The Geometric Maximum Traveling Salesman Problem

We consider the traveling salesman problem when the cities are points in R^d for some fixed d and distances are computed according to geometric distances, determined by some norm. We show that for any polyhedral norm, the problem of finding a tour of maximum length can be solved in polynomial time. If arithmetic operations are assumed to take unit time, our algorithms run in time O(n^{f-2} log n), where f is the number of facets of the polyhedron determining the polyhedral norm. Thus for example we have O(n^2 log n) algorithms for the cases of points in the plane under the Rectilinear and Sup norms. This is in contrast to the fact that finding a minimum length tour in each case is NP-hard. Our approach can be extended to the more general case of quasi-norms with not necessarily symmetric unit ball, where we get a complexity of O(n^{2f-2} log n). For the special case of two-dimensional metrics with f=4 (which includes the Rectilinear and Sup norms), we present a simple algorithm with O(n) running time. The algorithm does not use any indirect addressing, so its running time remains valid even in comparison based models in which sorting requires Omega(n \log n) time. The basic mechanism of the algorithm provides some intuition on why polyhedral norms allow fast algorithms. Complementing the results on simplicity for polyhedral norms, we prove that for the case of Euclidean distances in R^d for d>2, the Maximum TSP is NP-hard. This sheds new light on the well-studied difficulties of Euclidean distances.Comment: 24 pages, 6 figures; revised to appear in Journal of the ACM. (clarified some minor points, fixed typos

A CLUE for CLUster Ensembles

Cluster ensembles are collections of individual solutions to a given clustering problem which are useful or necessary to consider in a wide range of applications. The R package clue provides an extensible computational environment for creating and analyzing cluster ensembles, with basic data structures for representing partitions and hierarchies, and facilities for computing on these, including methods for measuring proximity and obtaining consensus and "secondary" clusterings.

Approximation Algorithms for Resource Allocation

This thesis is devoted to designing new techniques and algorithms for combinatorial optimization problems arising in various applications of resource allocation. Resource allocation refers to a class of problems where scarce resources must be distributed among competing agents maintaining certain optimization criteria. Examples include scheduling jobs on one/multiple machines maintaining system performance; assigning advertisements to bidders, or items to people maximizing profit/social fairness; allocating servers or channels satisfying networking requirements etc. Altogether they comprise a wide variety of combinatorial optimization problems. However, a majority of these problems are NP-hard in nature and therefore, the goal herein is to develop approximation algorithms that approximate the optimal solution as best as possible in polynomial time. The thesis addresses two main directions. First, we develop several new techniques, predominantly, a new linear programming rounding methodology and a constructive aspect of a well-known probabilistic method, the Lov\'{a}sz Local Lemma (LLL). Second, we employ these techniques to applications of resource allocation obtaining substantial improvements over known results. Our research also spurs new direction of study; we introduce new models for achieving energy efficiency in scheduling and a novel framework for assigning advertisements in cellular networks. Both of these lead to a variety of interesting questions. Our linear programming rounding methodology is a significant generalization of two major rounding approaches in the theory of approximation algorithms, namely the dependent rounding and the iterative relaxation procedure. Our constructive version of LLL leads to first algorithmic results for many combinatorial problems. In addition, it settles a major open question of obtaining a constant factor approximation algorithm for the Santa Claus problem. The Santa Claus problem is a $NP$-hard resource allocation problem that received much attention in the last several years. Through out this thesis, we study a number of applications related to scheduling jobs on unrelated parallel machines, such as provisionally shutting down machines to save energy, selectively dropping outliers to improve system performance, handling machines with hard capacity bounds on the number of jobs they can process etc. Hard capacity constraints arise naturally in many other applications and often render a hitherto simple combinatorial optimization problem difficult. In this thesis, we encounter many such instances of hard capacity constraints, namely in budgeted allocation of advertisements for cellular networks, overlay network design, and in classical problems like vertex cover, set cover and k-median

Tropical medians by transportation

Fermat-Weber points with respect to an asymmetric tropical distance function are studied. It turns out that they correspond to the optimal solutions of a transportation problem. The results are applied to obtain a new method for computing consensus trees in phylogenetics. This method has several desirable properties; e.g., it is Pareto and co-Pareto on rooted triplets.Comment: 23 pages, 9 figures, computational experiments adde

Impact of Symmetries in Graph Clustering

Diese Dissertation beschäftigt sich mit der durch die Automorphismusgruppe definierten Symmetrie von Graphen und wie sich diese auf eine Knotenpartition, als Ergebnis von Graphenclustering, auswirkt. Durch eine Analyse von nahezu 1700 Graphen aus verschiedenen Anwendungsbereichen kann gezeigt werden, dass mehr als 70 % dieser Graphen Symmetrien enthalten. Dies bildet einen Gegensatz zum kombinatorischen Beweis, der besagt, dass die Wahrscheinlichkeit eines zufälligen Graphen symmetrisch zu sein bei zunehmender Größe gegen Null geht. Das Ergebnis rechtfertigt damit die Wichtigkeit weiterer Untersuchungen, die auf mögliche Auswirkungen der Symmetrie eingehen. Bei der Analyse werden sowohl sehr kleine Graphen (10 000 000 Knoten/>25 000 000 Kanten) berücksichtigt. Weiterhin wird ein theoretisches Rahmenwerk geschaffen, das zum einen die detaillierte Quantifizierung von Graphensymmetrie erlaubt und zum anderen Stabilität von Knotenpartitionen hinsichtlich dieser Symmetrie formalisiert. Eine Partition der Knotenmenge, die durch die Aufteilung in disjunkte Teilmengen definiert ist, wird dann als stabil angesehen, wenn keine Knoten symmetriebedingt von der einen in die andere Teilmenge abgebildet werden und dadurch die Partition verändert wird. Zudem wird definiert, wie eine mögliche Zerlegbarkeit der Automorphismusgruppe in unabhängige Untergruppen als lokale Symmetrie interpretiert werden kann, die dann nur Auswirkungen auf einen bestimmten Bereich des Graphen hat. Um die Auswirkungen der Symmetrie auf den gesamten Graphen und auf Partitionen zu quantifizieren, wird außerdem eine Entropiedefinition präsentiert, die sich an der Analyse dynamischer Systeme orientiert. Alle Definitionen sind allgemein und können daher für beliebige Graphen angewandt werden. Teilweise ist sogar eine Anwendbarkeit für beliebige Clusteranalysen gegeben, solange deren Ergebnis in einer Partition resultiert und sich eine Symmetrierelation auf den Datenpunkten als Permutationsgruppe angeben lässt. Um nun die tatsächliche Auswirkung von Symmetrie auf Graphenclustering zu untersuchen wird eine zweite Analyse durchgeführt. Diese kommt zum Ergebnis, dass von 629 untersuchten symmetrischen Graphen 72 eine instabile Partition haben. Für die Analyse werden die Definitionen des theoretischen Rahmenwerks verwendet. Es wird außerdem festgestellt, dass die Lokalität der Symmetrie eines Graphen maßgeblich beeinflusst, ob dessen Partition stabil ist oder nicht. Eine hohe Lokalität resultiert meist in einer stabilen Partition und eine stabile Partition impliziert meist eine hohe Lokalität. Bevor die obigen Ergebnisse beschrieben und definiert werden, wird eine umfassende Einführung in die verschiedenen benötigten Grundlagen gegeben. Diese umfasst die formalen Definitionen von Graphen und statistischen Graphmodellen, Partitionen, endlichen Permutationsgruppen, Graphenclustering und Algorithmen dafür, sowie von Entropie. Ein separates Kapitel widmet sich ausführlich der Graphensymmetrie, die durch eine endliche Permutationsgruppe, der Automorphismusgruppe, beschrieben wird. Außerdem werden Algorithmen vorgestellt, die die Symmetrie von Graphen ermitteln können und, teilweise, auch das damit eng verwandte Graphisomorphie Problem lösen. Am Beispiel von Graphenclustering gibt die Dissertation damit Einblicke in mögliche Auswirkungen von Symmetrie in der Datenanalyse, die so in der Literatur bisher wenig bis keine Beachtung fanden

Advancing Divide-And-Conquer Phylogeny Estimation Using Robinson-Foulds Supertrees

One of the Grand Challenges in Science is the construction of the Tree of Life, an evolutionary tree containing several million species, spanning all life on earth. However, the construction of the Tree of Life is enormously computationally challenging, as all the current most accurate methods are either heuristics for NP-hard optimization problems or Bayesian MCMC methods that sample from tree space. One of the most promising approaches for improving scalability and accuracy for phylogeny estimation uses divide-and-conquer: a set of species is divided into overlapping subsets, trees are constructed on the subsets, and then merged together using a "supertree method". Here, we present Exact-RFS-2, the first polynomial-time algorithm to find an optimal supertree of two trees, using the Robinson-Foulds Supertree (RFS) criterion (a major approach in supertree estimation that is related to maximum likelihood supertrees), and we prove that finding the RFS of three input trees is NP-hard. We also present GreedyRFS (a greedy heuristic that operates by repeatedly using Exact-RFS-2 on pairs of trees, until all the trees are merged into a single supertree). We evaluate Exact-RFS-2 and GreedyRFS, and show that they have better accuracy than the current leading heuristic for RFS

A Survey on Approximation in Parameterized Complexity: Hardness and Algorithms

Parameterization and approximation are two popular ways of coping with NP-hard problems. More recently, the two have also been combined to derive many interesting results. We survey developments in the area both from the algorithmic and hardness perspectives, with emphasis on new techniques and potential future research directions

Optimizing a global alignment of protein interaction networks

Motivation: The global alignment of protein interaction networks is a widely studied problem. It is an important first step in understanding the relationship between the proteins in different species and identifying functional orthologs. Furthermore, it can provide useful insights into the species’ evolution. Results: We propose a novel algorithm, PISwap, for optimizing global pairwise alignments of protein interaction networks, based on a local optimization heuristic that has previously demonstrated its effectiveness for a variety of other intractable problems. PISwap can begin with different types of network alignment approaches and then iteratively adjust the initial alignments by incorporating network topology information, trading it off for sequence information. In practice, our algorithm efficiently refines other well-studied alignment techniques with almost no additional time cost. We also show the robustness of the algorithm to noise in protein interaction data. In addition, the flexible nature of this algorithm makes it suitable for different applications of network alignment. This algorithm can yield interesting insights into the evolutionary dynamics of related species. Availability: Our software is freely available for non-commercial purposes from our Web site, http://piswap.csail.mit.edu/.National Institutes of Health (U.S.) (Grant GM081871

LIPIcs, Volume 248, ISAAC 2022, Complete Volume

LIPIcs, Volume 248, ISAAC 2022, Complete Volum