Reconstructing Ultrametric Trees from Noisy Experiments

TL;DR

This paper develops efficient algorithms for reconstructing ultrametric evolutionary trees from noisy experimental data, establishing conditions under which topology and edge weights can be accurately recovered despite stochastic noise.

Contribution

It introduces a new noise model and provides algorithms with provable guarantees for reconstructing tree topology and weights when edges are sufficiently long.

Findings

Reconstruction is feasible when edges are at least  O(1/\u221A n)) in length.

Topology reconstruction becomes impossible if edges are shorter than this threshold.

Edge weights can be approximately reconstructed under the same conditions for a specific noise model.

Abstract

The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the results of `experiments' on triples of leaves (a,b,c), which return the pair with the deepest least common ancestor. If the tree is assumed to be an ultrametric (i.e., all root-leaf paths have the same length), the experiment can be equivalently seen to return the closest pair of leaves. In this model, efficient algorithms are known for tree reconstruction. In reality, since the data on which these `experiments' are run is itself generated by the stochastic process of evolution, these experiments are noisy. In all reasonable models of evolution, if the branches leading to the leaves in a triple separate from each other at common ancestors that are very close to each other in the tree, the result of the experiment should be close to uniformly random. Motivated by this, we consider a model where the noise on any triple is just dependent on the three pairwise distances (referred to as distance based noise). Our results are the following: 1. Suppose the length of every edge in the unknown tree is at least $\tilde{O}(\frac{1}{\sqrt n})$ fraction of the length of a root-leaf path. Then, we give an efficient algorithm to reconstruct the topology of the tree for a broad family of distance-based noise models. Further, we show that if the edges are asymptotically shorter, then topology reconstruction is information-theoretically impossible. 2. Further, for a specific distance-based noise model--which we refer to as the homogeneous noise model--we show that the edge weights can also be approximately reconstructed under the same quantitative lower bound on the edge lengths.