Scholarly publishing and argument in hyperspace

The World Wide Web is opening up access to documents and data for scholars. However it has not yet impacted on one of the primary activities in research: assessing new findings in the light of current knowledge and debating it with colleagues. The ClaiMaker system uses a directed graph model with similarities to hypertext, in which new ideas are published as nodes, which other contributors can build on or challenge in a variety of ways by linking to them. Nodes and links have semantic structure to facilitate the provision of specialist services for interrogating and visualizing the emerging network. By way of example, this paper is grounded in a ClaiMaker model to illustrate how new claims can be described in this structured way.

Software Testing and Documenting Automation

This article describes some approaches to problem of testing and documenting automation in information systems with graphical user interface. Combination of data mining methods and theory of finite state machines is used for testing automation. Automated creation of software documentation is based on using metadata in documented system. Metadata is built on graph model. Described approaches improve performance and quality of testing and documenting processes.

About Methods of Mathematical Modelling in the Development of Information Systems

This article describes the approach, which allows to develop information systems without taking into consideration details of physical storage of the relational model and type database management system. Described in terms of graph model, this approach allows to construct several algorithms, for example, for verification application domain. This theory was introduced into operation testing as a part of CASE-system METAS.

Access Rights Inheritance in Information Systems Controlled by Metadata

All information systems have to be protected. As the number of information objects and the number of users increase the task of information system’s protection becomes more difficult. One of the most difficult problems is access rights assignment. This paper describes the graph model of access rights inheritance. This model takes into account relations and dependences between different objects and between different users. The model can be implemented in the information systems controlled by the metadata, describing information objects and connections between them, such as the systems based on CASE-technology METAS.

Learning Technology in Scheduling Based on the Mixed Graphs

We propose the adaptive algorithm for solving a set of similar scheduling problems using learning technology. It is devised to combine the merits of an exact algorithm based on the mixed graph model and heuristics oriented on the real-world scheduling problems. The former may ensure high quality of the solution by means of an implicit exhausting enumeration of the feasible schedules. The latter may be developed for certain type of problems using their peculiarities. The main idea of the learning technology is to produce effective (in performance measure) and efficient (in computational time) heuristics by adapting local decisions for the scheduling problems under consideration. Adaptation is realized at the stage of learning while solving a set of sample scheduling problems using a branch-and-bound algorithm and structuring knowledge using pattern recognition apparatus.

Design, development and control of a new generation high performance linear actuator for parallel robots and other applications

The main focus of this research is to design and develop a high performance linear actuator based on a four bar mechanism. The present work includes the detailed analysis (kinematics and dynamics), design, implementation and experimental validation of the newly designed actuator. High performance is characterized by the acceleration of the actuator end effector. The principle of the newly designed actuator is to network the four bar rhombus configuration (where some bars are extended to form an X shape) to attain high acceleration. Firstly, a detailed kinematic analysis of the actuator is presented and kinematic performance is evaluated through MATLAB simulations. A dynamic equation of the actuator is achieved by using the Lagrangian dynamic formulation. A SIMULINK control model of the actuator is developed using the dynamic equation. In addition, Bond Graph methodology is presented for the dynamic simulation. The Bond Graph model comprises individual component modeling of the actuator along with control. Required torque was simulated using the Bond Graph model. Results indicate that, high acceleration (around 20g) can be achieved with modest (3 N-m or less) torque input. A practical prototype of the actuator is designed using SOLIDWORKS and then produced to verify the proof of concept. The design goal was to achieve the peak acceleration of more than 10g at the middle point of the travel length, when the end effector travels the stroke length (around 1 m). The actuator is primarily designed to operate in standalone condition and later to use it in the 3RPR parallel robot. A DC motor is used to operate the actuator. A quadrature encoder is attached with the DC motor to control the end effector. The associated control scheme of the actuator is analyzed and integrated with the physical prototype. From standalone experimentation of the actuator, around 17g acceleration was achieved by the end effector (stroke length was 0.2m to 0.78m). Results indicate that the developed dynamic model results are in good agreement. Finally, a Design of Experiment (DOE) based statistical approach is also introduced to identify the parametric combination that yields the greatest performance. Data are collected by using the Bond Graph model. This approach is helpful in designing the actuator without much complexity.

Petri Net Siphon Analysis and Network Centrality Measures for Identifying Combination Therapies in Signaling Pathways

Aberrant behavior of biological signaling pathways has been implicated in diseases such as cancers. Therapies have been developed to target proteins in these networks in the hope of curing the illness or bringing about remission. However, identifying targets for drug inhibition that exhibit good therapeutic index has proven to be challenging since signaling pathways have a large number of components and many interconnections such as feedback, crosstalk, and divergence. Unfortunately, some characteristics of these pathways such as redundancy, feedback, and drug resistance reduce the efficacy of single drug target therapy and necessitate the employment of more than one drug to target multiple nodes in the system. However, choosing multiple targets with high therapeutic index poses more challenges since the combinatorial search space could be huge. To cope with the complexity of these systems, computational tools such as ordinary differential equations have been used to successfully model some of these pathways. Regrettably, for building these models, experimentally-measured initial concentrations of the components and rates of reactions are needed which are difficult to obtain, and in very large networks, they may not be available at the moment. Fortunately, there exist other modeling tools, though not as powerful as ordinary differential equations, which do not need the rates and initial conditions to model signaling pathways. Petri net and graph theory are among these tools. In this thesis, we introduce a methodology based on Petri net siphon analysis and graph network centrality measures for identifying prospective targets for single and multiple drug therapies. In this methodology, first, potential targets are identified in the Petri net model of a signaling pathway using siphon analysis. Then, the graph-theoretic centrality measures are employed to prioritize the candidate targets. Also, an algorithm is developed to check whether the candidate targets are able to disable the intended outputs in the graph model of the system or not. We implement structural and dynamical models of ErbB1-Ras-MAPK pathways and use them to assess and evaluate this methodology. The identified drug-targets, single and multiple, correspond to clinically relevant drugs. Overall, the results suggest that this methodology, using siphons and centrality measures, shows promise in identifying and ranking drugs. Since this methodology only uses the structural information of the signaling pathways and does not need initial conditions and dynamical rates, it can be utilized in larger networks.

An enforced cooperation : understanding scientific assessments in adversarial polities through Quebec shale gas policymaking, 2010-2014

Les biotechnologies, le réchauffement climatique, les ressources naturelles et la gestion des écosystèmes sont tous représentatifs de la “nouvelle politique de la nature” (Hajer 2003), un terme englobant les enjeux marqués par une grande incertitude scientifique et un encadrement réglementaire inadapté aux nouvelles réalités, suscitant de fait un conflit politique hors du commun. Dans l'espoir de diminuer ces tensions et de générer un savoir consensuel, de nombreux gouvernements se tournent vers des institutions scientifiques ad hoc pour documenter l'élaboration des politiques et répondre aux préoccupations des partie-prenantes. Mais ces évaluations scientifiques permettent-elles réellement de créer une compréhension commune partagée par ces acteurs politiques polarisés? Alors que l'on pourrait croire que celles-ci génèrent un climat d'apprentissage collectif rassembleur, un environnement politique conflictuel rend l'apprentissage entre opposant extrêmement improbable. Ainsi, cette recherche documente le potentiel conciliateur des évaluation scientifique en utilisant le cas des gaz de schiste québécois (2010-2014). Ce faisant, elle mobilise la littérature sur les dimensions politiques du savoir et de la science afin de conceptualiser le rôle des évaluations scientifiques au sein d'une théorie de la médiation scientifique (scientific brokerage). Une analyse de réseau (SNA) des 5751 références contenues dans les documents déposés par 268 organisations participant aux consultations publiques de 2010 et 2014 constitue le corps de la démonstration empirique. Précisément, il y est démontré comment un médiateur scientifique peut rediriger le flux d'information afin de contrer l'incompatibilité entre apprentissage collectif et conflit politique. L'argument mobilise les mécanismes cognitifs traditionnellement présents dans la théorie des médiateurs de politique (policy broker), mais introduit aussi les jeux de pouvoir fondamentaux à la circulation de la connaissance entre acteurs politiques.

An enforced cooperation : understanding scientific assessments in adversarial polities through Quebec shale gas policymaking, 2010-2014

Les biotechnologies, le réchauffement climatique, les ressources naturelles et la gestion des écosystèmes sont tous représentatifs de la “nouvelle politique de la nature” (Hajer 2003), un terme englobant les enjeux marqués par une grande incertitude scientifique et un encadrement réglementaire inadapté aux nouvelles réalités, suscitant de fait un conflit politique hors du commun. Dans l'espoir de diminuer ces tensions et de générer un savoir consensuel, de nombreux gouvernements se tournent vers des institutions scientifiques ad hoc pour documenter l'élaboration des politiques et répondre aux préoccupations des partie-prenantes. Mais ces évaluations scientifiques permettent-elles réellement de créer une compréhension commune partagée par ces acteurs politiques polarisés? Alors que l'on pourrait croire que celles-ci génèrent un climat d'apprentissage collectif rassembleur, un environnement politique conflictuel rend l'apprentissage entre opposant extrêmement improbable. Ainsi, cette recherche documente le potentiel conciliateur des évaluation scientifique en utilisant le cas des gaz de schiste québécois (2010-2014). Ce faisant, elle mobilise la littérature sur les dimensions politiques du savoir et de la science afin de conceptualiser le rôle des évaluations scientifiques au sein d'une théorie de la médiation scientifique (scientific brokerage). Une analyse de réseau (SNA) des 5751 références contenues dans les documents déposés par 268 organisations participant aux consultations publiques de 2010 et 2014 constitue le corps de la démonstration empirique. Précisément, il y est démontré comment un médiateur scientifique peut rediriger le flux d'information afin de contrer l'incompatibilité entre apprentissage collectif et conflit politique. L'argument mobilise les mécanismes cognitifs traditionnellement présents dans la théorie des médiateurs de politique (policy broker), mais introduit aussi les jeux de pouvoir fondamentaux à la circulation de la connaissance entre acteurs politiques.

An integer programming model for the minimum interval graph completion problem

The minimum interval graph completion problem consists of, given a graph G = ( V, E ), finding a supergraph H = ( V, E ∪ F ) that is an interval graph, while adding the least number of edges |F| . We present an integer programming formulation for solving the minimum interval graph completion problem recurring to a characteri- zation of interval graphs that produces a linear ordering of the maximal cliques of the solution graph.

Software evolution: a graph based model

A model based on graph isomorphisms is used to formalize software evolution. Step by step we narrow the search space by an informed selection of the attributes based on the current state-of-the-art in software engineering and generate a seed solution. We then traverse the resulting space using graph isomorphisms and other set operations over the vertex sets. The new solutions will preserve the desired attributes. The goal of defining an isomorphism based search mechanism is to construct predictors of evolution that can facilitate the automation of ’software factory’ paradigm. The model allows for automation via software tools implementing the concepts.

Software evolution: a graph based model

A model based on graph isomorphisms is used to formalize software evolution. Step by step we narrow the search space by an informed selection of the attributes based on the current state-of-the-art in software engineering and generate a seed solution. We then traverse the resulting space using graph isomorphisms and other set operations over the vertex sets. The new solutions will preserve the desired attributes. The goal of defining an isomorphism based search mechanism is to construct predictors of evolution that can facilitate the automation of ’software factory’ paradigm. The model allows for automation via software tools implementing the concepts.

Connections between the Sznajd model with general confidence rules and graph theory

The Sznajd model is a sociophysics model that is used to model opinion propagation and consensus formation in societies. Its main feature is that its rules favor bigger groups of agreeing people. In a previous work, we generalized the bounded confidence rule in order to model biases and prejudices in discrete opinion models. In that work, we applied this modification to the Sznajd model and presented some preliminary results. The present work extends what we did in that paper. We present results linking many of the properties of the mean-field fixed points, with only a few qualitative aspects of the confidence rule (the biases and prejudices modeled), finding an interesting connection with graph theory problems. More precisely, we link the existence of fixed points with the notion of strongly connected graphs and the stability of fixed points with the problem of finding the maximal independent sets of a graph. We state these results and present comparisons between the mean field and simulations in Barabasi-Albert networks, followed by the main mathematical ideas and appendices with the rigorous proofs of our claims and some graph theory concepts, together with examples. We also show that there is no qualitative difference in the mean-field results if we require that a group of size q > 2, instead of a pair, of agreeing agents be formed before they attempt to convince other sites (for the mean field, this would coincide with the q-voter model).