In this paper, we consider different constrained partition problems for weighted trees and cactus graphs. We focus on the (l,u)-partition problem, which is the problem of partitioning a weighted graph into connected clusters such that each cluster fulfills the lower and upper weight constraints l and u. Partitioning into a minimum, maximum or a fixed number of clusters is known to be NP-hard in general, but polynomial-time solvable on trees. We prove that these three variants of the (l,u)-partition problem can be solved for cactus graphs as well by presenting a polynomial-time algorithm. Additionally, we present an efficient method to compute the corresponding partitions. For other optimization goals or additional constraints, the partition problem becomes NP-hard - even on trees and for a lower weight bound equal to zero. We show that our method can be used as an algorithmic framework to solve other partition problems for weighted trees and cactus graphs with a pseudopolynomial runtime.
The weighted $k$-center problem in graphs is a classical facility location problem where we place $k$ centers on the graph, which minimize the maximum weighted distance of a vertex to its nearest center. We study this problem when the underlying graph is a cactus with $n$ vertices and present an $O(n \log^2 n)$ time algorithm for the same. This time complexity improves upon the $O(n^2)$ time algorithm by Ben-Moshe et al. [TCS 2007], which is the current state-of-the-art.
In the paper, we write a linear algorithm for calculating the weighted domination number of a vertex-weighted cactus. The algorithm is based on the well known depth first search (DFS) structure. Our algorithm needs less than $12n+5b$ additions and $9n+2b$ $\min$-operations where $n$ is the number of vertices and $b$ is the number of blocks in the cactus.
Partitioning oracles were introduced by Hassidim et al. (FOCS 2009) as a generic tool for constant-time algorithms. For any epsilon > 0, a partitioning oracle provides query access to a fixed partition of the input bounded-degree minor-free graph, in which every component has size poly(1/epsilon), and the number of edges removed is at most epsilon*n, where n is the number of vertices in the graph. However, the oracle of Hassidimet al. makes an exponential number of queries to the input graph to answer every query about the partition. In this paper, we construct an efficient partitioning oracle…
We introduce a method and an algorithm for computing the weighted Moore-Penrose inverse of multiple-variable polynomial matrix and the related algorithm which is appropriated for sparse polynomial matrices. These methods and algorithms are generalizations of algorithms developed in [M.B. Tasic, P.S. Stanimirovic, M.D. Petkovic, Symbolic computation of weighted Moore-Penrose inverse using partitioning method, Appl. Math. Comput. 189 (2007) 615-640] to multiple-variable rational and polynomial matrices and improvements of these algorithms on sparse matrices. Also, these methods are generalizatio…
The Partitioning Min-Max Weighted Matching (PMMWM) problem is an NP-hard problem that combines the problem of partitioning a group of vertices of a bipartite graph into disjoint subsets with limited size and the classical Min-Max Weighted Matching (MMWM) problem. Kress et al. proposed this problem in 2015 and they also provided several algorithms, among which MP$_{\text{LS}}$ is the state-of-the-art. In this work, we observe there is a time bottleneck in the matching phase of MP$_{\text{LS}}$. Hence, we optimize the redundant operations during the matching iterations, and propose an efficient …
We propose a method and algorithm for computing the weighted Moore-Penrose inverse of one-variable rational matrices. Continuing this idea, we develop an algorithm for computing the weighted Moore-Penrose inverse of one-variable polynomial matrix. These methods and algorithms are generalizations of the method for computing the weighted Moore-Penrose inverse for constant matrices, originated in Wang and Chen [G.R. Wang, Y.L. Chen, A recursive algorithm for computing the weighted Moore-Penrose inverse AMN, J. Comput. Math. 4 (1986) 74-85], and the partitioning method for computing the Moore-Penr…
In a network, a $k$-plex represents a subset of $n$ vertices where the degree of each vertex in the subnetwork induced by this subset is at least $n-k$. The maximum edge-weight $k$-plex partitioning problem (Max-EkPP) is to find the $k$-plex partitioning in edge-weighted network, such that the sum of edge weights is maximal. The Max-EkPP has an important role in discovering new information in large sparse biological networks. We propose a variable neighborhood search (VNS) algorithm for solving Max-EkPP. The VNS implements a local search based on the 1-swap first improvement strategy and the o…
The balanced hypergraph partitioning problem is to partition a hypergraph into $k$ disjoint blocks of bounded size such that the sum of the number of blocks connected by each hyperedge is minimized. We present an improvement to the flow-based refinement framework of KaHyPar-MF, the current state-of-the-art multilevel $k$-way hypergraph partitioning algorithm for high-quality solutions. Our improvement is based on the recently proposed HyperFlowCutter algorithm for computing bipartitions of unweighted hypergraphs by solving a sequence of incremental maximum flow problems. Since vertices and hyp…
The objective of clustering is to discover natural groups in datasets and to identify geometrical structures which might reside there, without assuming any prior knowledge on the characteristics of the data. The problem can be seen as detecting the inherent separations between groups of a given point set in a metric space governed by a similarity function. The pairwise similarities between all data objects form a weighted graph adjacency matrix which contains all necessary information for the clustering process, which can consequently be formulated as a graph partitioning problem. In this cont…
This paper studies optimal matroid partitioning problems for various objective functions. In the problem, we are given a finite set $E$ and $k$ weighted matroids $(E, \mathcal{I}_i, w_i)$, $i = 1, \dots, k$, and our task is to find a minimum partition $(I_1,\dots,I_k)$ of $E$ such that $I_i \in \mathcal{I}_i$ for all $i$. For each objective function, we give a polynomial-time algorithm or prove NP-hardness. In particular, for the case when the given weighted matroids are identical and the objective function is the sum of the maximum weight in each set (i.e., $\sum_{i=1}^k\max_{e\in I_i}w_i(e)$…
In this paper new algorithm for calculating power indices is described. The complexity class of the problem is #P-complete and even calculating power index of the biggest player is NP-hard task. Constructed algorithm is a mix of ideas of two algorithms: Klinz & Woeginger partitioning algorithm and Mann & Shapley generating functions algorithm. Time and space complexities of the algorithm are analysed and compared with other known algorithms for the problem. Constructed algorithm has pessimistic time complexity O(n 2^(n/2))and pseudopolynomial complexity O(nq), where q is quota of the voting ga…
In this paper we study a max-min $k$-partition problem on a weighted graph, that could model a robust $k$-coalition formation. We settle the computational complexity of this problem as complete for class $Σ_2^P$. This hardness holds even for $k=2$ and arbitrary weights, or $k=3$ and non-negative weights, which matches what was known on \textsc{MaxCut} and \textsc{Min-3-Cut} one level higher in the polynomial hierarchy.
Online algorithms process their inputs piece by piece, taking irrevocable decisions for each data item. This model is too restrictive for most partitioning problems, since data that is yet to arrive may render it impossible to extend partial partitionings to the entire data set reasonably well. In this work, we show that preemption might be a potential remedy. We consider the problem of partitioning online sequences, where $p-1$ separators need to be inserted into a sequence of integers that arrives online so as to create $p$ contiguous partitions of similar weight. While without preemption no…
We introduce an improved structure of distance sensitivity oracle (DSO). The task is to pre-process a non-negatively weighted graph so that a data structure can quickly answer replacement path length for every triple of source, terminal and failed vertex. The previous best algorithm constructs in time $\tilde{O}(mn)$ a distance sensitivity oracle of size $O(n^2\log n)$ that processes queries in $O(1)$ time. As an improvement, our oracle takes up $O(n^2)$ space, while preserving $O(1)$ query efficiency and $\tilde{O}(mn)$ preprocessing time. One should notice that space complexity and query tim…
This paper introduces a discrete relaxation for the class of combinatorial optimization problems which can be described by a set partitioning formulation under packing constraints. We present two combinatorial relaxations based on computing maximum weighted matchings in suitable graphs. Besides providing dual bounds, the relaxations are also used on a variable reduction technique and a matheuristic. We show how that general method can be tailored to sample applications, and also perform a successful computational evaluation with benchmark instances of a problem in maritime logistics.
An exact algorithm is presented for solving edge weighted graph partitioning problems. The algorithm is based on a branch and bound method applied to a continuous quadratic programming formulation of the problem. Lower bounds are obtained by decomposing the objective function into convex and concave parts and replacing the concave part by an affine underestimate. It is shown that the best affine underestimate can be expressed in terms of the center and the radius of the smallest sphere containing the feasible set. The concave term is obtained either by a constant diagonal shift associated with…
The balanced hypergraph partitioning problem (HGP) is to partition the vertex set of a hypergraph into k disjoint blocks of bounded weight, while minimizing an objective function defined on the hyperedges. Whereas real-world applications often use vertex and edge weights to accurately model the underlying problem, the HGP research community commonly works with unweighted instances. In this paper, we argue that, in the presence of vertex weights, current balance constraint definitions either yield infeasible partitioning problems or allow unnecessarily large imbalances and propose a new definit…
We study the approximability of multiway partitioning problems, examples of which include Multiway Cut, Node-weighted Multiway Cut, and Hypergraph Multiway Cut. We investigate these problems from the point of view of two possible generalizations: as Min-CSPs, and as Submodular Multiway Partition problems. These two generalizations lead to two natural relaxations, the Basic LP, and the Lovasz relaxation. We show that the Lovasz relaxation gives a (2-2/k)-approximation for Submodular Multiway Partition with $k$ terminals, improving a recent 2-approximation. We prove that this factor is optimal i…
In the k-partition problem (k-PP), one is given an edge-weighted undirected graph, and one must partition the node set into at most k subsets, in order to minimise (or maximise) the total weight of the edges that have their end-nodes in the same cluster. Various hierarchical variants of this problem have been studied in the context of data mining. We consider a 'two-level' variant that arises in mobile wireless communications. We show that an exact algorithm based on intelligent preprocessing, cutting planes and symmetry-breaking is capable of solving small- and medium-size instances to proven…
We present a new combinatorial model for identifying regulatory modules in gene co-expression data using a decomposition into weighted cliques. To capture complex interaction effects, we generalize the previously-studied weighted edge clique partition problem. As a first step, we restrict ourselves to the noise-free setting, and show that the problem is fixed parameter tractable when parameterized by the number of modules (cliques). We present two new algorithms for finding these decompositions, using linear programming and integer partitioning to determine the clique weights. Further, we impl…
A graph $G=(V,E)$ with a vertex set $V$ and an edge set $E$ is called a pairwise compatibility graph (PCG, for short) if there are a tree $T$ whose leaf set is $V$, a non-negative edge weight $w$ in $T$, and two non-negative reals $d_{\min}\leq d_{\max}$ such that $G$ has an edge $uv\in E$ if and only if the distance between $u$ and $v$ in the weighted tree $(T,w)$ is in the interval $[d_{\min}, d_{\max}]$. PCG is a new graph class motivated from bioinformatics. In this paper, we give some necessary and sufficient conditions for PCG based on cut-vertices and twins, which provide reductions amo…
We propose an optimal algorithm for solving the longest path problem in undirected weighted graphs. By using graph partitioning and dynamic programming, we obtain an algorithm that is significantly faster than other state-of-the-art methods. This enables us to solve instances that have previously been unsolved.
In this paper we show how graph structure can be used to drastically reduce the computational bottleneck of the Breadth First Search algorithm (the foundation of many graph traversal techniques). In particular, we address parallel implementations where the bottleneck is the number of messages between processors emitted at the peak iteration. First, we derive an expression for the expected degree distribution of vertices in the frontier of the algorithm which is shown to be highly skewed. Subsequently, we derive an expression for the expected message along an edge in a particular iteration. Thi…
Consider the problem of partitioning an arbitrary metric space into pieces of diameter at most Δ, such every pair of points is separated with relatively low probability. We propose a rate-based algorithm inspired by multiplicatively-weighted Voronoi diagrams, and prove it has optimal trade-offs. This also gives us another logarithmic approximation algorithm for the 0-extension problem.
Determining the interaction strength between proteins and small molecules is key to analyzing their biological function. Quantum-mechanical calculations such as \emph{Density Functional Theory} (DFT) give accurate and theoretically well-founded results. With common implementations the running time of DFT calculations increases quadratically with molecule size. Thus, numerous subsystem-based approaches have been developed to accelerate quantum-chemical calculations. These approaches partition the protein into different fragments, which are treated separately. Interactions between different frag…
Finding the origin of short phrases propagating through the web has been formalized by Leskovec et al. [ACM SIGKDD 2009] as DAG Partitioning: given an arc-weighted directed acyclic graph on $n$ vertices and $m$ arcs, delete arcs with total weight at most $k$ such that each resulting weakly-connected component contains exactly one sink---a vertex without outgoing arcs. DAG Partitioning is NP-hard. We show an algorithm to solve DAG Partitioning in $O(2^k \cdot (n+m))$ time, that is, in linear time for fixed $k$. We complement it with linear-time executable data reduction rules. Our experiments s…
In this paper, we develop the idea to partition the edges of a weighted graph in order to uncover overlapping communities of its nodes. Our approach is based on the construction of different types of weighted line graphs, i.e. graphs whose nodes are the links of the original graph, that encapsulate differently the relations between the edges. Weighted line graphs are argued to provide an alternative, valuable representation of the system's topology, and are shown to have important applications in community detection, as the usual node partition of a line graph naturally leads to an edge partit…
We study the problem of computing a minimum cut in a simple, undirected graph and give a deterministic $O(m \log^2 n \log\log^2 n)$ time algorithm. This improves both on the best previously known deterministic running time of $O(m \log^{12} n)$ (Kawarabayashi and Thorup, STOC 2015) and the best previously known randomized running time of $O(m \log^{3} n)$ (Karger, J.ACM 2000) for this problem, though Karger's algorithm can be further applied to weighted graphs. Moreover, our result extends to balanced directed graphs, where the balance of a directed graph captures how close the graph is to bei…
Dealing with NP-hard problems, kernelization is a fundamental notion for polynomial-time data reduction with performance guarantees: in polynomial time, a problem instance is reduced to an equivalent instance with size upper-bounded by a function of a parameter chosen in advance. Kernelization for weighted problems particularly requires to also shrink weights. Marx and Végh [ACM Trans. Algorithms 2015] and Etscheid et al. [J. Comput. Syst. Sci. 2017] used a technique of Frank and Tardos [Combinatorica 1987] to obtain polynomial-size kernels for weighted problems, mostly with additive goal func…
Interval scheduling is a basic problem in the theory of algorithms and a classical task in combinatorial optimization. We develop a set of techniques for partitioning and grouping jobs based on their starting and ending times, that enable us to view an instance of interval scheduling on many jobs as a union of multiple interval scheduling instances, each containing only a few jobs. Instantiating these techniques in dynamic and local settings of computation leads to several new results. For $(1+\varepsilon)$-approximation of job scheduling of $n$ jobs on a single machine, we develop a fully dyn…
In a breakthrough work, Kawarabayashi and Thorup (J.~ACM'19) gave a near-linear time deterministic algorithm for minimum cut in a simple graph $G = (V,E)$. A key component is finding the $(1+\varepsilon)$-KT partition of $G$, the coarsest partition $\{P_1, \ldots, P_k\}$ of $V$ such that for every non-trivial $(1+\varepsilon)$-near minimum cut with sides $\{S, \bar{S}\}$ it holds that $P_i$ is contained in either $S$ or $\bar{S}$, for $i=1, \ldots, k$. Here we give a near-linear time randomized algorithm to find the $(1+\varepsilon)$-KT partition of a weighted graph. Our algorithm is quite dif…
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 $k$ disjoint trees within $G$ such that each vertex of $G$ is contained in one of the trees and the weight of the largest tree is as small as possible. We are unable to find this problem in the graph partitioning literature, but we show that the problem is NP-complete. We then propose two approximation algorithms, one that uses a spectral clustering approach…
We propose an exact algorithm for solving the longest simple path problem between two given vertices in undirected weighted graphs. By using graph partitioning and dynamic programming, we obtain an algorithm that is significantly faster than other state-of-the-art methods. This enables us to solve instances that were previously unsolved and solve hard instances significantly faster. Lastly, we present a scalable parallelization which yields the first efficient parallel algorithm for the problem.
There has recently been much progress on exact algorithms for the (un)weighted graph (bi)partitioning problem using branch-and-bound and related methods. In this note we present and improve an easily computable, purely combinatorial lower bound for the weighted bipartitioning problem. The bound is computable in $O(n\log n+m)$ time steps for weighted graphs with $n$ vertices and $m$ edges. In the branch-and-bound setting, the bound for each new subproblem can be updated in $O(n+(m/n)\log n)$ time steps amortized over a series of $n$ branching steps; a rarely triggered tightening of the bound re…
Many load balancing problems that arise in scientific computing applications ask to partition a graph with weights on the vertices and costs on the edges into a given number of almost equally-weighted parts such that the maximum boundary cost over all parts is small. Here, this partitioning problem is considered for bounded-degree graphs G=(V,E) with edge costs c: E->R+ that have a p-separator theorem for some p>1, i.e., any (arbitrarily weighted) subgraph of G can be separated into two parts of roughly the same weight by removing a vertex set S such that the edges incident to S in the subgrap…
We consider the problem of partitioning the set of vertices of a given unit disk graph (UDG) into a minimum number of cliques. The problem is NP-hard and various constant factor approximations are known, with the current best ratio of 3. Our main result is a {\em weakly robust} polynomial time approximation scheme (PTAS) for UDGs expressed with edge-lengths, it either (i) computes a clique partition or (ii) gives a certificate that the graph is not a UDG; for the case (i) that it computes a clique partition, we show that it is guaranteed to be within $(1+\eps)$ ratio of the optimum if the inpu…
Boolean-width is a recently introduced graph parameter. Many problems are fixed parameter tractable when parametrized by boolean-width, for instance "Minimum Weighted Dominating Set" (MWDS) problem can be solved in $O^*(2^{3k})$ time given a boolean-decomposition of width $k$, hence for all graph classes where a boolean-decomposition of width $O(\log n)$ can be found in polynomial time, MWDS can be solved in polynomial time. We study graph classes having boolean-width $O(\log n)$ and problems solvable in $O^*(2^{O(k)})$, combining these two results to design polynomial algorithms. We show that…
Correlation clustering is a fundamental combinatorial optimization problem arising in many contexts and applications that has been the subject of dozens of papers in the literature. In this problem we are given a general weighted graph where each edge is labeled positive or negative. The goal is to obtain a partitioning (clustering) of the vertices that minimizes disagreements - weight of negative edges trapped inside a cluster plus positive edges between different clusters. Most of the papers on this topic mainly focus on minimizing total disagreement, a global objective for this problem. In …
We introduce the balanced crown decomposition that captures the structure imposed on graphs by their connected induced subgraphs of a given size. Such subgraphs are a popular modeling tool in various application areas, where the non-local nature of the connectivity condition usually results in very challenging algorithmic tasks. The balanced crown decomposition is a combination of a crown decomposition and a balanced partition which makes it applicable to graph editing as well as graph packing and partitioning problems. We illustrate this by deriving improved kernelization and approximation al…
