In this paper we propose the first experimental study of the fully dynamic single source shortest paths problem on directed graphs with positive real edge weights. In particular, we perform an experimental analysis of three different algorithms: Dijkstra's algorithm, and the two output bounded algorithms proposed by Ramalingam and Reps in [31] and by Frigioni, Marchetti-Spaccamela and Nanni in [18], respectively. The main goal of this paper is to provide a first experimental evidence for: (a) the effectiveness of dynamic algorithms for shortest paths with respect to a traditional static approach to this problem; (b) the validity of the theoretical model of output boundedness to analyze dynamic graph algorithms. Beside random generated graphs, useful to capture the "asymptotic" behavior of algorithms, we also develope experiments by considering a widely used graph from the real world, i.e., the Internet graph. Work partially supported by the ESPRIT Long Term Research Project...

In this paper, we propose to extend current practice in schema matching with the simultaneous use of top-K schema mappings rather than a single best mapping. This is a natural extension of existing methods (which can be considered to fall into the top-1 category), taking into account the imprecision inherent in the schema matching process. The essence of this method is the simultaneous generation and examination of K best schema mappings to identify useful mappings. The paper discusses efficient methods for generating top-K methods and propose a generic methodology for the simultaneous utilization of top-K mappings. We also propose a concrete heuristic that aims at improving precision at the cost of recall. We have tested the heuristic on real as well as synthetic data and anlyze the emricial results. The novelty of this paper lies in the robust extension of existing methods for schema matching, one that can gracefully accommodate less-than-perfect scenarios in which the exact mapping cannot be identified in a single iteration. Our proposal represents a step forward in achieving fully automated schema matching, which is currently semiautomated at best. 1

In molecular biology sequence alignment is a crucial tool in studying structure and function of molecules as well as evolution of species. In the segment-to-segment variation of the multiple alignment problem the input can be seen as a set of runs of non-gapped matches (diagonals) between pairs of sequences. Given a weight function that assigns a weight score to every possible diagonal, the goal is to choose a consistent set of diagonals of maximum weight. We show that the segment-to-segment multiple alignment problem is equivalent to a novel formulation of the Maximum Weight Trace (MWT) problem. Solving the generalized MWT (GMWT) problem to optimality therefore improves upon the previous greedy strategies that are used for solving the segment-to-segment multiple sequence alignment problem. We show that the GMWT can be stated in terms of an integer linear program and then solve the integer linear program using methods from polyhedral combinatorics. This leads to a branch-and...

Dominance constraints are logical descriptions of trees. E- cient algorithms for the subclass of normal dominance constraints were proposed recently. We present a new and simpler graph algorithm which solves more expressive weakly normal dominance constraints. We thereby improve on the best previously known algorithm for normal dominance constraints in eciency, coverage, and applicability.

We investigate the label number maximisation problem (lnm): Given a set of labels , each of which belongs to a point feature in the plane, the task is to nd a largest subset P of so that each 2 P labels the corresponding point feature and no two labels from P overlap. Our approach is based on two so-called constraint graphs which code horizontal and vertical positioning relations. The key idea is to link the two graphs by a set of additional constraints, thus characterising all feasible solutions of lnm. This enables us to formulate a zero-one integer linear program whose solution leads to an optimal labelling. We can express lnm in both the discrete and the slider labelling models. The slider models allow a continuous movement of a label around its point feature, leading to a signicantly higher number of labels that can be placed. To our knowledge, we present the rst algorithm that computes provably optimal solutions in the slider models. We nd it remarkable that our approach is independent of the labelling model and results in a discrete algorithm even if the problem is of continuous nature as in the slider models. Extensive experimental results on both real-world instances and point sets created by a widely used benchmark generator show that the new approach is applicable in practice. 1

We present the first experimental study of the fully dynamic single-source shortest paths problem in digraphs with arbitrary (negative and non-negative) arc weights. We implemented and tested several variants of the theoretically fastest fully dynamic algorithms proposed in the literature, plus a new algorithm devised to be as simple as possible while matching the best worst-case bounds for the problem. According to experiments performed on randomly generated test sets, all the considered dynamic algorithms are faster by several orders of magnitude than recomputing from scratch with the best static algorithm. The experiments also reveal that, although the simple dynamic algorithm we suggest is usually the fastest in practice, other dynamic algorithms proposed in the literature yield better results for specific kinds of test sets. 1

Many multiple alignment methods implicitly or explicitly try to minimize the amount of biological change implied by an alignment. At the level of sequences, biological change is measured along a phylogenetic tree, a structure frequently being predicted only after the multiple alignment instead of together with it. The Generalized Tree Alignment problem addresses both questions simultaneously. It can formally be viewed as a Steiner tree problem in sequence space and our approach merges a path heuristic for the construction of a Steiner tree with a clustering method as usually applied only to distance data. This combination is achieved using sequence graphs, a data structure for efficient representation of similar sequences. Although somewhat slower in practice than an earlier method by Hein (Mol. Biol. Evol., 6:649--668,1989) the current approach achieves significantly better results in terms of the underlying scoring function. Furthermore, a variant of the algorithm is intr...

Many geometric algorithms that are usually formulated for points and segments generalize easily to inputs also containing rays and lines. The sweep algorithm for segment intersection is a prototypical example. Implementations of such algorithms do, in general, not extend easily. For example,

ing with credit is permitted. To copy otherwise, to republish, to post on servers, to redistribute to lists, or to use any component of this work in other works, requires prior specific permission and/or a fee. Permissions may be requested from Publications Dept, ACM Inc., 1515 Broadway, New York, NY 10036 USA, fax +1 (212) 869-0481, or permissions@acm.org. 2 \Delta R. Iyer and D.R. Karger and H. S. Rahul and M. Thorup We present an experimental study of different variants of the amortized O(log 2 n)-time fullydynamic connectivity algorithm of Holm, de Lichtenberg, and Thorup (STOC'98). The experiments build upon experiments provided by Alberts, Cattaneo, and Italiano (SODA'96) on the randomized amortized O(log 3 n) fully-dynamic connectivity algorithm of Henzinger and King (STOC'95). Our experiments shed light upon similarities and differences between the two algorithms. We also present a slightly modified version of the Henzinger-King algorithm that runs in O(log 2 n) time, wh...

Introduction Geometric problems arise in many areas. Computer graphics, robotics, manufacturing, and geographic information systems are some examples. Often the same geometric subproblems are to be solved. Hence a library providing solutions for core problems in geometric computing has a wide range of applications and can be very useful. The success of LEDA [16], a library of efficient data types and algorithms, has shown that the existence of a library can make a tremendous difference for taking advanced techniques in data structures and algorithms from theory to practice. The field of computational geometry is now very close to a state where it can provide such a library of geometric algorithms. Over the past twenty years many algorithms for geometric problems have been developed by computational geometers. Many of these algorithms clearly have no direct impact for geometric computing in practice, because they are efficient compared to other solutions only for huge problem i