17445618
A Formal Definition of Hierarchical Predicate Transition Nets
Hierarchical predicate transition nets have recently been introduced as a visual formalism for specifying complex reactive systems. They extend predicate transition nets with hierarchical structures so that large systems can be specified and understood stepwisely, and thus are more suitable for real-world applications. In this paper, we provide a formal syntax and an algebraic semantics for hierarchical predicate transition nets, which establish the theory of hierarchical predicate transition nets for precise specification and formal reasoning.
28965788
A useful approach to developing reverse engineering metrics
If software metrics are useful in a forward software engineering environment, they are vital in a reverse engineering environment. We are endeavouring to discover approaches to developing reverse engineering metrics for software engineers who need them for reverse engineering legacy systems. The major contribution of the paper is the presentation of a systematic research base and a hierarchical approach to the development of software metrics for reverse engineering. Measurement is fundamental to the software engineering discipline as a whole. A software metric is a quantitative measure of the degree to which a system, component, or process possesses a given attribute (N.E. Fenton and S.L. Pfleeger, 1996). Software reverse engineering is the process of analysing a subject system to: identify the system's components and their interrelationships; and create representations of the system at a higher level of abstraction (E.J. Chikofsky and J.H. Cross II, 1990). The goal of developing reverse engineering metrics is to identify measures that are needed for assessing the status of reverse engineering projects, products, processes and resources, and helping engineers to understand both what is happening and what will happen during reverse engineering procedures. Consequently, these concrete reverse engineering measures make more visible to us aspects of process and product in reverse engineering, in particular, the product of specifications and the process of abstractions and transformations. This makes it possible to control reverse engineering projects. Aspects of measurement in reverse engineering are outlined.
28830107
Introducing software architecture specification and analysis in SAM through an example
Abstract Software architecture study has become one of the most active research areas in software engineering in the recent years. Although there have been many published results on specification and analysis method of software architectures, information on sound systematic methodology for modeling and analyzing software architectures is lacking. In this article, we present a formal systematic software architecture specification and analysis methodology called SAM and show how to apply SAM to specify a command control (C2) system and to analyze its real-time constraints.
20141160
A method for analyzing properties of hierarchical predicate transition nets
Hierarchical high level Petri nets have been proposed in recent years as a powerful formal method for modeling large concurrent and distributed systems but they are even more difficult to analyze than flat high level Petri nets, which are also lacking effective analysis methods themselves. A method for analyzing properties of hierarchical predicate transition Petri nets is proposed. The method employs two temporal induction techniques, one for safety properties and the other for liveness properties, without using temporal logic formalism. Within each induction technique, a hybrid reasoning technique combining net structural and behavioral reasoning, and ordinary first order logic reasoning is used.
14218377
A Methodology for Constructing Predicate Transition Net Specifications
In this paper, a methodology for constructing hierarchical and structured predicate transition net specifications is developed, which includes new systematic notation extensions for supporting various transformation techniques upon predicate transition nets and several rules for applying such transformation techniques. The levelling technique in data-flow diagrams is adapted in the refinement and the abstraction techniques, and the state decomposition idea in state-charts is employed in designing various label formulation operators. The methodology is illustrated through the specification of a lift system. The methodology can significantly reduce the constructing complexity and enhance the comprehensibility of large predicate transition net specifications.
12973064
Integrating predicate transition nets with first order temporal logic in the specification and verification of concurrent systems
This paper presents some results of integrating predicate transition nets with first order temporal logic in the specification and verification of concurrent systems. The intention of this research is to use predicate transition nets as a specification method and to use first order temporal logic as a verification method so that their strengths — the easy comprehension of predicate transition nets and the reasoning power of first order temporal logic can be combined. In this paper, a theoretical relationship between the computation models of these two formalisms is presented; an algorithm for systematically translating a predicate transition net into a corresponding temporal logic system is outlined; and a special temporal refutation proof technique is proposed and illustrated in verifying various concurrent properties of the predicate transition net specification of the five dining philosophers problem.
18826487
On Even Triangulations of 2-Connected Embedded Graphs
Recently, Hoffmann and Kriegel proved an important combinatorial theorem [4]: Every 2-connected bipartite plane graph G has a triangulation in which all vertices have even degree (it's called an even triangulation). Combined with a classical Whitney's Theorem, this result implies that every such a graph has a 3-colorable plane triangulation. Using this theorem, Hoffmann and Kriegel significantly improved the upper bounds of several art gallery and prison guard problems. In [7], Zhang and He presented a linear time algorithm which relies on the complicated algebraic proof in [4]. This proof cannot be extended to similar graphs embedded on high genus surfaces. It's not known whether Hoffmann and Kriegel's Theorem is true for such graphs. 
 
In this paper, we describe a totally independent and much simpler proof of the above theorem, using only graph-theoretic arguments. Our new proof can be easily extend to show the existence of even triangulations for similar graphs on high genus surfaces. Hence we show that Hoffmann and Kriegel's theorem remains valid for such graphs. Our new proof leads to a very simple linear time algorithm for finding even triangulations.
1711864
Automatically Generating Gene Summaries from Biomedical Literature
Biologists often need to find information about genes whose function is not described in the genome databases. Currently they must try to search disparate biomedical literature to locate relevant articles, and spend considerable efforts reading the retrieved articles in order to locate the most relevant knowledge about the gene. We describe our software, the first that automatically generates gene summaries from biomedical literature. We present a two-stage summarization method, which involves first retrieving relevant articles and then extracting the most informative sentences from the retrieved articles to generate a structured gene summary. The generated summary explicitly covers multiple aspects of a gene, such as the sequence information, mutant phenotypes, and molecular interaction with other genes. We propose several heuristic approaches to improve the accuracy in both stages. The proposed methods are evaluated using 10 randomly chosen genes from FlyBase and a subset of Medline abstracts about Drosophila. The results show that the precision of the top selected sentences in the 6 aspects is typically about 50-70%, and the generated summaries are quite informative, indicating that our approaches are effective in automatically summarizing literature information about genes. The generated summaries not only are directly useful to biologists but also serve as useful entry points to enable them to quickly digest the retrieved literature articles.
11889495
On Even Triangulations of 2-Connected Embedded Graphs
Recently, Hoffmann and Kriegel proved an important combinatorial theorem [SIAM J. Discrete Math., 9 (1996), pp. 210--224]: Every 2-connected bipartite plane multigraph G without 2-cycle faces has a triangulation in which all vertices have even degree (this is called an even triangulation). Combined with the classical Whitney's theorem, this result implies that every such graph has a 3-colorable plane triangulation. Using this theorem, Hoffmann and Kriegel significantly improved the upper bounds of several art gallery and prison guard problems. A complicated O(n2) time algorithm was obtained in [SIAM J. Discrete Math., 9 (1996), pp. 210--224] for constructing an even triangulation of G. Hoffmann and Kriegel conjectured that there is an O(n3/2) time algorithm for solving this problem. 
In this paper, we develop a simple proof of the above theorem. Our proof reveals and relies on a natural correspondence between even triangulations of G and certain orientations of G. Based on this new proof, we obtain a very simple O(n) time algorithm for finding an even triangulation of G. We also extend our proof to show the existence of even triangulations for similar graphs on high genus surface.
206769424
Neighborhood preserving embedding
Recently there has been a lot of interest in geometrically motivated approaches to data analysis in high dimensional spaces. We consider the case where data is drawn from sampling a probability distribution that has support on or near a submanifold of Euclidean space. In this paper, we propose a novel subspace learning algorithm called neighborhood preserving embedding (NPE). Different from principal component analysis (PCA) which aims at preserving the global Euclidean structure, NPE aims at preserving the local neighborhood structure on the data manifold. Therefore, NPE is less sensitive to outliers than PCA. Also, comparing to the recently proposed manifold learning algorithms such as Isomap and locally linear embedding, NPE is defined everywhere, rather than only on the training data points. Furthermore, NPE may be conducted in the original space or in the reproducing kernel Hilbert space into which data points are mapped. This gives rise to kernel NPE. Several experiments on face database demonstrate the effectiveness of our algorithm
14477095
Learning and Incorporating Top-Down Cues in Image Segmentation
Bottom-up approaches, which rely mainly on continuity principles, are often insufficient to form accurate segments in natural images. In order to improve performance, recent methods have begun to incorporate top-down cues, or object information, into segmentation. In this paper, we propose an approach to utilizing category-based information in segmentation, through a formulation as an image labelling problem. Our approach exploits bottom-up image cues to create an over-segmented representation of an image. The segments are then merged by assigning labels that correspond to the object category. The model is trained on a database of images, and is designed to be modular: it learns a number of image contexts, which simplify training and extend the range of object classes and image database size that the system can handle. The learning method estimates model parameters by maximizing a lower bound of the data likelihood. We examine performance on three real-world image databases, and compare our system to a standard classifier and other conditional random field approaches, as well as a bottom-up segmentation method.