Faster and More Unifying Algorithm for Comparing Trees via Unbalanced Bipartite Matchings
Ming-Yang Kao, Tak-Wah Lam, Wing-Kin Sung +1
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is onl…
A Decomposition Theorem for Maximum Weight Bipartite Matchings
Ming-Yang Kao, Tak-Wah Lam, Wing-Kin Sung +1
Let G be a bipartite graph with positive integer weights on the edges and without isolated nodes. Let n, N and W be the node count, the largest edge weight and the total weight of…