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Recovering a tree that represents the evolutionary history of a group of species is a key task in phylogenetics. Performing this task using sequence data from multiple genetic markers poses two key challenges. The first is the discordance…

Populations and Evolution · Quantitative Biology 2026-03-12 Ortal Reshef , Ofer Glassman , Or Zuk , Yariv Aizenbud , Boaz Nadler , Ariel Jaffe

The $k$-defective clique model relaxes the strict completeness constraint of the traditional clique by allowing up to $k$ missing edges, providing a robust formulation for detecting cohesive structures in noisy graphs. Consequently, the…

Databases · Computer Science 2026-05-19 Kewu Yang , Kaiqiang Yu , Shengxin Liu , Zhaoquan Gu

We consider a new semidefinite programming relaxation for directed edge expansion, which is obtained by adding triangle inequalities to the reweighted eigenvalue formulation. Applying the matrix multiplicative weight update method to this…

Data Structures and Algorithms · Computer Science 2023-06-16 Lap Chi Lau , Kam Chuen Tung , Robert Wang

We introduce a new Steiner-type problem for directed graphs named \textsc{$q$-Root Steiner Tree}. Here one is given a directed graph $G=(V,A)$ and two subsets of its vertices, $R$ of size $q$ and $T$, and the task is to find a minimum size…

Data Structures and Algorithms · Computer Science 2016-04-19 Ondřej Suchý

Clustering bipartite graphs is a fundamental task in network analysis. In the high-dimensional regime where the number of rows $n_1$ and the number of columns $n_2$ of the associated adjacency matrix are of different order, existing methods…

Statistics Theory · Mathematics 2023-02-28 Guillaume Braun , Hemant Tyagi

Iterative rounding and relaxation have arguably become the method of choice in dealing with unconstrained and constrained network design problems. In this paper we extend the scope of the iterative relaxation method in two directions: (1)…

Data Structures and Algorithms · Computer Science 2015-05-18 Nikhil Bansal , Rohit Khandekar , Jochen Konemann , Viswanath Nagarajan , Britta Peis

Moss and Rabani[12] study constrained node-weighted Steiner tree problems with two independent weight values associated with each node, namely, cost and prize (or penalty). They give an O(log n)-approximation algorithm for the…

Data Structures and Algorithms · Computer Science 2013-04-30 MohammadHossein Bateni , MohammadTaghi Hajiaghayi , Vahid Liaghat

A remarkable connection has been established for antiferromagnetic 2-spin systems, including the Ising and hard-core models, showing that the computational complexity of approximating the partition function for graphs with maximum degree D…

Computational Complexity · Computer Science 2014-11-05 Andreas Galanis , Daniel Stefankovic , Eric Vigoda

Boolean quadratic optimization problems occur in a number of applications. Their mixed integer-continuous nature is challenging, since it is inherently NP-hard. For this motivation, semidefinite programming relaxations (SDR's) are proposed…

Optimization and Control · Mathematics 2020-03-20 V. Cerone , S. M. Fosson , D. Regruto

The Steiner Forest problem, also known as the Generalized Steiner Tree problem, is a fundamental optimization problem on edge-weighted graphs where, given a set of vertex pairs, the goal is to select a minimum-cost subgraph such that each…

Data Structures and Algorithms · Computer Science 2025-04-16 Ali Ahmadi , Iman Gholami , MohammadTaghi Hajiaghayi , Peyman Jabbarzade , Mohammad Mahdavi

We present an algorithm for recovering planted solutions in two well-known models, the stochastic block model and planted constraint satisfaction problems, via a common generalization in terms of random bipartite graphs. Our algorithm…

Data Structures and Algorithms · Computer Science 2015-04-30 Vitaly Feldman , Will Perkins , Santosh Vempala

We significantly improve known time bounds for solving the minimum cut problem on undirected graphs. We use a ``semi-duality'' between minimum cuts and maximum spanning tree packings combined with our previously developed random sampling…

Data Structures and Algorithms · Computer Science 2007-05-23 David R. Karger

We give an FPTAS and an efficient sampling algorithm for the high-fugacity hard-core model on bounded-degree bipartite expander graphs and the low-temperature ferromagnetic Potts model on bounded-degree expander graphs. The results apply,…

Data Structures and Algorithms · Computer Science 2020-03-25 Matthew Jenssen , Peter Keevash , Will Perkins

Hypergraphs allow modeling problems with multi-way high-order relationships. However, the computational cost of most existing hypergraph-based algorithms can be heavily dependent upon the input hypergraph sizes. To address the…

Machine Learning · Computer Science 2021-12-22 Ali Aghdaei , Zhiqiang Zhao , Zhuo Feng

The most commonly used method to tackle the graph partitioning problem in practice is the multilevel approach. During a coarsening phase, a multilevel graph partitioning algorithm reduces the graph size by iteratively contracting nodes and…

Distributed, Parallel, and Cluster Computing · Computer Science 2014-03-26 Henning Meyerhenke , Peter Sanders , Christian Schulz

We consider a variant of the prize collecting Steiner tree problem in which we are given a \emph{directed graph} $D=(V,A)$, a monotone submodular prize function $p:2^V \rightarrow \mathbb{R}^+ \cup \{0\}$, a cost function $c:V \rightarrow…

Data Structures and Algorithms · Computer Science 2022-10-04 Gianlorenzo D'Angelo , Esmaeil Delfaraz , Hugo Gilbert

We introduce a novel method for clustering using a semidefinite programming (SDP) relaxation of the Max k-Cut problem. The approach is based on a new methodology for rounding the solution of an SDP relaxation using iterated linear…

Optimization and Control · Mathematics 2022-07-07 Pedro Felzenszwalb , Caroline Klivans , Alice Paul

We present a tree structure algorithm for optimal control problems with state constraints. We prove a convergence result for a discrete time approximation of the value function based on a novel formulation of the constrained problem. Then…

Numerical Analysis · Mathematics 2020-09-29 Alessandro Alla , Maurizio Falcone , Luca Saluzzi

Suppose we are given a bipartite graph that admits a perfect matching and an adversary may delete any edge from the graph with the intention of destroying all perfect matchings. We consider the task of adding a minimum cost edge-set to the…

Data Structures and Algorithms · Computer Science 2018-12-06 Felix Hommelsheim , Moritz Mühlenthaler , Oliver Schaudt

We consider the densest $k$-subgraph problem, which seeks to identify the $k$-node subgraph of a given input graph with maximum number of edges. This problem is well-known to be NP-hard, by reduction to the maximum clique problem. We…

Optimization and Control · Mathematics 2019-04-09 Polina Bombina , Brendan Ames