Strong Connectivity in Directed Hypergraphs and its Application to the Atomic Decomposition of Ontologies

Los hipergrafos dirigidos se han empleado en problemas relacionados con lógica proposicional, bases de datos relacionales, linguística computacional y aprendizaje automático. Los hipergrafos dirigidos han sido también utilizados como alternativa a los grafos (bipartitos) dirigidos para facilitar el estudio de las interacciones entre componentes de sistemas complejos que no pueden ser fácilmente modelados usando exclusivamente relaciones binarias. En este contexto, este tipo de representación es conocida como hiper-redes. Un hipergrafo dirigido es una generalización de un grafo dirigido especialmente adecuado para la representación de relaciones de muchos a muchos. Mientras que una arista en un grafo dirigido define una relación entre dos de sus nodos, una hiperarista en un hipergrafo dirigido define una relación entre dos conjuntos de sus nodos. La conexión fuerte es una relación de equivalencia que divide el conjunto de nodos de un hipergrafo dirigido en particiones y cada partición define una clase de equivalencia conocida como componente fuertemente conexo. El estudio de los componentes fuertemente conexos de un hipergrafo dirigido puede ayudar a conseguir una mejor comprensión de la estructura de este tipo de hipergrafos cuando su tamaño es considerable. En el caso de grafo dirigidos, existen algoritmos muy eficientes para el cálculo de los componentes fuertemente conexos en grafos de gran tamaño. Gracias a estos algoritmos, se ha podido averiguar que la estructura de la WWW tiene forma de “pajarita”, donde más del 70% del los nodos están distribuidos en tres grandes conjuntos y uno de ellos es un componente fuertemente conexo. Este tipo de estructura ha sido también observada en redes complejas en otras áreas como la biología. Estudios de naturaleza similar no han podido ser realizados en hipergrafos dirigidos porque no existe algoritmos capaces de calcular los componentes fuertemente conexos de este tipo de hipergrafos. En esta tesis doctoral, hemos investigado como calcular los componentes fuertemente conexos de un hipergrafo dirigido. En concreto, hemos desarrollado dos algoritmos para este problema y hemos determinado que son correctos y cuál es su complejidad computacional. Ambos algoritmos han sido evaluados empíricamente para comparar sus tiempos de ejecución. Para la evaluación, hemos producido una selección de hipergrafos dirigidos generados de forma aleatoria inspirados en modelos muy conocidos de grafos aleatorios como Erdos-Renyi, Newman-Watts-Strogatz and Barabasi-Albert. Varias optimizaciones para ambos algoritmos han sido implementadas y analizadas en la tesis. En concreto, colapsar los componentes fuertemente conexos del grafo dirigido que se puede construir eliminando ciertas hiperaristas complejas del hipergrafo dirigido original, mejora notablemente los tiempos de ejecucion de los algoritmos para varios de los hipergrafos utilizados en la evaluación. Aparte de los ejemplos de aplicación mencionados anteriormente, los hipergrafos dirigidos han sido también empleados en el área de representación de conocimiento. En concreto, este tipo de hipergrafos se han usado para el cálculo de módulos de ontologías. Una ontología puede ser definida como un conjunto de axiomas que especifican formalmente un conjunto de símbolos y sus relaciones, mientras que un modulo puede ser entendido como un subconjunto de axiomas de la ontología que recoge todo el conocimiento que almacena la ontología sobre un conjunto especifico de símbolos y sus relaciones. En la tesis nos hemos centrado solamente en módulos que han sido calculados usando la técnica de localidad sintáctica. Debido a que las ontologías pueden ser muy grandes, el cálculo de módulos puede facilitar las tareas de re-utilización y mantenimiento de dichas ontologías. Sin embargo, analizar todos los posibles módulos de una ontología es, en general, muy costoso porque el numero de módulos crece de forma exponencial con respecto al número de símbolos y de axiomas de la ontología. Afortunadamente, los axiomas de una ontología pueden ser divididos en particiones conocidas como átomos. Cada átomo representa un conjunto máximo de axiomas que siempre aparecen juntos en un modulo. La decomposición atómica de una ontología es definida como un grafo dirigido de tal forma que cada nodo del grafo corresponde con un átomo y cada arista define una dependencia entre una pareja de átomos. En esta tesis introducimos el concepto de“axiom dependency hypergraph” que generaliza el concepto de descomposición atómica de una ontología. Un modulo en una ontología correspondería con un componente conexo en este tipo de hipergrafos y un átomo de una ontología con un componente fuertemente conexo. Hemos adaptado la implementación de nuestros algoritmos para que funcionen también con axiom dependency hypergraphs y poder de esa forma calcular los átomos de una ontología. Para demostrar la viabilidad de esta idea, hemos incorporado nuestros algoritmos en una aplicación que hemos desarrollado para la extracción de módulos y la descomposición atómica de ontologías. A la aplicación la hemos llamado HyS y hemos estudiado sus tiempos de ejecución usando una selección de ontologías muy conocidas del área biomédica, la mayoría disponibles en el portal de Internet NCBO. Los resultados de la evaluación muestran que los tiempos de ejecución de HyS son mucho mejores que las aplicaciones más rápidas conocidas. ABSTRACT Directed hypergraphs are an intuitive modelling formalism that have been used in problems related to propositional logic, relational databases, computational linguistic and machine learning. Directed hypergraphs are also presented as an alternative to directed (bipartite) graphs to facilitate the study of the interactions between components of complex systems that cannot naturally be modelled as binary relations. In this context, they are known as hyper-networks. A directed hypergraph is a generalization of a directed graph suitable for representing many-to-many relationships. While an edge in a directed graph defines a relation between two nodes of the graph, a hyperedge in a directed hypergraph defines a relation between two sets of nodes. Strong-connectivity is an equivalence relation that induces a partition of the set of nodes of a directed hypergraph into strongly-connected components. These components can be collapsed into single nodes. As result, the size of the original hypergraph can significantly be reduced if the strongly-connected components have many nodes. This approach might contribute to better understand how the nodes of a hypergraph are connected, in particular when the hypergraphs are large. In the case of directed graphs, there are efficient algorithms that can be used to compute the strongly-connected components of large graphs. For instance, it has been shown that the macroscopic structure of the World Wide Web can be represented as a “bow-tie” diagram where more than 70% of the nodes are distributed into three large sets and one of these sets is a large strongly-connected component. This particular structure has been also observed in complex networks in other fields such as, e.g., biology. Similar studies cannot be conducted in a directed hypergraph because there does not exist any algorithm for computing the strongly-connected components of the hypergraph. In this thesis, we investigate ways to compute the strongly-connected components of directed hypergraphs. We present two new algorithms and we show their correctness and computational complexity. One of these algorithms is inspired by Tarjan’s algorithm for directed graphs. The second algorithm follows a simple approach to compute the stronglyconnected components. This approach is based on the fact that two nodes of a graph that are strongly-connected can also reach the same nodes. In other words, the connected component of each node is the same. Both algorithms are empirically evaluated to compare their performances. To this end, we have produced a selection of random directed hypergraphs inspired by existent and well-known random graphs models like Erd˝os-Renyi and Newman-Watts-Strogatz. Besides the application examples that we mentioned earlier, directed hypergraphs have also been employed in the field of knowledge representation. In particular, they have been used to compute the modules of an ontology. An ontology is defined as a collection of axioms that provides a formal specification of a set of terms and their relationships; and a module is a subset of an ontology that completely captures the meaning of certain terms as defined in the ontology. In particular, we focus on the modules computed using the notion of syntactic locality. As ontologies can be very large, the computation of modules facilitates the reuse and maintenance of these ontologies. Analysing all modules of an ontology, however, is in general not feasible as the number of modules grows exponentially in the number of terms and axioms of the ontology. Nevertheless, the modules can succinctly be represented using the Atomic Decomposition of an ontology. Using this representation, an ontology can be partitioned into atoms, which are maximal sets of axioms that co-occur in every module. The Atomic Decomposition is then defined as a directed graph such that each node correspond to an atom and each edge represents a dependency relation between two atoms. In this thesis, we introduce the notion of an axiom dependency hypergraph which is a generalization of the atomic decomposition of an ontology. A module in the ontology corresponds to a connected component in the hypergraph, and the atoms of the ontology to the strongly-connected components. We apply our algorithms for directed hypergraphs to axiom dependency hypergraphs and in this manner, we compute the atoms of an ontology. To demonstrate the viability of this approach, we have implemented the algorithms in the application HyS which computes the modules of ontologies and calculate their atomic decomposition. In the thesis, we provide an experimental evaluation of HyS with a selection of large and prominent biomedical ontologies, most of which are available in the NCBO Bioportal. HyS outperforms state-of-the-art implementations in the tasks of extracting modules and computing the atomic decomposition of these ontologies.

Recommendations for Soil and Water Conservation Programs

The United States Department of Agriculture employs soil and water conservation programs to assist with the sustainable use of natural resources in balance with economic vitality in rural America. This capstone project analyzed soil and water conservation programs to identify strengths, weaknesses, and methods to maximize environmental benefits. There are many requirements for participation in these programs which are difficult for most agricultural producers to comprehend. Research indicates in order to accomplish the goals of federal conservation programs and assist individuals, a method must be developed to effectively present information in a concise manner. This capstone project created a communicative measure, a template, to disseminate pertinent knowledge on soil and water conservation programs, thereby filling a void in existing literature.

A combined probabilistic framework for learning gestures and actions

In this paper we introduce a probabilistic approach to support visual supervision and gesture recognition. Task knowledge is both of geometric and visual nature and it is encoded in parametric eigenspaces. Learning processes for compute modal subspaces (eigenspaces) are the core of tracking and recognition of gestures and tasks. We describe the overall architecture of the system and detail learning processes and gesture design. Finally we show experimental results of tracking and recognition in block-world like assembling tasks and in general human gestures.

Connecting Clinical Practices with Microbiological and Biochemical Technologies

The word technology refers to the knowledge of techniques, skills, methods or processes used to produce goods, services or to reach specific objectives (research, business, etc.). The concept technology can also be used to make reference to devices, computers and factories.

Performing Pedagogies and Exploring Embodied Knowledge

Performing Pedagogies was a week-long performance and exhibition series I organized that took place in Kingston, Ontario between March 15th - March 20th 2016. The motivation for this project came from a desire to explore performative modes of experiencing critical, embodied knowledge. The series featured five performances, a long distance collaboration between thirty-one Queen’s undergraduate students and a Vancouver artist-run free school (The School for Eventual Vacancy), a subsequent exhibition, a panel discussion, and a radical performance pedagogy workshop led by co-artistic director of the international performance art troupe, La Pocha Nostra. Artists featured included Golboo Amani, Basil AlZeri, Caitlin Chaisson, Justin Langlois, Saul Garcia-Lopez, Francisco-Fernando Granados, and Andrew Rabyniuk. By curating examples of performance art that variously incorporated embodied pedagogical interventions, I examined the processes of performance as pedagogy. Performing Pedagogies explored interventions into contemporary contours of neoliberal education paradigms through embodied encounters—fostering conversations about the meanings and limitations of knowledge dissemination and education today and posing questions about possibilities for radical pedagogies, embodied knowledge, and counter curricula.

Lost in Translation? Russian Media Portrayals and Laypersons’ Interpretations of Angelina Jolie’s Breast Cancer Discourse

In May 2013, Angelina Jolie revealed that because she had a family history of breast and ovarian cancer and carried a rare BRCA gene mutation, she had undergone a preventive double mastectomy. Media coverage has been extensive around the world, including in Russia, not an English-language country, where all global news is inevitably filtered by translation. After examining the reactions of Russian mass media and members of the public to Jolie’s disclosure, I consider what transformations have occurred with Jolie’s message in the process of cross-cultural transfer. I explore the mass media portrayal of Jolie’s announcement, laypersons’ immediate and prolonged reactions, and the reflections of patients involved directly in the field of hereditary breast cancer. To my knowledge, this multifaceted and bilingual project is the first conceptualization of Jolie’s story as it has been translated in a different sociocultural environment. I start with examination of offline and online publications that appeared in Russia within two months after Jolie’s announcement. In this part of my analysis, I conceptualize the representation of Jolie’s case in Russian mass media and grasp what sociocultural waves were generated by this case among general lay audiences. Another part of my study contains the results of qualitative in-depth interviews. Eight women with a family history of hereditary breast cancer were recruited to participate in the research. The findings represent Jolie’s case through the eyes of Russian women with the same gene mutation as Jolie. Consolidating my findings, I argue that Jolie’s announcement was misinterpreted and misrepresented by Russian mass media, as well as misunderstood by a considerable part of the media audience. Jolie’s perspective on hereditary breast cancer mostly remained unheard among members of the Russian public. I make suggestions about the reasons for such a phenomenon, and demonstrate how Jolie’s case is implicated in politics, economics, and the culture of contemporary Russia.

Prepared for a Symposium on Country Development at the European Meeting on Cybernetics and Systems Research, Vienna, Austria, April 2012 (Untitled). ACES Working Papers, April 2012

In Kazakhstan doctoral students are not expected to make a contribution to knowledge, as is required at Western universities. Rather, their task is to become familiar with what is known and then make policy recommendations for Kazakhstan. For example, how can the human capital in Kazakhstan be improved? This is a very broad subject for a PhD dissertation. However, it does require a holistic perspective, and such dissertation topics may create an opportunity for systems scientists. When Russell Ackoff created the Social Systems Sciences PhD program at the Wharton School of the University of Pennsylvania, he had his students solve practical problems for business or government managers. That program graduated a large number of people who became consultants. A few became academics in several countries. The program created a philosophy and methods for holistic management. Large issues in developing countries may be a source of clients for systems scientists who want to further develop philosophy, theories and methods by working with large social systems.

Maclear & Co.'s Canadian almanac, and repository of useful knowledge.

Vols. for 1855-1856 called also 8th-9th.

Atlantic journal, and friend of knowledge. In eight numbers. Containing about 160 original articles and tracts on natural and historical sciences, the description of about 150 new plants, and 100 new animals or fossils. Many vocabularies of languages, historical and geological facts, &c.

Caption title: nos. 1-4, Atlantic journal, and firend of knowledge; a cyclopedic journal and review of universal science and knowledge: historical, natural, and medical arts and sciences. -- nos. 5-8, Atlantic journal and friend of knowledge; a quarterly journal of historical and natural sciences, useful knowledge, &c.

Allen's commercial organic analysis; a treatise on the properties, modes of assaying, and proximate analytical examination of the various organic chemicals and products employed in the arts, manufactures, medicine, etc., with concise methods for the detection and estimation of their impurities, adulterations, and products of decomposition ...

Vols. 3-9 edited by W.A. Davis and Samuel S. Sadtler.

Literacy Content and Core Practices: Teacher Educator Pedagogy as the Bridge Between Knowing and Doing

Thesis (Ph.D.)--University of Washington, 2016-04

Gaussian quantum operator representation for bosons

We introduce a Gaussian quantum operator representation, using the most general possible multimode Gaussian operator basis. The representation unifies and substantially extends existing phase-space representations of density matrices for Bose systems and also includes generalized squeezed-state and thermal bases. It enables first-principles dynamical or equilibrium calculations in quantum many-body systems, with quantum uncertainties appearing as dynamical objects. Any quadratic Liouville equation for the density operator results in a purely deterministic time evolution. Any cubic or quartic master equation can be treated using stochastic methods.

Knowledge beliefs and attitudes of squash venue operators relating to use of protective eyewear

Sports venues are in a position to potentially influence the safety practices of their patrons. This study examined the knowledge, beliefs and attitudes of venue operators that could influence the use of protective eyewear by squash players. A 50% random sample of all private and public squash venues affiliated with the Victorian Squash Federation in metropolitan Melbourne was selected. Face-to-face interviews were conducted with 15 squash venue operators during August 2001. Interviews were transcribed and content and thematic analyses were performed. The content of the interviews covered five topics: (1) overall injury risk perception, (2) eye injury occurrence, (3) knowledge, behaviors, attitudes and beliefs associated with protective eyewear, (4) compulsory protective eyewear and (5) availability of protective eyewear at venues. Venue operators were mainly concerned with the severe nature of eye injuries, rather than the relatively low incidence of these injuries. Some venue operators believed that players should wear any eyewear, rather than none at all, and believed that more players should use protective eyewear. Generally, they did not believe that players with higher levels of experience and expertise needed to wear protective eyewear when playing. Only six venues had at least one type of eyewear available for players to hire or borrow or to purchase. Operators expressed a desire to be informed about correct protective eyewear. Appropriate protective eyewear is not readily available at squash venues. Better-informed venue operators may be more likely to provide suitable protective eyewear.

Practice challenges at the intersection of child protection and mental health

This paper examines the complexity of collaboration between child protection and mental health services, where a parent has a mental illness and there are protection concerns for children. The paper reports on data from focused in-depth interviews with 36 child protection workers, adult mental health workers and child and youth mental health workers. Data were analysed thematically, using NVivo to facilitate data management and analysis. Two dimensions were identified. The first, the process of collaboration, relates to four factors that assisted the collaborative process: communication, knowledge, role clarity and resources. The second dimension considers the challenges presented to collaborative work when a parent has a mental illness and a child is in need of protection, and identifies issues that are inherent in cases of this kind. Two types of challenge were identified. The first related to characteristics of mental illness, and included the episodic and/or unpredictable nature of mental illness, incorporating information from psychiatric and parenting capacity assessments, and the provision of ongoing support. The second type of challenge concerned the tension between the conflicting needs of parents and their children, and how this was viewed from both the adult mental health and the child protection perspective. Implications for policy and practice are identified in relation to the need for service models that provide ongoing, flexible support that can be intensified or held back as needed.