Related papers: On the minimum quartet tree cost problem
Finding a minimum spanning tree (MST) for $n$ points in an arbitrary metric space is a fundamental primitive for hierarchical clustering and many other ML tasks, but this takes $\Omega(n^2)$ time to even approximate. We introduce a…
Several important tasks in medical image analysis can be stated in the form of an optimization problem whose feasible solutions are connected subgraphs. Examples include the reconstruction of neural or vascular structures under…
This paper addresses combinatorial optimization scheme for solving the multicriteria Steiner tree problem for communication network topology design (e.g., wireless mesh network). The solving scheme is based on several models: multicriteria…
Min-Cut queries are fundamental: Preprocess an undirected edge-weighted graph, to quickly report a minimum-weight cut that separates a query pair of nodes $s,t$. The best data structure known for this problem simply builds a cut-equivalent…
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…
As the development of distributed systems progresses, more and more challenges arise and the need for developing optimized systems and for optimizing existing systems from multiple perspectives becomes more stringent. In this paper I…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
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…
A quadratic minimum spanning tree (QMST) problem is to determine a minimum spanning tree of a connected graph having edges which are associated with linear and quadratic weights. The linear weights are the edge costs which are associated…
One of the key problems in tensor network based quantum circuit simulation is the construction of a contraction tree which minimizes the cost of the simulation, where the cost can be expressed in the number of operations as a proxy for the…
Determining the evolutionary history of a given biological data is an important task in biological sciences. Given a set of quartet topologies over a set of taxa, the Maximum Quartet Consistency (MQC) problem consists of computing a global…
Correlation clustering is arguably the most natural formulation of clustering. Given n objects and a pairwise similarity measure, the goal is to cluster the objects so that, to the best possible extent, similar objects are put in the same…
We study the query complexity of the metric Steiner Tree problem, where we are given an $n \times n$ metric on a set $V$ of vertices along with a set $T \subseteq V$ of $k$ terminals, and the goal is to find a tree of minimum cost that…
The Minimum Branch Vertices Spanning Tree problem aims to find a spanning tree $T$ in a given graph $G$ with the fewest branch vertices, defined as vertices with a degree three or more in $T$. This problem, known to be NP-hard, has…
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 the problem of connecting the parts of a multipartite graph using a minimum number of edges under a matching constraint. We introduce interconnection trees, defined as matchings whose projections onto the quotient graph form a…
We study the explainable clustering problem first posed by Moshkovitz, Dasgupta, Rashtchian, and Frost (ICML 2020). The goal of explainable clustering is to fit an axis-aligned decision tree with $K$ leaves and minimal clustering cost…
The Minimum Spanning Tree Problem with Conflicts consists in finding the minimum conflict-free spanning tree of a graph, i.e., the spanning tree of minimum cost, including no pairs of edges that are in conflict. In this paper, we solve this…
One of the challenging scientific computing problems is topology optimization, where searching through the combinatorially complex configurations and solving the constraints of partial differential equations need to be done simultaneously.…
The optimal connecting network problem generalizes many models of structure optimization known from the literature, including communication and transport network topology design, graph cut and graph clustering, structure identification from…