Metagenomic systems biology: frameworks for modeling and characterizing the gut microbiome

Thesis (Ph.D.)--University of Washington, 2014

Optimization and Machine Learning Frameworks for Complex Network Analysis

Thesis (Ph.D.)--University of Washington, 2016-06

Toward a Theory of Structure in Information Organization Frameworks

This paper outlines a formal and systematic approach to explication of the role of structure in information organization. It presents a preliminary set of constructs that are useful for understanding the similarities and differences that obtain across information organization systems. This work seeks to provide necessary groundwork for development of a theory of structure that can serve as a lens through which to observe patterns across systems of information organization.

The Economic and Aesthetic Axis of Information Organization Frameworks

This paper argues that in order to systematically comprehend the diversity of information organization frameworks, we must look at how aesthetic concerns and economic concerns manifest in decisions made about designing and deploying work practices, structures, and discourse. In order to do this I construct an analytical rubric borne by a definition of aesthetic and economics pertinent to indexing regimes. I take the position that we need to move into a more descriptive stance on practices of knowledge organization, not only in documentary heritage institutions (libraries, archives, and museums), but also into the cultural and artistic realms. By expanding the scope of inquiry we can interrogate the integrity of my assertion above, namely, that a chief concern in systematically understanding information organization frameworks, lies in understanding how such frameworks wrestle with, and manifest along a spectrum drawn from economic to aesthetic decision-making.

Modeling the Aesthetic Axis of Information Organization Frameworks, Part 1: Theoretical Basis

Purpose – The purpose of this paper is to propose a theoretical framework, based on contemporary philosophical aesthetics, from which principled assessments of the aesthetic value of information organization frameworks may be conducted.Design/methodology/approach – This paper identifies appropriate discourses within the field of philosophical aesthetics, constructs from them a framework for assessing aesthetic properties of information organization frameworks. This framework is then applied in two case studies examining the Library of Congress Subject Headings (LCSH), and Sexual Nomenclature: A Thesaurus. Findings – In both information organization frameworks studied, the aesthetic analysis was useful in identifying judgments of the frameworks as aesthetic judgments, in promoting discovery of further areas of aesthetic judgments, and in prompting reflection on the nature of these aesthetic judgments. Research limitations/implications – This study provides proof-of-concept for the aesthetic evaluation of information organization frameworks. Areas of future research are identified as the role of cultural relativism in such aesthetic evaluation and identification of appropriate aesthetic properties of information organization frameworks.Practical implications – By identifying a subset of judgments of information organization frameworks as aesthetic judgments, aesthetic evaluation of such frameworks can be made explicit and principled. Aesthetic judgments can be separated from questions of economic feasibility, functional requirements, and user-orientation. Design and maintenance of information organization frameworks can be based on these principles.Originality/value – This study introduces a new evaluative axis for information organization frameworks based on philosophical aesthetics. By improving the evaluation of such novel frameworks, design and maintenance can be guided by these principles.Keywords Evaluation, Research methods, Analysis, Bibliographic systems, Indexes, Retrieval languages

Modeling the Aesthetic Axis of Information Organization Frameworks, Part 2: Case Studies

Purpose – The purpose of this paper is to propose a theoretical framework, based on contemporary philosophical aesthetics, from which principled assessments of the aesthetic value of information organization frameworks may be conducted.Design/methodology/approach – This paper identifies appropriate discourses within the field of philosophical aesthetics, constructs from them a framework for assessing aesthetic properties of information organization frameworks. This framework is then applied in two case studies examining the Library of Congress Subject Headings (LCSH), and Sexual Nomenclature: A Thesaurus. Findings – In both information organization frameworks studied, the aesthetic analysis was useful in identifying judgments of the frameworks as aesthetic judgments, in promoting discovery of further areas of aesthetic judgments, and in prompting reflection on the nature of these aesthetic judgments. Research limitations/implications – This study provides proof-of-concept for the aesthetic evaluation of information organization frameworks. Areas of future research are identified as the role of cultural relativism in such aesthetic evaluation and identification of appropriate aesthetic properties of information organization frameworks.Practical implications – By identifying a subset of judgments of information organization frameworks as aesthetic judgments, aesthetic evaluation of such frameworks can be made explicit and principled. Aesthetic judgments can be separated from questions of economic feasibility, functional requirements, and user-orientation. Design and maintenance of information organization frameworks can be based on these principles.Originality/value – This study introduces a new evaluative axis for information organization frameworks based on philosophical aesthetics. By improving the evaluation of such novel frameworks, design and maintenance can be guided by these principles.Keywords Evaluation, Analysis, Bibliographic systems, Indexes, Retrieval languages, Philosophy

Function, Purpose, Predication, and Context of Information Organization Frameworks

This paper outlines the purposes, predications, functions, and contexts of information organization frameworks; including: bibliographic control, information retrieval, resource discovery, resource description, open access scholarly indexing, personal information management protocols, and social tagging in order to compare and contrast those purposes, predications, functions, and contexts. Information organization frameworks, for the purpose of this paper, consist of information organization systems (classification schemes, taxonomies, ontologies, bibliographic descriptions, etc.), methods of conceiving of and creating the systems, and the work processes involved in maintaining these systems. The paper first outlines the theoretical literature of these information organization frameworks. In conclusion, this paper establishes the first part of an evaluation rubric for a function, predication, purpose, and context analysis.