The structure of a protein molecule is highly correlated to its function. Some diseases such as cystic fibrosis are the result of a change in the structure of a protein so that this change interferes or inhibits its function. Often these changes in structure are caused by a misfolding of the protein molecule. To assist computational biologists, there is a database of proteins together with their misfolded versions, called decoys, that can be used to test the accuracy of protein structure prediction algorithms. In our work we use a nested graph model to quantify a selected set of proteins that have two single misfold decoys. The graph theoretic model used is a three tiered nested graph. Measures based on the vertex weights are calculated and we compare the quantification of the proteins with their decoys. Our method is able to separate the misfolded proteins from the correctly folded proteins.

Flexible approaches for eliciting preferences of decision makers involved in a conflict are developed along with applications to real-world disputes. More specifically, two multiple criteria decision making approaches are proposed for capturing the relative preferences of a decision maker participating in a conflict situation. A case study in logistics concerned with the conflict arising over the expansion of port facilities on the west coast of North America as well as a transportation negotiation dispute are used to illustrate how these approaches can be integrated with the Graph Model for Conflict Resolution, a practical conflict analysis methodology. Ascertaining the preferences of the decision makers taking part in a conflict constitutes a key element in the construction of a formal conflict model. In practice, the relative preferences, which reflect each decision maker’s objectives or goals in a given situation, are rather difficult to obtain. The first method for preference elicitation is to integrate an Analytic Hierarchy Process (AHP) preference ranking method with the Graph Model for Conflict Resolution. The AHP approach is used to elicit relative preferences of decision makers, and this preference information is then fed into a graph model for further stability analyses. The case study of the Canadian west coast port congestion conflict is investigated using this integrated model. Another approach is based on a fuzzy multiple criteria out-ranking technique called ELECTRE III. It is also employed for ranking states or possible scenarios in a conflict from most to least preferred, with ties allowed, by the decision maker according to his or her own value system. The model is applied to a transportation negotiation dispute between the two key parties consisting of shippers and carriers.

Theoretical procedures are developed to account for the effect of emotion and perception in strategic conflict. The <em>possibility principle</em> facilitates modeling the effects of emotions on future scenarios contemplated by decision makers; <em>perceptual graph models</em> and a <em>graph model system</em> permit the decision makers (DMs) to experience and view the conflict independently; and <em>perceptual stability analysis</em>, which is based on individual- and meta-stability analysis techniques, is employed in analyzing graph model systems when the DMs have inconsistent perceptions. These developments improve the methodology of the Graph Model for Conflict Resolution by reconciling emotion, perception, and strategy to make predictions consistent with the actual unfolding of events. <br /><br /> Current research in neuroscience suggests that emotions are a necessary component of cognitive processes such as memory, attention, and reasoning. The somatic marker hypothesis, for example, holds that feelings are necessary to reasoning, especially during social interactions (Damasio, 1994, 2003). Somatic markers are memories of past emotions: we use them to predict future outcomes. To incorporate the effect of emotion in conflict, the underlying principle of Damasio?s hypothesis is used in developing the possibility principle, which significantly expands the paradigm of the Graph Model for Conflict Resolution of Fang, Hipel, and Kilgour (1993). <br /><br /> State identification is a crucial step in determining future scenarios for DMs. The possibility principle is integrated into the modeling stage of the Graph Model by refining the method of determining feasible states. The possibility principle enables analysts and DMs to include emotion in a conflict model, without sacrificing the parsimonious design of the Graph Model methodology, by focusing attention on two subsets of the set of feasible states: <em>hidden</em> and <em>potential</em> states. Hidden states are logically valid, feasible states that are invisible because of the presence of negative emotions such as anger and fear; potential states are logically valid, feasible states that are invisible because of missing positive emotions. Dissipating negative emotions will make the hidden states visible, while expressing the appropriate positive emotions will make the potential states visible. The possibility principle has been applied to a number of real world conflicts. In all cases, eliminating logically valid states not envisioned by any DM simplifies a conflict model substantially, expedites the analysis, and makes it an intuitive and a realistic description of the DMs' conceptualizations of the conflict. <br /><br /> A fundamental principle of the Graph Model methodology is that all DMs' directed graphs must have the same set of feasible states, which are integrated into a <em>standard</em> graph model. The possibility principle may modify the set of feasible states perceived by each DM according to his or her emotion, making it impossible to construct a single standard graph model. When logically valid states are no longer achievable for one or more DMs due to emotions, the apprehension of conflict becomes inconsistent, and resolution may become difficult to predict. Therefore, reconciling emotion and strategy requires that different apprehensions of the underlying decision problem be permitted, which can be accomplished using a perceptual graph model for each DM. A perceptual graph model inherits its primitive ingredients from a standard graph model, but reflects a DM's emotion and perception with no assumption of complete knowledge of other DMs' perceptions. <br /><br /> Each DM's perceptual graph model constitutes a complete standard graph model. Hence, conclusions drawn from a perceptual graph model provide a limited view of equilibria and predicted resolutions. A graph model system, which consists of a list of DMs' perceptual graph models, is defined to reconcile perceptions while facilitating conclusions that reflect each DM's viewpoint. However, since a DM may or may not be aware that other graph models differ from his or her own, different variants of graph model systems are required to describe conflicts. Each variant of graph model system corresponds to a configuration of awareness, which is a set of ordered combinations of DMs' viewpoints. <br /><br /> Perceptual stability analysis is a new procedure that applies to graph model systems. Its objective is to help an <em>outside</em> analyst predict possible resolutions, and gauge the robustness and sustainability of these predictions. Perceptual stability analysis takes a two-phase approach. In Phase 1, the stability of each state in each perceptual graph model is assessed from the point of view of the owner of the model, for each DM in the model, using standard or perceptual solution concepts, depending on the owner's awareness of others' perceptions. (In this research, only perceptual solution concepts for the 2-decision maker case are developed. ) In Phase 2, meta-stability analysis is employed to consolidate the stability assessments of a state in all perceptual graph models and across all variants of awareness. Distinctive modes of equilibria are defined, which reflect incompatibilities in DMs' perceptions and viewpoints but nonetheless provide important insights into possible resolutions of conflict. <br /><br /> The possibility principle and perceptual stability analysis are integrative techniques that can be used as a basis for empathetically studying the interaction of emotion and reasoning in the context of strategic conflict. In general, these new techniques expand current modeling and analysis capabilities, thereby facilitating realistic, descriptive models without exacting too great a cost in modeling complexity. In particular, these two theoretical advances enhance the applicability of the Graph Model for Conflict Resolution to real-world disputes by integrating emotion and perception, common ingredients in almost all conflicts. <br /><br /> To demonstrate that the new developments are practical, two illustrative applications to real-world conflicts are presented: the US-North Korea conflict and the confrontation between Russia and Chechen Rebels. In both cases, the analysis yields new strategic insights and improved advice.

Flexible approaches for eliciting preferences of decision makers involved in a conflict are developed along with applications to real-world disputes. More specifically, two multiple criteria decision making approaches are proposed for capturing the relative preferences of a decision maker participating in a conflict situation. A case study in logistics concerned with the conflict arising over the expansion of port facilities on the west coast of North America as well as a transportation negotiation dispute are used to illustrate how these approaches can be integrated with the Graph Model for Conflict Resolution, a practical conflict analysis methodology. Ascertaining the preferences of the decision makers taking part in a conflict constitutes a key element in the construction of a formal conflict model. In practice, the relative preferences, which reflect each decision maker’s objectives or goals in a given situation, are rather difficult to obtain. The first method for preference elicitation is to integrate an Analytic Hierarchy Process (AHP) preference ranking method with the Graph Model for Conflict Resolution. The AHP approach is used to elicit relative preferences of decision makers, and this preference information is then fed into a graph model for further stability analyses. The case study of the Canadian west coast port congestion conflict is investigated using this integrated model. Another approach is based on a fuzzy multiple criteria out-ranking technique called ELECTRE III. It is also employed for ranking states or possible scenarios in a conflict from most to least preferred, with ties allowed, by the decision maker according to his or her own value system. The model is applied to a transportation negotiation dispute between the two key parties consisting of shippers and carriers.

This thesis presents space-efficient algorithms to sample from random web graphs generated by two important stochastic graph models based on concept of copying: the linear copy model and the hostgraph model. The goal is to avoid constructing the entire random graph, and instead use an amount of space nearer to the desired (smaller) sample size. The efficiency of our algorithms is achieved by refraining from making unnecessary random decisions when constructing the sample. The construc- tion of a sample subgraph from a random graph with n nodes and k outgoing links on each node based on the linear copying model uses an expected O(klnn) words for each node in the sample subgraph. The construction of a sample subgraph from a random graph with n nodes based on the hostgraph model uses, for any small sample size, an expected n+o(n) words.

Ce travail introduit un ensemble de solutions pour extraire des graphes à partir des données de l'entreprise et pour aussi faciliter le processus de recherche d'information dans ces graphes. Premièrement, nous avons défini un nouveau modèle de données appelé SPIDER-Graph permettant de modéliser des objets complexes et de définir des graphes hétérogènes. Puis, nous avons développé un ensemble d'algorithmes pour extraire le contenu des bases de données de l'entreprise et les transformer suivant ce nouveau modèle de graphe. Cette représentation permet de mettre à jour des relations non explicites entre objets, relations existantes mais non visibles dans le modèle relationnel. Par ailleurs, pour unifier la représentation de toutes les données dans l'entreprise, nous avons développé, dans une deuxième approche, une méthode de constitution d’une ontologie d'entreprise contenant les concepts et les relations les plus importantes d'une entreprise, et ceci, à partir de l’extraction des données non structurés de cette même entreprise. Ensuite, après le processus d'extraction des différents graphes de données l'entreprise, nous avons proposé une approche qui permettent d'extraire des graphes d'interactions entre des objets hétérogènes modélisant l'entreprise. Cette approche permet d'extraire des graphes de réseaux sociaux ou des graphes d'interactions. Ensuite, nous avons proposé un nouveau langage d'interrogation visuel appelé GraphVQL ( Graph Visual Query Langauge) qui permet aux utilisateurs non experts de poser leurs requêtes visuellement sous forme de patron de graphe. Ce langage propose plusieurs types de requêtes de la simple sélection et agrégation jusqu'à l'analyse des réseaux sociaux. Il permet aussi d'interroger différent type de graphes SPIDER-Graph, RDF ou GraphML en se basant sur des algorithmes de pattern matching ou de translation des requêtes sous forme de SPARQL. / The present work introduces a set of solutions to extract graphs from enterprise data and facilitate the process of information search on these graphs. First of all we have defined a new graph model called the SPIDER-Graph, which models complex objects and permits to define heterogeneous graphs. Furthermore, we have developed a set of algorithms to extract the content of a database from an enterprise and to represent it in this new model. This latter representation allows us to discover relations that exist in the data but are hidden due to their poor compatibility with the classical relational model. Moreover, in order to unify the representation of all the data of the enterprise, we have developed a second approach which extracts from unstructured data an enterprise's ontology containing the most important concepts and relations that can be found in a given enterprise. Having extracted the graphs from the relational databases and documents using the enterprise ontology, we propose an approach which allows the users to extract an interaction graph between a set of chosen enterprise objects. This approach is based on a set of relations patterns extracted from the graph and the enterprise ontology concepts and relations. Finally, information retrieval is facilitated using a new visual graph query language called GraphVQL, which allows users to query graphs by drawing a pattern visually for the query. This language covers different query types from the simple selection and aggregation queries to social network analysis queries.

How are arms export choices made within a state? In this dissertation I use a foreign policy analysis framework to examine this question. I focus on examining each of the three primary levels of analysis in international relations as it relates to the main question. I begin with a typical international relations level and examine the characteristics of the two states that dominate the world arms trade: The United States and Russia. I then examine the full network of relations among all states in the international system that are involved in the sale or purchase of arms. To do this I use an Exponential Random Graph Model (ERGM) to examine these relations, which I derived from data on arms sales from the Stockholm International Peace Research Institute (SIPRI). I examine the arms sales in each decade from 1950 through 2010. In order to answer the question of how arms decisions are made within the state, I focus my inquiry on the United States and Russia. It is these states that have the practical capability to use arms transfers as a foreign policy tool. I examine the foreign policy making mechanisms in each of these states to determine how arms transfers can be used as a foreign policy tool. I examine and the bureaucratic institutions within each state and come up with a state ordering preference for how arms decisions are evaluated in each state. Finally, I use case studies to examine arms relations between the both the U.S. and Russia and three other states in each case. The other states were selected based on the pattern of sales between the two countries. I examine these sales to determine the impact of bureaucratic maneuvering and interest politics on the decision-making process within Russia and the United States. I find in my network analysis that the traditional measures of state power - military spending, regime type, and military alliances - do not account for the overall structure of the arms sale network. The most important factors in the formation of the arms sale network in each of the six decades that I study are specific configurations of triadic relations that suggest a continued hierarchy in the arms sale network. I find in my case study chapters that a simple model of state interest as a decision-making rule accounts for the decisions made by the different bureaucratic actors in the U.S. Russian arms sales are driven by a state imperative to increase Russia's market share, and there is high-level involvement in making different arms deals with other countries.

Floods are among some of the most damaging natural disasters. They can cause major interruptions to buildings and infrastructure and can have lasting impacts. In the case of flood damage estimation to buildings, structural and non-structural damages are of interest to most flood risk research. Very few studies, conversely analyze the impact of the recovery timeline on losses. There is a challenge to clearly understand the cause of failures within an interconnected system such as a building, and the requirements for accelerating restoration to overcome the adverse results of flood in the most convenient way possible. This work seeks to map the various components involved in functional failures of flood damaged buildings to understand their recovery. A novel model of a residential building is constructed using the Graph Model for Operational Resilience (GMOR) to model the complex interaction among dependencies in building systems to understand the cascade of failure of restoration. A case study is performed to generate recovery model to simulate the restoration of a single residential building in a flood prone neighborhood of Surrey, BC, Canada. The depth-damage functions, along with construction and repair guides, are used to identify restoration dependencies and to formulate a unique sequence of flood recovery steps for several possible flood depths. This study demonstrates how restoration can be delayed and probable solutions to improve the resilience of the city through recovery planning of flooded buildings. The results provide insights that should be useful to help emergency managers and other decision makers to develop and implement resilience thinking while revealing the economic benefits associated with increased flood risk management. In future, the custom flood model can be adapted to other locations. / Graduate / 2020-12-04

京都大学 / 0048 / 新制・課程博士 / 博士(情報学) / 甲第17927号 / 情博第509号 / 新制||情||90(附属図書館) / 30747 / 京都大学大学院情報学研究科社会情報学専攻 / (主査)教授 吉川 正俊, 教授 石田 亨, 教授 田中 克己 / 学位規則第4条第1項該当 / Doctor of Informatics / Kyoto University / DGAM

The electromagnetic machines like the dc, induction, synchronous motor/generator and the transformer have an energy flow framework that is similar. All these machines deal with electrical energy in the electrical domain that is interfaced with the magnetic domain. Except for the transformer, the other machines also have one more energy interface i.e. with the mechanical domain. In all these machines, the magnetic domain acts as the silent energy manager. The electrical and the mechanical domain energies will have to pass through the magnetic domain and appropriately get routed. In recognition of the commonality of this pattern of energy flow, this thesis proposes a generalised model of a multiphase electromagnetic device wherein the dc machine, induction machine, synchronous machine and the transformers are special cases of the proposed generalised model. This is derived using bond graphs that is based on the underlining principle of Energy Flow rooted in the concept of Conservation of Energy. A model is a set of mathematical equations representing a physical system. A model is as good as a modeller understanding of the physical system and the underlying approximation he makes while writing down the equations describing the models behaviour to the stimulus. A modelling language tool, which can cut down the approximations made by using the power of identified analogous characteristics across the physical domain, can help make a model more close to real life situation. Bond Graph is such a modelling language which is powerful enough to model the non-linear, multi-disciplinary, hybrid continuous-discrete phenomena encountered in a real life physical system. Bond graphs as a modelling tool was introduced by Professor H.Paynter at Massachusetts Institute of Technology in 1959. The Bond Graph methodology is based on consideration of energy flows between the ports of the components of an engineering system. Bond Graph methodology enables one to develop a graphical model that is consistent with the first principle of energy conservation without having the need to start with establishing and reformulating equations. The derivation of a mathematical model from the graphical description is automated by software tools. As a consequence, a modeller using this methodology can focus on modelling of the physical system. In the graphical representation of bond graph the vertices of a bond graph denote subsystems, system components or elements, while the edges, called power bonds, represent energy flows between them. The nodes of a bond graph have power ports where energy can enter or exit. Bond graph models are developed in a hierarchical top-down or bottom-up approach by using component models or elements from model libraries. An electromagnetic machine is a black box having an assemblage of windings in iron resulting in a combination of input/output ports on shaft and electrical terminals. Abstraction of an machine model by a modeller matching the vision of the observer above is an ideal goal. Bond graph methodology is an appropriate tool for trying to reach this goal as it is based on object oriented modelling techniques. There have been few attempts to model electric machine in bond graph earlier. A well established DC motor bond graph has been widely used in all bond graph literature. But AC rotating machine being a higher order nonlinear system poses a tougher challenge. Here too, there have been few attempts in modelling AC machines. It is observed that majority of AC machine bond graph models have been built up from their mathematical models. But as the bond graph modelling technique is based on the unifying theory of energy exchange, better insight into the system is achievable if the model is conceptualised from its physical structure. This thesis starts from the basic theory of energy port to conceptualise the generalised model from physical correspondence. In this thesis a Rotating Electrical Machine is studied as a physical system. The energy ports inside this physical system is identified. When a physical system receives the energy through its energy port in one energy cycle, it processes this energy in one of the three ways. The received energy is converted into useful work or it is dissipated or stored. The storage can further be classified into two ways, either as kinetic energy or as potential energy. For a rotating electric machine the input-output port for energy exchange are either in electrical or mechanical domain depending on the class of the machine. The magnetic domain across all class of electromagnetic device acts as the energy manager. In order to capture the features of the energy jumping across the air gap in a rotating electrical machine, wherein the magnetic fields from spatially distributed windings of the stator and rotor interplay, an Axis Rotator (AR) element -a mathematical commutator, is introduced in this thesis as a new bond graph element. In a multiphase device, the energy from the various phases and spatial axes are transferred through the axis rotator element. The Axis Rotator is a critical element which helps distinguish between the various classes of electromagnetic devices. The defining features of the Axis Rotator helps in deriving the various special electromagnetic devices (such as the dc machine, induction machine, synchronous machine and the transformer) from the generalised model. The Axis Rotator exists in the magnetic domain. It naturally inherits the characteristics of the magnetic domain. The Axis Rotator as a bond graph element is complex. In a specific case of 3φ Induction Motor an alternative bond graph model with all integral elements is developed. By one to one correspondence with the AR bond graph model, the inner component of ’AR’ can be identified. Another advantage of using this model is that saturable and non-saturable magnetic permeance can be separated out, a useful feature in the nonlinear model discussed next. One of the most distinguishing features of the magnetic domain is the existence of Magnetic Hysteresis. Magnetic Hysteresis is a well understood and studied subject. But this physical process is wilfully ignored by the modelling community at large. The main reason for this is the difficulty of modelling a nonlinear phenomena. The bond graph modelling naturally allows the inclusion of such non-idealities within its framework. This thesis proposes the generalised model along with the inclusion of magnetic non-linearities and non-idealities into the model of the system. This inherent strength of bond graph model flows from the fact that the models in bond graph are developed from the first principles of energy conversation and the mathematical equations are derived later from the evolved graph. The tools that are available for bond graph simulation are not adequate for power electronics systems. The existing tools do not address space vectors and frame transformations. As a consequence it is difficult to simulate the electromagnetic device models developed in this thesis. The need for a bond graph tool to address vectors and frame transformations, a common occurrence in electric machines dynamic model study was acutely felt. This necessitated a support for handling complex data class from the underlying mathematical engine of the software. MATLAB/Simulink is the commonly available mathematical tool which has a support for complex variables. Therefore during the course of this research work a new software tool box was developed which meets the need of electromagnetic machines in particular and other engineering domains in general. For developing the new bond graph simulation software, the language extender approach was chosen, as it combines the capabilities of existing popular mathematical engine with its tested graphical frontend and the flexibility of combining different modelling technique like bond graph, block diagram, equations etc. It also ensures portability as they are compiled by interpreted language compiler of the mathematical engine and are thus independent of the computer operating system. C-MEX S-function methodology was used to develop the software as it has access to lower level functions and methods of the underlying mathematical engine. This helps in speeding up the software execution time alongwith the flexibility in defining new complex elements like the Nonlinear Axis Rotator. In conclusion, this thesis makes the following contributions: (i) The Axis rotator concept to handle space vectors and frame transformations, (ii) generalised model of the electromagnetic device, (iii) introduction of the saturation and hysteresis non-linearity in the magnetic domain, (iv) development of the bond graph toolbox to handle vector and frame transformations.