2022/06/15 by Eshwar Ram Arunachaleswaran, Anindya De, Arunachaleswaran, Eshwar Ram +3 · 1 citation
Biochemistry, Genetics and Molecular Biology · Computer Science · #Data Structures and Algorithms (cs.DS) #FOS: Computer and information sciences #Single-cell and spatial transcriptomics #Topological and Geometric Data Analysis #cs.DS
paper · pdf · doi:10.48550/arxiv.2206.07672
arxiv created 2022/06/15 · openalex publication_date 2022/06/15 · arxiv updated 2022/06/16 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
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 O((1)/(√ 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.