Related papers: UPGMA and the normalized equidistant minimum evolu…
The Partitioning Min-Max Weighted Matching (PMMWM) problem, being a practical NP-hard problem, integrates the task of partitioning the vertices of a bipartite graph into disjoint sets of limited size with the classical Maximum-Weight…
Given an $n$-vertex non-negatively real-weighted graph $G$, whose vertices are partitioned into a set of $k$ clusters, a \emph{clustered network design problem} on $G$ consists of solving a given network design optimization problem on $G$,…
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…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
Motivated by the fact that in several cases a matching in a graph is stable if and only if it is produced by a greedy algorithm, we study the problem of computing a maximum weight greedy matching on weighted graphs, termed GreedyMatching.…
The Minimum Linear Arrangement problem (MLA) consists of finding a mapping $\pi$ from vertices of a graph to distinct integers that minimizes $\sum_{\{u,v\}\in E}|\pi(u) - \pi(v)|$. In that setting, vertices are often assumed to lie on a…
A common problem in phylogenetics is to try to infer a species phylogeny from gene trees. We consider different variants of this problem. The first variant, called Unrestricted Minimal Episodes Inference, aims at inferring a species tree…
In the past few years powerful generalizations to the Euclidean k-means problem have been made, such as Bregman clustering [7], co-clustering (i.e., simultaneous clustering of rows and columns of an input matrix) [9,18], and tensor…
Many discrete optimization problems amount to selecting a feasible set of edges of least weight. We consider in this paper the context of spatial graphs where the positions of the vertices are uncertain and belong to known uncertainty sets.…
PPGMMGA is a Projection Pursuit (PP) algorithm aimed at detecting and visualizing clustering structures in multivariate data. The algorithm uses the negentropy as PP index obtained by fitting Gaussian Mixture Models (GMMs) for density…
We study the {\em min-cost chain-constrained spanning-tree} (abbreviated \mcst) problem: find a min-cost spanning tree in a graph subject to degree constraints on a nested family of node sets. We devise the {\em first} polytime algorithm…
The largest common embeddable subtree problem asks for the largest possible tree embeddable into two input trees and generalizes the classical maximum common subtree problem. Several variants of the problem in labeled and unlabeled rooted…
Although recovering an Euclidean distance matrix from noisy observations is a common problem in practice, how well this could be done remains largely unknown. To fill in this void, we study a simple distance matrix estimate based upon the…
The Steiner tree problem is one of the classic and most fundamental $\mathcal{NP}$-hard problems: given an arbitrary weighted graph, seek a minimum-cost tree spanning a given subset of the vertices (terminals). Byrka \emph{et al}. proposed…
We consider the minimum spanning tree problem on a weighted complete bipartite graph $K_{n_R, n_B}$ whose $n=n_R+n_B$ vertices are random, i.i.d. uniformly distributed points in the unit cube in $d$ dimensions and edge weights are the…
We study how to utilize (possibly erroneous) predictions in a model for computing under uncertainty in which an algorithm can query unknown data. Our aim is to minimize the number of queries needed to solve the minimum spanning tree…
Randomized experiments have been critical tools of decision making for decades. However, subjects can show significant heterogeneity in response to treatments in many important applications. Therefore it is not enough to simply know which…
The tree inclusion problem is, given two node-labeled trees $P$ and $T$ (the ``pattern tree'' and the ``target tree''), to locate every minimal subtree in $T$ (if any) that can be obtained by applying a sequence of node insertion operations…
The expectation-maximization (EM) algorithm is an iterative method for finding maximum likelihood estimates when data are incomplete or are treated as being incomplete. The EM algorithm and its variants are commonly used for parameter…
We consider the rooted prize-collecting walks (PCW) problem, wherein we seek a collection $C$ of rooted walks having minimum prize-collecting cost, which is the (total cost of walks in $C$) + (total node-reward of nodes not visited by any…