20756797
Algebraic specification of interconnection network relationships by permutation voltage graph mappings
Symmetries of large networks are used to simplify the specification of a guest-host network relationship. The relevant kinds of symmetries occur not only in Cayley graphs and in group-action graphs, but elsewhere as well. In brief, the critical topological symmetry property of a guest or host is that it is algebraically specifiable as a covering space of a smaller graph. A first objective is to understand the circumstances under which a mapping (a.k.a. “embedding”) between two base graphs can be lifted topologically to a mapping between their respective coverings. A suitable assignment of algebraic elements called “permutation voltages” to a base graph for the intended host network facilitates the construction not only of the intended host, but also of the intended guest and of the intended mapping of the guest into the host. Explicit formulas are derived for measurement of the load, of the congestion, and of the dilation of the lifted mapping. A concluding example suggests how these new formulas open the opportunity to develop optimization methods for algebraically specified guest-host mappings.
5242879
Interactive rind modeling
In this paper, we describe a technique, with roots in topological graph theory, that we call rind modeling. It provides for the easy creation of surfaces resembling peeled and punctured rinds. We show how the method's two main steps of: 1) creation of a shell or crust like the rind of an orange, and 2) opening holes in the crust by punching or peeling can be encapsulated into a real time semi-automatic interactive algorithm. We include a number of worked examples, some by students in a first modeling course, that demonstrate the ease with which a large variety of intricate rind shapes can be created.
16331940
Optimal Parallel Routing in Star Networks
Star networks have recently been proposed as attractive alternatives to the popular hypercube for interconnecting processors on a parallel computer. In this paper, we present an efficient algorithm that constructs an optimal parallel routing in star networks. Our result improves previous results for the problem.
2261180
Graph Ear Decompositions and Graph Embeddings
Ear decomposition of a graph has been extensively studied in relation to graph connectivity. In this paper, a connection of ear decomposition to graph embeddings is exhibited. It is shown that constructing a maximum-paired ear decomposition of a graph and constructing a maximum-genus embedding of the graph are polynomial-time equivalent. Applications of this connection are discussed.
1021255
A minimal and complete set of operators for the development of robust manifold mesh modelers
In this paper, we identify a minimal and complete set of fundamental operators, which is necessary and sufficient for performing all homeomorphic and topological operations on 2- manifold mesh structures. Efficient algorithms are developed for the implementation of these operators. We also developed a set of powerful, user-friendly, and effective operators at the level of user-interface. Using these operators, we have developed a prototype system for robust, interactive, and user-friendly modeling of orientable 2-manifold meshes. Users of our system can perform a large set of homeomorphic and topological changes with these user-interface level operators. Our system is topologically robust in the sense that users will never create invalid 2-manifold mesh structure with these operators. In our system, the homeomorphic and topological surgery operations can be applied alternatively on 2-manifold meshes. With our system, users can blend surfaces, construct rinds, and open holes on these rind shapes. With our system, the shapes that look like solid, non-manifold, or 2-manifold with boundary can be manipulated. The system also provides automatic texture mapping during topology changes.
31382426
Strong Fault-Tolerance: Parallel Routing in Networks with Faults
A d-regular network G is strongly fault-tolerant if for any copy Gf of G with at most d - 2 faulty nodes, every pair of nonfaulty nodes u and v in Gf admits min{df(u), df (v)} node-disjoint paths in Gf from u to v, where df(u) and df(v) are the degrees of the nodes u and v in Gf. We show that popular network structures, such as hypercube and star networks, are strongly fault-tolerant. We develop efficient algorithms that construct the maximum number of node-disjoint paths of optimal or nearly optimal length in these networks with faulty nodes. Our algorithms are optimal in terms of their running time.
1561831
Discovering reliable protein interactions from high-throughput experimental data using network topology
OBJECTIVE
Current protein-protein interaction (PPI) detection via high-throughput experimental methods, such as yeast-two-hybrid has been reported to be highly erroneous, leading to potentially costly spurious discoveries. This work introduces a novel measure called IRAP, i.e. "interaction reliability by alternative path", for assessing the reliability of protein interactions based on the underlying topology of the PPI network.


METHODS AND MATERIALS
A candidate PPI is considered to be reliable if it is involved in a closed loop in which the alternative path of interactions between the two interacting proteins is strong. We devise an algorithm called AlternativePathFinder to compute the IRAP value for each interaction in a complex PPI network. Validation of the IRAP as a measure for assessing the reliability of PPIs is performed with extensive experiments on yeast PPI data. All the data used in our experiments can be downloaded from our supplementary data web site at .


RESULTS
Results show consistently that IRAP measure is an effective way for discovering reliable PPIs in large datasets of error-prone experimentally-derived PPIs. Results also indicate that IRAP is better than IG2, and markedly better than the more simplistic IG1 measure.


CONCLUSION
Experimental results demonstrate that a global, system-wide approach-such as IRAP that considers the entire interaction network instead of merely local neighbors-is a much more promising approach for assessing the reliability of PPIs.
24126539
A Behavior-Based Classification and Retrieval Technique for Object-Oriented Specification Reuse
This paper presents a classification and retrieval technique for object-oriented specification reuse, based on the assumption that existing specifications exhibiting behaviors similar to that of the system under development are appropriate for reuse. Existing specifications are classified and retrieved according to the semantic networks abstracted from their behaviors. Since semantic networks attach semantic meanings to certain degrees of detail, our technique is rather precise. Primary behavior is used to classify specifications because it can be obtained in the early phases of system analysis. Therefore, our technique allows early reuse. Moreover, subspecifications and classes of existing specifications are classified independently so that they can be retrieved for reuse separately. Thus, our technique encourages reusing subspecifications as well as classes. Since a subspecification is composed of classes and their relationships, reusing it corresponds to reusing all those classes and relationships. A technique that reuses subspecifications as well as classes is thus expected to save more time than those that reuse only classes.
36905463
Quasi-threshold Graphs
Abstract Quasi-threshold graphs are defined recursively by the following rules: 1. (1) K1 is a quasi-threshold graph, 2. (2) adding a new vertex adjacent to all vertices of a quasi-threshold graph results in a quasi-threshold graph, 3. (3) the disjoint union of two quasi-threshold graphs is a quasi-threshold graph. This paper gives some new equivalent definitions of a quasi-threshold graph. From them, linear time recognition algorithms follow. We also give linear time algorithms for the edge domination problem and the bandwidth problem in this class of graphs.
2647804
Extended DBP for (m, k)-Firm Based QoS
In this paper, an extended DBP (E_DBP) scheme is studied for (m,k)-firm constraint. The basic idea of the proposed algorithm takes into account the distance to exit a failure state, which is a symmetrical notion of distance to fall into a failure state in DBP. Quality of Service (QoS) in terms of dynamic failure and delay is evaluated. Simulation results reveal the effectiveness of E_DBP to provide better QoS.
8882088
Design of Nearest Neighbor Classifiers Using an Intelligent Multi-objective Evolutionary Algorithm
The goal of designing optimal nearest neighbor classifiers is to maximize classification accuracy while minimizing the sizes of both reference and feature sets. A usual way is to adaptively weight the three objectives as an objective function and then use a single-objective optimization method for achieving this goal. This paper proposes a multi-objective approach to cope with the weight tuning problem for practitioners. A novel intelligent multi-objective evolutionary algorithm IMOEA is utilized to simultaneously edit compact reference and feature sets for nearest neighbor classification. Two comparison studies are designed to evaluate performance of the proposed approach. It is shown empirically that the IMOEA-designed classifiers have high classification accuracy and small sizes of reference and feature sets. Moreover, IMOEA can provide a set of good solutions for practitioners to choose from in a single run. The simulation results indicate that the IMOEA-based approach is an expedient method to design nearest neighbor classifiers, compared with an existing single- objective approach.