Generation and Applications of Knowledge Graphs in Systems and Networks Biology

The acceleration in the generation of data in the biomedical domain has necessitated the use of computational approaches to assist in its interpretation. However, these approaches rely on the availability of high quality, structured, formalized biomedical knowledge. This thesis has the two goals to improve methods for curation and semantic data integration to generate high granularity biological knowledge graphs and to develop novel methods for using prior biological knowledge to propose new biological hypotheses. The first two publications describe an ecosystem for handling biological knowledge graphs encoded in the Biological Expression Language throughout the stages of curation, visualization, and analysis. Further, the second two publications describe the reproducible acquisition and integration of high-granularity knowledge with low contextual specificity from structured biological data sources on a massive scale and support the semi-automated curation of new content at high speed and precision. After building the ecosystem and acquiring content, the last three publications in this thesis demonstrate three different applications of biological knowledge graphs in modeling and simulation. The first demonstrates the use of agent-based modeling for simulation of neurodegenerative disease biomarker trajectories using biological knowledge graphs as priors. The second applies network representation learning to prioritize nodes in biological knowledge graphs based on corresponding experimental measurements to identify novel targets. Finally, the third uses biological knowledge graphs and develops algorithmics to deconvolute the mechanism of action of drugs, that could also serve to identify drug repositioning candidates. Ultimately, the this thesis lays the groundwork for production-level applications of drug repositioning algorithms and other knowledge-driven approaches to analyzing biomedical experiments

Mysticism and schizophrenia:A phenomenological exploration of the structure of consciousness in the schizophrenia spectrum disorders

AbstractMysticism and schizophrenia are different categories of human existence and experience. Nonetheless, they exhibit important phenomenological affinities, which, however, remain largely unaddressed. In this study, we explore structural analogies between key features of mysticism and major clinical-phenomenological aspects of the schizophrenia spectrum disorders—i.e. attitudes, the nature of experience, and the ‘other’, mystical or psychotic reality. Not only do these features gravitate around the issue of the basic dimensions of consciousness, they crucially seem to implicate and presuppose a specific alteration of the very structure of consciousness. This finding has bearings for the understanding of consciousness and its psychopathological distortions

Developing dwelling as an approach to landscape and place: The cases of long-distance transhumance and Easter processions

Approaches to place and landscape have concerned geographers, at least throughout Modern history. In geographical place and landscape writings, notions of dwelling have been taken up and developed since the 1970s to indicate the lived and practised character of the relationships between human beings and their environment. Dwelling has experienced a controversial history in geography, and bears some negative or limiting connotations: it would be backward-looking, exclusionary, static, nostalgic, and hindered by the idea of rootedness and the authentic / non-authentic life split.This thesis critically considers in what ways seminal dwelling literatures (those written by Martin Heidegger and Tim Ingold) might be problematical and / or enriching for place and landscape writing. In this thesis I argue that the theoretical complexity of seminal dwelling literatures is often overlooked while I also argue that some understandings of the relational, the incomplete, and the contingent are largely missing or problematically conceptualised in seminal dwelling literatures.Taking into account this reflection on the theoretical background of dwelling, the thesis explores possibilities for integrating dwelling in a framework inspired by non-representational theory (NRT). Such links are made in the thesis’ case studies: communities practising (a) long-distance transhumant herding in rural Spain (in which herders and herd journey biennially for about four weeks in response to environmental changes caused by the seasonal cycle), and (b) Easter processions in central Seville (in which brotherhoods celebrate the Resurrection of Jesus Christ). Place and landscape practices are accessed through ethnographical engagements, in which herding - and processional landscapes become the lived contexts for reflection. In the case studies, dwelling is redeveloped through a framework that prioritises posthumanism, relationality and openness, as well as issues of rhythmicity, and nearness (as people care for - and attune to happenings). In long-distance transhumance the rural, the ecological and the practical are privileged, whereas in Easter processions the urban, the spiritual, and to the sheer beauty of life are emphasised. As such, the case studies offer distinct perspectives on the possibilities for developments of dwelling in place and landscape writing, while the case studies share denominators such as journeying, seasonality, embodiment, and practice richness

Heidegger, Lonergan, and the Modern Philosophic Tradition

This dissertation begins from the guiding notion that Bernard Lonergan and Martin Heidegger, by virtue of their dialogue with the Western philosophic tradition and their attempt to overcome the modern paradigm of knowing and of the human person, and when read together, offer a unique and broad horizon wherein to situate a robust philosophical anthropology, taking the human person as both an intellectual being and as fully situated in a history and culture. The basic thesis is that, taken together, Lonergan and Heidegger offer a framework for getting beyond or sublating the impasses of modern thought. The dissertation first lays out the basis of the claim that Lonergan and Heidegger can be read as responding specifically to the problematic set by modern philosophy. It then presents each thinker’s formulation of that problem. The bulk of the dissertation lays out, as running parallel, some of the central features of each thinker’s master works—Insight and Being and Time—with an eye to allowing their complementarity stand forth. As regards Lonergan, we treat first the notion of insight, followed by the patterns of experience as pre-reflective organizing principles of experience; then we move on to a treatment of history and the place of fully-human knowing in that history, with a discussion of the self-affirmation of the knower. With Heidegger, we begin with a discussion of Being-in-the-world, move through a treatment of historicity and facticity—Dasein’s “thrownness”—and then proceed to a discussion of judgment and the ways in which knowing must be regarded as a founded (or non-primary) mode of access to reality. Finally, we compare both thinkers’ understandings of being in a final chapter, and suggest that these understandings of being are an essential part of both thinkers’ understandings of the human person. The dissertation concludes with a brief assessment of the possible avenues of further investigation, with a special emphasis on the possible development of a philosophical anthropology taking its bearings from the insights of Lonergan and Heidegger

Theology, science and the topos of the Logos: a stable, dynamic topology of Creation

This thesis argues that an integrated, dynamically stable theo-science may be explored by considering scientific and theological perspectives regarding stability itself, combining them in one overarching framework by embedding a scientific conception of stability within a broader theological conception thereof. Our very capacity to perceive ‘reality’ in a functionally consistent manner is dependent upon the physical cosmos presenting a particular, dynamic stability, allowing for the sustainable emergence of life in the first place. Stability is hierarchically qualified, with higher-order functional systems such as those pertaining to life being an emergent result of particular modes of interaction between lower-level degrees of stability, ultimately right down to fundamental particles or fields. Theologically, any stability inherent to ‘reality’ must furthermore be considered to derive from the fact that such reality is, at its profoundest, a manifestation of God’s revealing, Creative Activity through the Logos. The thesis considers, qualitatively, the scientific and theological ‘place’ and relevance of stability from a holistic perspective regarding our anthropological development. Scientifically this is viewed in layered, evolutionary terms. Theologically, the Incarnation is considered of central relevance to our anthropological journey, transfiguring the process of its development so as to draw human nature into its intended eschatological stability ‘at the right hand of the Father’. Since stability can be considered scientifically in topological terms, the framework is developed by means of a ‘theological topology’ centred, as the etymology suggests, on the idea of a sacramentally stable, pervasive topos indicative of God’s ‘motioning’, Creative Activity through the Logos. Such Activity becomes sense-objectified in the Incarnation, considered figuratively-speaking as a ‘phase transition’, the net effect of which is argued as a ‘drawing in’ (cf. John 12:32), reordering and enhancing all meaningful, creaturely contribution to the ‘content’ of Creation – content actively generated according to our iconic, creative capacity for conceiving (of) the Logos

The place of value in Whitehead's thought

Thesis (Ph.D.)--Boston UniversityThe purpose of this dissertation is the investigation of the development of Whitehead's conception of value and its basic categories and the function of value as an integrating factor for his general metaphysical position

Invisible Geographies: Oil, Time, and Ecology in Venezuelan Cultural Production.

Despite its political and economic significance in Venezuela, cultural critics have often argued that oil has remained absent in the country’s cultural production. Invisible Geographies disputes the idea of oil’s cultural absence in Venezuela. It does so, in part, by engaging with a wide range of overlooked texts, which deal with oil’s social, material and ecological impact. The project’s chief aim, however, is to challenge the conceptual practices that have rendered oil invisible in the Venezuelan cultural imaginary—in particular, the conventional modes of conceptualizing the nation’s territory and history. Through analyses of regionalist literature, early twentieth-century poetry, state documents, and oil industry propaganda, the project first shows how representations of nature as a timeless realm at the margins of human history, have been deployed to veil oil’s ecological imprint. A reading of the overlooked subgenre of la novela del petróleo delves into how sites of extraction and their literary representations have been exiled to a “no place” (a term famously used by Amitav Ghosh’s) imagined to exist outside the proper bounds of the nation. When reinserted into visions of the Venezuelan nation, these sites of extraction unsettle the usual ways of periodizing political change. The effects of oil’s invisibility in urban life and consumer culture are explored in relation to the literary work of Arturo Uslar Pietri, as well as the films produced by the Shell Oil Film Unit. Of particular interest in this portion of the project is the extent to which mid twentieth-century urban growth in Venezuela as well as in much of the world implicitly depended on the oil industry’s promise to liberate modern societies from the material and temporal limits. The project closes by examining the unwillingness to contend with long-term ecological harm as a political problem by delving into the controversy unleashed by the documentary Nuestro petróleo y otros cuentos (2005). As a whole, Invisible Geographies argues that the global ecological crises of the twenty-first century require a reexamination of the spatial and temporal categories that have been central to the idea of the modern nation.PhDRomance Languages and Literatures: SpanishUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/133323/1/barriose_1.pd

Makings of imagination in alternative cultural spaces in Cairo

To speak of space as a concept, how it is produced, de/reconstructed, and imagined is a process that involves multiplicities of understanding about the makings that take place. My concern is in this research is exploring the dynamic relationships that take place between cultural spaces in Cairo, the subjectivities of their participants and the possibilities that might be offered through these relations for a different social imagination that could be manifested in the details of their everydayness. The main question of my thesis is; In which ways and conditions can some of the contemporary cultural spaces in Cairo situate their presence and serve as a liberating spaces that nurture imaginations capable of transfiguring the status quo whether intellectual, social or political. My research questions are anchored in four focal theoretical concepts: space, subjectivity, imagination and how these concepts are manifested in everydayness. I will not deal with them as separate, linear or static concepts but as dimensions that are constantly in dynamic change in relation to each other. I will not attempt a cause/effect analysis and I am not after a comparative or a descriptive analysis of the two cultural spaces I chose ( Nahda Association- Jesuit\u27s culture centre in Cairo, The Choir Project of Cairo). I believe this different and dynamic configuration of theorizing will enable different moods of thinking and greater capacity of exploration to acquire different kind of knowledge about the contemporary moment in Cairo\u27s cultural scene, which is rapidly changing and how they can possibly provide fertile conditions for a different social imagination to take place