5864946
Linear-Time Algorithms for Partial \boldmathk -Tree Complements
Abstract. It is known that a graph decision problem can be solved in linear time over partial k -trees if the problem can be defined in Monadic Second-order (or MS) logic. MS logic allows quantification of vertex and edge subsets, with respect to which logical sentences can encode many different conditions that an input graph must satisfy. It is not always clear, however, which graph problems can be expressed in such a way. In this paper we consider problems stated as logical conditions on subsets of the vertices and nonedges of the input graph. If such a problem can be defined in MS logic (i.e., in terms of the vertices and edges of the input graph), then there is a linear-time algorithm to solve the problem over partial k -trees. This algorithm also provides a solution to some problem over the graph-theoretic complements of partial k -trees. We study several examples of these ``complement-problems.'' We introduce a variation of MS logic in which, if a graph-problem can be defined over the class of partial k -tree complements, then there is a linear-time algorithm to solve that problem over partial k -tree complements, and (equivalently) a linear-time algorithm to solve its complement-problem over partial k -trees.
204999323
Acyclic Directed Hypercubes may have Exponential Diameter
Abstract The diameter of a directed graph is the maximum of the lengths of the shortest paths between all pairs of vertices (if such paths exist). We prove that for every n , the edges of the n -dimensional hypercube can be acyclically oriented such that the diameter of the cube is F n + 1 , the ( n + 1)st Fibonacci number.
2367227
Parallel Algorithms For Vehicle Routing Problems
Vehicle routing problems involve the navigation of one or more vehicles through a network of locations. Locations have associated handling times as well as time windows during which they are active. The arcs connecting locations have time costs associated with them. In this paper, we consider two different problems in single vehicle routing. The first is to find least time cost routes between all pairs of nodes in a network for navigating vehicles; we call this the all pairs routing problem. We show that there is an O(log3 n) time parallel algorithm using a polynomial number of processors for this problem on a CREW PRAM. We next consider the problem in which a vehicle services all locations in a network. Here, locations can be passed through at any time but only serviced during their time window. The general problem is -complete under even fairly stringent restrictions but polynomial algorithms have been developed for some special cases. In particular, when the network is a line, there is no time cost in servicing a location, and all time windows are unbounded at either their lower or upper end, O(n2) algorithms have been developed. We show that under the same conditions, we can reduce this problem to the all pairs routing problem and therefore obtain an O(log3 n) time parallel algorithm on a CREW PRAM.
209133
Computing planar intertwines
The proof of Wagner's conjecture by N. Robertson and P. Seymour gives a finite description of any family of graphs which is closed under the minor ordering, called the obstructions of the family. Since the intersection and the union of two minor closed graph families are again a minor closed graph family, an interesting question is that of computing the obstructions of the new family given the obstructions for the original two families. It is easy to compute the obstructions of the intersection, but, until very recently, it was an open problem to compute the obstructions of the union. It is shown that if the original families are planar, then the obstructions of the union are no larger than n to the O(n/sup 2/) power, where n is the size of the largest obstruction of the original family.<<ETX>>
17058061
Sequential and Parallel Algorithms for Embedding Problems on Classes of Partial k-Trees
We present sequential and parallel algorithms for various embedding problems on bounded degree partial k-trees and k-connected partial k-trees; these include subgraph isomorphism and topological embedding, known to be NP-complete for general partial k-trees. As well as contributing to our understanding of the types of graphs for which these problems are tractable, this paper introduces methods for solving problems on graphs. In particular, we make use of the tree-decomposition of the graph to apply techniques used to solve problems on trees to solve problems on partial k-trees.
38885821
Embeddings of k-Connected Graphs of Pathwidth k
We present O(n3) embedding algorithms (generalizing subgraph isomorphism) for classes of graphs of bounded pathwidth, where n is the number of vertices in the graph. These include the first polynomialtime algorithm for minor containment and the first O(nc) algorithm (c a constant independent of k) for topological embedding of graphs from subclasses of partial k-trees. Of independent interest are structural properties of k-connected graphs of bounded pathwidth on which our algorithms are based. We also describe special cases which reduce to various generalizations of string matching, permitting more efficient solutions.
35215015
Coarse Grain Preconditioned Conjugate Gradient Solver for Large Sparse Systems
We explore a coarse grain parallel algorithm for the solution of large sparse linear systems with symmetric positive definite matrix, based on a preconditioned conjugate gradient method.
14760800
Deciding Separation Logic Formulae by SAT and Incremental Negative Cycle Elimination
Separation logic is a subset of the quantifier-free first order logic. It has been successfully used in the automated verification of systems that have large (or unbounded) integer-valued state variables, such as pipelined processor designs and timed systems. In this paper, we present a fast decision procedure for separation logic, which combines Boolean satisfiability (SAT) with a graph based incremental negative cycle elimination algorithm. Our solver abstracts a separation logic formula into a Boolean formula by replacing each predicate with a Boolean variable. Transitivity constraints over predicates are detected from the constraint graph and added on a need-to basis. Our solver handles Boolean and theory conflicts uniformly at the Boolean level. The graph based algorithm supports not only incremental theory propagation, but also constant time theory backtracking without using a cumbersome history stack. Experimental results on a large set of benchmarks show that our new decision procedure is scalable, and outperforms existing techniques for this logic.
25659803
BIRN-M: a semantic mediator for solving real-world neuroscience problems
A goal of the Biomedical Informatics Research Network (birn) project is to develop a multi-institution information management system for Neurosciences to gain a deeper understanding of several neurological disorders. Each institution specializes in a different subdiscipline and produces a database of its experimental or computationally derived data; a mediator module performs semantic integration over the databases to enable neuroscientists to perform analyses that could not be done from any single institution’s data. The overall system architecture of the birn system is that of a wrapper-mediator system. The information sources are various relational sources including Oracle 9i having userdefined packages, Oracle 8i with the Spatial Data Cartridge, and databases made available over the web. Sources also include computational resources that need to be “run” to produce data. A source can be either accessed directly by the mediator, or through a middleware called the Storage Resource Broker (SRB) to shield the mediator from keeping low-level information like data location and user authentication information, and from large object handling. Wrappers handle source registration, schema mapping, and translation from the mediator’s logic queries to the corresponding sql or web request. birn-m also admits knowledge sources, which host ontologies and domain-specific general knowledge in the form of logic rules. birn-m maintains a registry with semantic schemas from all sources, integrated views defined in a GAV fashion, and source query capabilities as binding patterns and special predicates or functions admissible by it. The registry also records the types of data a client can handle, and has an API for interactive custom-built clients.
9848793
Stochastic Steiner Trees Without a Root
This paper considers the Steiner tree problem in the model of two-stage stochastic optimization with recourse. This model, the focus of much recent research [11, 16, 8, 18], tries to capture the fact that many infrastructure planning problems have to be solved in the presence of uncertainty, and that we have make decisions knowing merely market forecasts (and not the precise set of demands); by the time the actual demands arrive, the costs may be higher due to inflation. 
 
In the context of the Stochastic Steiner Tree problem on a graph G = (V,E), the model can be paraphrased thus: on Monday, we are given a probability distribution π on subsets of vertices, and can build some subset EM of edges. On Tuesday, a set of terminals D materializes (drawn from the same distribution π). We now have to buy edges ET so that the set EM ∪ ET forms a Steiner tree on D. The goal is to minimize the expected cost of the solution. 
 
We give the first constant-factor approximation algorithm for this problem. To the best of our knowledge, this is the first O(1)-approximation for the stochastic version of a non sub-additive problem. In fact, algorithms for the unrooted stochastic Steiner tree problem we consider are powerful enough to solve the Multicommodity Rent-or-Buy problem, itself a topic of recent interest [3, 7, 15].
6701327
Towards a federated neuroscientific knowledge management system using brain atlases
Abstract The topic of federated databases has received much attention within the domain of neuroinformatics and is widely perceived as the eventual solution to the problems inherent in building truly interoperable informatics systems. We describe a feasibility study of a methodology strategy for building federated informatics systems with a specific example from informatics approaches involving the neuroscientific literature. We examine the logistical issues concerning linking two database systems (CoCoMac and NeuroScholar) via a method based on the use of transformations between neuroanatomical parcellations (Stephan et al., Phil. Trans. R. Soc. London B 335 (2000) 37–54).