Related papers: Provably Fast and Accurate Recovery of Evolutionar…
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…
We present the first sub-quadratic time algorithm that with high probability correctly reconstructs phylogenetic trees for short sequences generated by a Markov model of evolution. Due to rapid expansion in sequence databases, such very…
\begin{abstract} Greedy permutations, also known as Gonzalez Orderings or Farthest Point Traversals are a standard way to approximate $k$-center clustering and have many applications in sampling and approximating metric spaces. A greedy…
Recently, greedy algorithm has received much attention as a cost-effective means to reconstruct the sparse signals from compressed measurements. Much of previous work has focused on the investigation of a single candidate to identify the…
We present an algorithm for phylogenetic reconstruction using quartets that returns the correct topology for $n$ taxa in $O(n \log n)$ time with high probability, in a probabilistic model where a quartet is not consistent with the true…
A consensus tree is a phylogenetic tree that captures the similarity between a set of conflicting phylogenetic trees. The problem of computing a consensus tree is a major step in phylogenetic tree reconstruction. It also finds applications…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
Bidirectional motion planning often reduces planning time compared to its unidirectional counterparts. It requires connecting the forward and reverse search trees to form a continuous path. However, this process could fail and restart the…
Suppose a graph $G$ is stochastically created by uniformly sampling vertices along a line segment and connecting each pair of vertices with a probability that is a known decreasing function of their distance. We ask if it is possible to…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
We consider the reconciliation problem, in which the task is to find a mapping of a gene tree into a species tree, so as to maximize the likelihood of such fitting, given the available data. We describe a model for the evolution of the…
Background: The reconstruction of the phylogenetic tree topology of four taxa is, still nowadays, one of the main challenges in phylogenetics. Its difficulties lie in considering not too restrictive evolutionary models, and correctly…
Decision Tree is a classic formulation of active learning: given $n$ hypotheses with nonnegative weights summing to 1 and a set of tests that each partition the hypotheses, output a decision tree using the provided tests that uniquely…
Decision Trees (DTs) are commonly used for many machine learning tasks due to their high degree of interpretability. However, learning a DT from data is a difficult optimization problem, as it is non-convex and non-differentiable.…
Despite the great success of deep learning, recent works show that large deep neural networks are often highly redundant and can be significantly reduced in size. However, the theoretical question of how much we can prune a neural network…
Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…
Consider a collection of weighted subsets of a ground set N. Given a query subset Q of N, how fast can one (1) find the weighted sum over all subsets of Q, and (2) sample a subset of Q proportionally to the weights? We present a tree-based…
In this paper, we address the problem of learning the structure of a pairwise graphical model from samples in a high-dimensional setting. Our first main result studies the sparsistency, or consistency in sparsity pattern recovery,…
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families…