Related papers: Triplet Reconstruction and all other Phylogenetic …
This paper proposes a randomized optimization framework for constrained signal reconstruction, where the word "constrained" implies that data-fidelity is imposed as a hard constraint instead of adding a data-fidelity term to an objective…
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…
Molecular phylogenetic techniques do not generally account for such common evolutionary events as site insertions and deletions (known as indels). Instead tree building algorithms and ancestral state inference procedures typically rely on…
In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence a divergence arises between the true evolutionary distances and the differences…
A constraint satisfaction problem (CSP), $\textsf{Max-CSP}(\mathcal{F})$, is specified by a finite set of constraints $\mathcal{F} \subseteq \{[q]^k \to \{0,1\}\}$ for positive integers $q$ and $k$. An instance of the problem on $n$…
Hierarchical clustering is a critical task in numerous domains. Many approaches are based on heuristics and the properties of the resulting clusterings are studied post hoc. However, in several applications, there is a natural cost function…
The rooted subtree prune and regraft (rSPR) distance between two rooted binary phylogenetic trees is a well-studied measure of topological dissimilarity that is NP-hard to compute. Here we describe an improved linear kernel for the problem.…
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…
While first-order stationary points (FOSPs) are the traditional targets of non-convex optimization, they often correspond to undesirable strict saddle points. To circumvent this, attention has shifted towards second-order stationary points…
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…
We study approximation algorithms for satisfiable and nearly satisfiable instances of ordering constraint satisfaction problems (ordering CSPs). Ordering CSPs arise naturally in ranking and scheduling, yet their approximability remains…
An active topic in the study of random constraint satisfaction problems (CSPs) is the geometry of the space of satisfying or almost satisfying assignments as the function of the density, for which a precise landscape of predictions has been…
The computational complexity of solving random 3-Satisfiability (3-SAT) problems is investigated. 3-SAT is a representative example of hard computational tasks; it consists in knowing whether a set of alpha N randomly drawn logical…
The three-in-a-tree problem asks for an induced tree of the input graph containing three mandatory vertices. In 2006, Chudnovsky and Seymour [Combinatorica, 2010] presented the first polynomial time algorithm for this problem, which has…
Stable Marriage is a fundamental problem to both computer science and economics. Four well-known NP-hard optimization versions of this problem are the Sex-Equal Stable Marriage (SESM), Balanced Stable Marriage (BSM), max-Stable Marriage…
In phylogenetics, the consensus problem consists in summarizing a set of phylogenetic trees that all classify the same set of species into a single tree. Several definitions of consensus exist in the literature; in this paper we focus on…
A number of recent works have employed decision trees for the construction of explainable partitions that aim to minimize the $k$-means cost function. These works, however, largely ignore metrics related to the depths of the leaves in the…
Constraint satisfaction problem (CSP) is a well-studied combinatorial search problem, in which we are asked to find an assignment of values to given variables so as to satisfy all of given constraints. We study a reconfiguration variant of…
We present Fast Approximate Minimum Spanning Tree (FAMST), a novel algorithm that addresses the computational challenges of constructing Minimum Spanning Trees (MSTs) for large-scale and high-dimensional datasets. FAMST utilizes a…
A kernelization algorithm for a computational problem is a procedure which compresses an instance into an equivalent instance whose size is bounded with respect to a complexity parameter. For the Boolean satisfiability problem (SAT), and…