A branch-&-price approach to the unrooted maximum agreement forest problem

2024/10/05 by Frohn, Martin, Kelk, Steven, Vychytilova, Simona · 1 citation
#Data Structures and Algorithms (cs.DS) #FOS: Biological sciences #FOS: Computer and information sciences #FOS: Mathematics #Optimization and Control (math.OC) #Populations and Evolution (q-bio.PE)

paper · doi:10.48550/arxiv.2410.04122

Abstract

We propose the first branch-&-price algorithm for the maximum agreement forest problem on unrooted binary trees: given two unrooted X-labelled binary trees we seek to partition X into a minimum number of blocks such that the induced subtrees are disjoint and have the same topologies in both trees. We provide a dynamic programming algorithm for the weighted maximum agreement subtree problem to solve the pricing problem. When combined with rigorous polynomial-time pre-processing our branch-&-price algorithm exhibits (beyond) state-of-the-art performance.

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