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We introduce a graph partitioning problem motivated by computational topology and propose two algorithms that produce approximate solutions. Specifically, given a weighted, undirected graph $G$ and a positive integer $k$, we desire to find…
Given a graph G, the {\em maximum internal spanning tree problem} (MIST for short) asks for computing a spanning tree T of G such that the number of internal vertices in T is maximized. MIST has possible applications in the design of…
This paper presents a new anytime algorithm for the marginal MAP problem in graphical models. The algorithm is described in detail, its complexity and convergence rate are studied, and relations to previous theoretical results for the…
Classically, a mainstream approach for solving a convex-concave min-max problem is to instead solve the variational inequality problem arising from its first-order optimality conditions. Is it possible to solve min-max problems faster by…
Among all trees on $n$ vertices with a given degree sequence, how do we maximise or minimise the sum over all adjacent pairs of vertices $x$ and $y$ of $f(\mathrm{deg} x, \mathrm{deg} y)$? Here $f$ is a fixed symmetric function satisfying a…
Inverse scattering problems have many important applications. In this paper, given limited aperture data, we propose a Bayesian method for the inverse acoustic scattering to reconstruct the shape of an obstacle. The inverse problem is…
We consider the problem of drawing multiple gene trees inside a single species tree in order to visualize multispecies coalescent trees. Specifically, the drawing of the species tree fills a rectangle in which each of its edges is…
Two kinds of approximation algorithms exist for the k-BALANCED PARTITIONING problem: those that are fast but compute unsatisfying approximation ratios, and those that guarantee high quality ratios but are slow. In this paper we prove that…
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…
In this paper we analyze several inexact fast augmented Lagrangian methods for solving linearly constrained convex optimization problems. Mainly, our methods rely on the combination of excessive-gap-like smoothing technique developed in…
The well-known Eulerian path problem can be solved in polynomial time (more exactly, there exists a linear time algorithm for this problem). In this paper, we model the problem using a string matching framework, and then initiate an…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…
Considering a 2D matrix of positive and negative numbers, how might one draw a rectangle within it whose contents sum higher than all other rectangles'? This fundamental problem, commonly known the maximum rectangle problem or subwindow…
This paper discusses the graph covering problem in which a set of edges in an edge- and node-weighted graph is chosen to satisfy some covering constraints while minimizing the sum of the weights. In this problem, because of the large…
The maximum/minimum bisection problems are, given an edge-weighted graph, to find a bipartition of the vertex set into two sets whose sizes differ by at most one, such that the total weight of edges between the two sets is…
Finite metric trees are known to have strict 1-negative type. In this paper we introduce a new family of inequalities that quantify the extent of the "strictness" of the 1-negative type inequalities for finite metric trees. These…
Polytrees are a subclass of Bayesian networks that seek to capture the conditional dependencies between a set of $n$ variables as a directed forest and are motivated by their more efficient inference and improved interpretability. Since the…
We consider two problems for a directed graph $G$, which we show to be closely related. The first one is to find $k$ edge-disjoint forests in $G$ of maximal size such that the indegree of each vertex in these forests is at most $k$. We…
In the $k$-dispersion problem, we need to select $k$ nodes of a given graph so as to maximize the minimum distance between any two chosen nodes. This can be seen as a generalization of the independent set problem, where the goal is to…