Computing a Maximum Clique in Geometric Superclasses of Disk Graphs

In the classical problem of scheduling on unrelated parallel machines, a set of jobs has to be assigned to a set of machines. The jobs have a processing time depending on the machine and the goal is to minimize the makespan, that is, the maximum machine load. It is well known that this problem is NP-hard and does not allow polynomial time approximation algorithms with approximation guarantees smaller than 1.5 unless P = NP. We consider the case that there are only a constant number K of machine types. Two machines have the same type if all jobs have the same processing time for them. This variant of the problem is strongly NP-hard already for $$K=1$$ . We present an efficient polynomial time approximation scheme (EPTAS) for the problem, that is, for any $$\varepsilon > 0$$ an assignment with makespan of length at most $$(1+\varepsilon )$$ times the optimum can be found in polynomial time in the input length and the exponent is independent of $$1/\varepsilon $$ . In particular, we achieve a running time of $$2^{{\mathcal {O}}(K\log (K) \nicefrac {1}{\varepsilon }\log ^4 \nicefrac {1}{\varepsilon })}+\mathrm {poly}(|I|)$$ , where |I| denotes the input length. Furthermore, we study three other problem variants and present an EPTAS for each of them: The Santa Claus problem, where the minimum machine load has to be maximized; the case of scheduling on unrelated parallel machines with a constant number of uniform types, where machines of the same type behave like uniformly related machines; and the multidimensional vector scheduling variant of the problem where both the dimension and the number of machine types are constant. For the Santa Claus problem we achieve the same running time. The results are achieved, using mixed integer linear programming and rounding techniques.

A (unit) disk graph is the intersection graph of closed (unit) disks in the plane. Almost three decades ago, an elegant polynomial-time algorithm was found for M AXIMUM C LIQUE on unit disk graphs [Clark, Colbourn, Johnson; Discrete Mathematics ’90]. Since then, it has been an intriguing open question whether or not tractability can be extended to general disk graphs. We show that the disjoint union of two odd cycles is never the complement of a disk graph nor of a unit (3-dimensional) ball graph. From that fact and existing results, we derive a simple QPTAS and a subexponential algorithm running in time 2 Õ( n 2/3 ) for M AXIMUM C LIQUE on disk and unit ball graphs. We then obtain a randomized EPTAS for computing the independence number on graphs having no disjoint union of two odd cycles as an induced subgraph, bounded VC-dimension, and linear independence number. This, in combination with our structural results, yields a randomized EPTAS for M AX C LIQUE on disk and unit ball graphs. M AX C LIQUE on unit ball graphs is equivalent to finding, given a collection of points in R 3 , a maximum subset of points with diameter at most some fixed value. In stark contrast, M AXIMUM C LIQUE on ball graphs and unit 4-dimensional ball graphs, as well as intersection graphs of filled ellipses (even close to unit disks) or filled triangles is unlikely to have such algorithms. Indeed, we show that, for all those problems, there is a constant ratio of approximation that cannot be attained even in time 2 n 1−ɛ , unless the Exponential Time Hypothesis fails.

In this paper, we study the problem of designing in-place algorithms for finding the maximum clique in the intersection graphs of axis-parallel rectangles and disks in 2D. We first propose O(n 2logn) time in-place algorithms for finding the maximum clique of the intersection graphs of a set of axis-parallel rectangles of arbitrary sizes. For the rectangle intersection graph of fixed height rectangles, the time complexity can be slightly improved to O(nlogn + nK), where K is the size of the maximum clique. For disk graphs, we consider two variations of the maximum clique problem, namely geometric clique and graphical clique. The time complexity of our algorithm for finding the largest geometric clique is O(n 2logn), and it works for disks of arbitrary radii. For graphical clique, our proposed algorithm works for unit disks (i.e., of same radii) and the worst case time complexity is O(n 2 + mK 4); m is the number of edges in the unit disk intersection graph, and K is the size of the largest clique in that graph. It uses O(n 4) time in-place computation of maximum matching in a bipartite graph, which is of independent interest. All these algorithms need O(1) work space in addition to the input array \(\cal R\).KeywordsBipartite GraphUnit DiskBottom BoundaryMaximum CliqueIntersection GraphThese keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

The results of this paper provide an Efficient Polynomial-Time Approximation Scheme (EPTAS) for approximating the genus (and non-orientable genus) of dense graphs. The running time of the algorithm is quadratic. Moreover, we extend the algorithm to output an embedding (rotation system), whose genus is arbitrarily close to the minimum genus. This second algorithm is an Efficient Polynomial-time Randomized Approximation Scheme (EPRAS) and the expected running time is also quadratic.

The main results of this paper provide an Efficient Polynomial-Time Approximation Scheme (EPTAS) for approximating the genus (and non-orientable genus) of dense graphs. By dense we mean that \(|E(G)|\ge \alpha \, |V(G)|^2\) for some fixed \(\alpha \gt 0\) . While a constant-factor approximation is trivial for this class of graphs, approximations with factor arbitrarily close to 1 need a sophisticated algorithm and complicated mathematical justification. More precisely, we provide an algorithm that for a given (dense) graph G of order n and given \(\varepsilon \gt 0\) , returns an integer g such that G has an embedding in a surface of genus g , and this is ɛ-close to a minimum genus embedding in the sense that the minimum genus \(\mathsf {g}(G)\) of G satisfies: \(\mathsf {g}(G)\le g\le (1+\varepsilon)\mathsf {g}(G)\) . The running time of the algorithm is \(O(f(\varepsilon)\,n^2)\) , where \(f(\cdot)\) is an explicit function. Next, we extend this algorithm to also output an embedding (rotation system) whose genus is g . This second algorithm is an Efficient Polynomial-time Randomized Approximation Scheme (EPRAS) and runs in time \(O(f_1(\varepsilon)\,n^2)\) . Our algorithms are based on the analysis of minimum genus embeddings of quasirandom graphs. We use a general notion of quasirandom graphs [ 25 ]. We start with a regular partition obtained via an algorithmic version of the Szemerédi Regularity Lemma (due to Frieze and Kannan [ 17 ] and to Fox, Lovász, and Zhao [ 14 , 15 ]). We then partition the input graph into a bounded number of quasirandom subgraphs, which are preselected in such a way that they admit embeddings using as many triangles and quadrangles as faces as possible. Here we provide an ɛ-approximation \(\nu (G)\) for the maximum number of edge-disjoint triangles in G . The value \(\nu (G)\) can be computed by solving a linear program whose size is bounded by certain value \(f_2(\varepsilon)\) depending only on ɛ. After solving the linear program, the genus can be approximated (see Corollary 1.7 ). The proof of this result is long and will be of independent interest in topological graph theory.

We are given a set of weighted unit disks and a set of points in Euclidean plane. The minimum weight unit disk cover (WUDC) problem asks for a subset of disks of minimum total weight that covers all given points. WUDC is one of the geometric set cover problems, which have been studied extensively for the past two decades (for many different geometric range spaces, such as (unit) disks, halfspaces, rectangles, triangles). It is known that the unweighted WUDC problem is NP-hard and admits a polynomial-time approximation scheme (PTAS). For the weighted WUDC problem, several constant approximations have been developed. However, whether the problem admits a PTAS has been an open question. In this paper, we answer this question affirmatively by presenting the first PTAS for WUDC. Our result implies the first PTAS for the minimum weight dominating set problem in unit disk graphs. Combining with existing ideas, our result can also be used to obtain the first PTAS for the maxmimum lifetime coverage problem and an improved constant approximation ratio for the connected dominating set problem in unit disk graphs.

This paper presents an algorithm for constructing a spanner for ad hoc networks whose nodes have variabletransmission range. Almost all previous spanner constructions for ad hoc networks assumed that all nodes in the network have the same transmission range. This allowed a succinct representation of the network as a unit disk graph, serving as the basis for the construction. In contrast, when nodes have variable transmission range, the ad hoc network must be modeled by a general disk graph. Whereas unit disk graphs are undirected, general disk graphs are directed. This complicates the construction of a spanner for the network, since currently there are no efficient constructions of low-stretch spanners for general directed graphs. Nevertheless, in this paper it is shown that the class of disk graphs enjoys (efficiently constructible) spanners of quality similar to that of unit disk graph spanners. Moreover, it is shown that the new construction can be done in a localized fashion.

We consider basic problems of non-preemptive scheduling on uniformly related machines. For a given schedule, defined by a partition of the jobs into m subsets corresponding to the m machines, $$C_i$$ C i denotes the completion time of machine i. Our goal is to find a schedule that minimizes or maximizes $$\sum _{i=1}^m C_i^p$$ ? i = 1 m C i p for a fixed value of p such that $$0 1$$ p > 1 the minimization problem is equivalent to the well-known problem of minimizing the $$\ell _p$$ l p norm of the vector of the completion times of the machines, and for $$0<p<1$$ 0 < p < 1 , the maximization problem is of interest. Our main result is an efficient polynomial time approximation scheme (EPTAS) for each one of these problems. Our schemes use a non-standard application of the so-called shifting technique. We focus on the work (total size of jobs) assigned to each machine and introduce intervals of work that are forbidden. These intervals are defined so that the resulting effect on the goal function is sufficiently small. This allows the partition of the problem into sub-problems (with subsets of machines and jobs) whose solutions are combined into the final solution using dynamic programming. Our results are the first EPTAS's for this natural class of load balancing problems.

NC-Approximation Schemes for NP- and PSPACE-Hard Problems for Geometric Graphs

A central question in computational biology is the design of genetic markers to distinguish between two given sets of (DNA) sequences. This question is formalized as the NP-complete Distinguishing Substring Selection problem (DSSS for short) which asks, given a set of "good" strings and a set of "bad" strings, for a solution string which is, with respect to the Hamming metric, "away" from the good strings and "close" to the bad strings. More precisely, given integers dg, db, and L, we ask for a length-L string s such that s has Hamming distance at least dg to every length-L substring of the good strings and such that every bad string has a length-L substring with Hamming distance at most db to s. Studying the parameterized complexity of DSSS, we show that, already for binary alphabet, DSSS is W[1]-hard with respect to its natural parameters. This, in particular, implies that a recently given polynomial-time approximation scheme (PTAS) by Deng et al. cannot be replaced by a so-called efficient polynomial-time approximation scheme (EPTAS) unless an unlikely collapse in parameterized complexity theory occurs. This is seemingly the first computational biology problem for which such a border between PTAS (which exists) and EPTAS (which is unlikely to exist) could be established. By way of contrast, for a special case of DSSS, we present an exact fixed-parameter algorithm solving the problem efficiently. In this way we also exhibit a sharp border between fixed-parameter tractability and intractability results.

We present an efficient polynomial-time approximation scheme (EPTAS) for the problem of scheduling jobs on parallel uniform machines that improves all previously known EPTAS for the problem. Our algorithm uses a Mixed Integer Linear Program (MILP) formulation for a relaxed version of the problem. We simplify the MILP by repeatedly removing carefully selected sets of jobs and machines until all integer variables have been removed. Then, we build up the solution through the use of a dynamic programming approach, enumeration, and linear program solving. Notable about our approach is that our algorithm only uses an LP solver, different from previous EPTAS approaches where MILP solvers are necessary.

We present two local approaches that yield polynomial-time approximation schemes (PTAS) for the Maximum Independent Set and Minimum Dominating Set problem in unit disk graphs. The algorithms run locally in each node and compute a (1+ε)-approximation to the problems at hand for any given ε &gt; 0. The time complexity of both algorithms is O(TMIS + log*! n/εO(1)), where TMIS is the time required to compute a maximal independent set in the graph, and n denotes the number of nodes. We then extend these results to a more general class of graphs in which the maximum number of pair-wise independent nodes in every r-neighborhood is at most polynomial in r. Such graphs of polynomially bounded growth are introduced as a more realistic model for wireless networks and they generalize existing models, such as unit disk graphs or coverage area graphs.

Maximum weight independent sets and cliques in intersection graphs of filaments

Given a graph G=(V,E) with node weight w:V→R+ and a subset S⊆V, find a minimum total weight tree interconnecting all nodes in S. This is the node-weighted Steiner tree problem which will be studied in this paper. In general, this problem is NP-hard and cannot be approximated by a polynomial time algorithm with performance ratio aln n for any 0<a<1 unless NP⊆DTIME(nO(log n)), where n is the number of nodes in s. In this paper, we are the first to show that even though for unit disk graphs, the problem is still NP-hard and it has a polynomial time constant approximation. We present a 2.5ρ-approximation where ρ is the best known performance ratio for polynomial time approximation of classical Steiner minimum tree problem in graphs. As a corollary, we obtain that there is a polynomial time (9.875+e)-approximation algorithm for minimum weight connected dominating set in unit disk graphs, and also there is a polynomial time (4.875+e)-approximation algorithm for minimum weight connected vertex cover in unit disk graphs.

In this paper, we give a comprehensive overview of the development of clique algorithms and their use for drug design based on the search for cliques in protein product graphs. The maximum clique problem is a computational problem of finding largest subsets of vertices in a graph that are all pairwise adjacent. A related problem is the maximum weight clique problem and the highest weight k-clique problem, which both extend the algorithm to weighted graphs. The review covers our developed algorithms, starting with our improved branch-and-bound algorithm for finding maximum cliques in undirected graphs from 2007 up to the recent developments of algorithms for weighted graphs in 2024. We show the application of these algorithms to early stages of drug discovery, in particular to protein binding site detection based on protein similarity search in large protein databases and to protein-ligand molecular docking.