Hierarchical graphs for rule-based modeling of biochemical systems

<p>Abstract</p> <p>Background</p> <p>In rule-based modeling, graphs are used to represent molecules: a colored vertex represents a component of a molecule, a vertex attribute represents the internal state of a component, and an edge represents a bond between components. Components of a molecule share the same color. Furthermore, graph-rewriting rules are used to represent molecular interactions. A rule that specifies addition (removal) of an edge represents a class of association (dissociation) reactions, and a rule that specifies a change of a vertex attribute represents a class of reactions that affect the internal state of a molecular component. A set of rules comprises an executable model that can be used to determine, through various means, the system-level dynamics of molecular interactions in a biochemical system.</p> <p>Results</p> <p>For purposes of model annotation, we propose the use of hierarchical graphs to represent structural relationships among components and subcomponents of molecules. We illustrate how hierarchical graphs can be used to naturally document the structural organization of the functional components and subcomponents of two proteins: the protein tyrosine kinase Lck and the T cell receptor (TCR) complex. We also show that computational methods developed for regular graphs can be applied to hierarchical graphs. In particular, we describe a generalization of Nauty, a graph isomorphism and canonical labeling algorithm. The generalized version of the Nauty procedure, which we call HNauty, can be used to assign canonical labels to hierarchical graphs or more generally to graphs with multiple edge types. The difference between the Nauty and HNauty procedures is minor, but for completeness, we provide an explanation of the entire HNauty algorithm.</p> <p>Conclusions</p> <p>Hierarchical graphs provide more intuitive formal representations of proteins and other structured molecules with multiple functional components than do the regular graphs of current languages for specifying rule-based models, such as the BioNetGen language (BNGL). Thus, the proposed use of hierarchical graphs should promote clarity and better understanding of rule-based models.</p

Thick 2D Relations for Document Understanding

We use a propositional language of qualitative rectangle relations to detect the reading order from document images. To this end, we define the notion of a document encoding rule and we analyze possible formalisms to express document encoding rules such as LATEX and SGML. Document encoding rules expressed in the propositional language of rectangles are used to build a reading order detector for document images. In order to achieve robustness and avoid brittleness when applying the system to real life document images, the notion of a thick boundary interpretation for a qualitative relation is introduced. The framework is tested on a collection of heterogeneous document images showing recall rates up to 89%

Intelligent multimedia indexing and retrieval through multi-source information extraction and merging

This paper reports work on automated meta-data\ud creation for multimedia content. The approach results\ud in the generation of a conceptual index of\ud the content which may then be searched via semantic\ud categories instead of keywords. The novelty\ud of the work is to exploit multiple sources of\ud information relating to video content (in this case\ud the rich range of sources covering important sports\ud events). News, commentaries and web reports covering\ud international football games in multiple languages\ud and multiple modalities is analysed and the\ud resultant data merged. This merging process leads\ud to increased accuracy relative to individual sources

Efficient Analysis of Complex Diagrams using Constraint-Based Parsing

This paper describes substantial advances in the analysis (parsing) of diagrams using constraint grammars. The addition of set types to the grammar and spatial indexing of the data make it possible to efficiently parse real diagrams of substantial complexity. The system is probably the first to demonstrate efficient diagram parsing using grammars that easily be retargeted to other domains. The work assumes that the diagrams are available as a flat collection of graphics primitives: lines, polygons, circles, Bezier curves and text. This is appropriate for future electronic documents or for vectorized diagrams converted from scanned images. The classes of diagrams that we have analyzed include x,y data graphs and genetic diagrams drawn from the biological literature, as well as finite state automata diagrams (states and arcs). As an example, parsing a four-part data graph composed of 133 primitives required 35 sec using Macintosh Common Lisp on a Macintosh Quadra 700.Comment: 9 pages, Postscript, no fonts, compressed, uuencoded. Composed in MSWord 5.1a for the Mac. To appear in ICDAR '95. Other versions at ftp://ftp.ccs.neu.edu/pub/people/futrell

Named Entity Extraction and Disambiguation: The Reinforcement Effect.

Named entity extraction and disambiguation have received much attention in recent years. Typical fields addressing these topics are information retrieval, natural language processing, and semantic web. Although these topics are highly dependent, almost no existing works examine this dependency. It is the aim of this paper to examine the dependency and show how one affects the other, and vice versa. We conducted experiments with a set of descriptions of holiday homes with the aim to extract and disambiguate toponyms as a representative example of named entities. We experimented with three approaches for disambiguation with the purpose to infer the country of the holiday home. We examined how the effectiveness of extraction influences the effectiveness of disambiguation, and reciprocally, how filtering out ambiguous names (an activity that depends on the disambiguation process) improves the effectiveness of extraction. Since this, in turn, may improve the effectiveness of disambiguation again, it shows that extraction and disambiguation may reinforce each other.\u

The REVERE project:Experiments with the application of probabilistic NLP to systems engineering

Despite natural language’s well-documented shortcomings as a medium for precise technical description, its use in software-intensive systems engineering remains inescapable. This poses many problems for engineers who must derive problem understanding and synthesise precise solution descriptions from free text. This is true both for the largely unstructured textual descriptions from which system requirements are derived, and for more formal documents, such as standards, which impose requirements on system development processes. This paper describes experiments that we have carried out in the REVERE1 project to investigate the use of probabilistic natural language processing techniques to provide systems engineering support

Tracking Report 2011 Adidas Group, Philippines 430259239J

This document is part of a digital collection provided by the Martin P. Catherwood Library, ILR School, Cornell University, pertaining to the effects of globalization on the workplace worldwide. Special emphasis is placed on labor rights, working conditions, labor market changes, and union organizing.FLA_2011_AdidasGroup_TR_Philippines_430259239J.pdf: 86 downloads, before Oct. 1, 2020

Version Control in Online Software Repositories

Software version control repositories provide a uniform and stable interface to manage documents and their version histories. Unfortunately, Open Source systems, for example, CVS, Subversion, and GNU Arch are not well suited to highly collaborative environments and fail to track semantic changes in repositories. We introduce document provenance as our Description Logic framework to track the semantic changes in software repositories and draw interesting results about their historic behaviour using a rule-based inference engine. To support the use of this framework, we have developed our own online collaborative tool, leveraging the fluency of the modern WikiWikiWeb

PHP/HTML design and build of a computer adaptive test to assess English fluency among native Spanish speakers

textThe following is a review of key findings from the implementation of a PHP/HTML web-based application to assess English fluency among native Spanish speakers. The scope of this professional report includes mainly the design, build, and implementation of a web based system accessible through www.babelous.com. This written portion is intended to briefly summarize initial results from the implementation of the successfully built application, provide information on how to replicate the application, and detail areas of focus for future development.Public AffairsBusiness Administratio