Functional Ontologies and Their Application to Hydrologic Modeling: Development of an Integrated Semantic and Procedural Knowledge Model and Reasoning Engine

This dissertation represents the research and development of new concepts and techniques for modeling the knowledge about the many concepts we as hydrologists must understand such that we can execute models that operate in terms of conceptual abstractions and have those abstractions translate to the data, tools, and models we use every day. This hydrologic knowledge includes conceptual (i.e. semantic) knowledge, such as the hydrologic cycle concepts and relationships, as well as functional (i.e. procedural) knowledge, such as how to compute the area of a watershed polygon, average basin slope or topographic wetness index. This dissertation is presented as three papers and a reference manual for the software created. Because hydrologic knowledge includes both semantic aspects as well as procedural aspects, we have developed, in the first paper, a new form of reasoning engine and knowledge base that extends the general-purpose analysis and problem-solving capability of reasoning engines by incorporating procedural knowledge, represented as computer source code, into the knowledge base. The reasoning engine is able to compile the code and then, if need be, execute the procedural code as part of a query. The potential advantage to this approach is that it simplifies the description of procedural knowledge in a form that can be readily utilized by the reasoning engine to answer a query. Further, since the form of representation of the procedural knowledge is source code, the procedural knowledge has the full capabilities of the underlying language. We use the term functional ontology to refer to the new semantic and procedural knowledge models. The first paper applies the new knowledge model to describing and analyzing polygons. The second and third papers address the application of the new functional ontology reasoning engine and knowledge model to hydrologic applications. The second paper models concepts and procedures, including running external software, related to watershed delineation. The third paper models a project scenario that includes integrating several models. A key advance demonstrated in this paper is the use of functional ontologies to apply metamodeling concepts in a manner that both abstracts and fully utilizes computational models and data sets as part of the project modeling process

Crossing the chasm: a 'tube-map' for agent-based social simulation of policy scenarios in spatially-distributed systems

Agent based models (ABMs) simulate actions and interactions of autonomous agents/groups and their effect on systems as a whole, accounting for learning without assuming perfect rationality or complete knowledge. ABMs are an increasingly popular approach to studying complex, spatially distributed socio-environmental systems, but have still to become an established approach in the sense of being one that is expected by those wanting to explore scenarios in such systems. Partly, this is an issue of awareness – ABM is still new enough that many people have not heard of it; partly, it is an issue of confidence – ABM has more to do to prove itself if it is to become a preferred method. This paper will identify advances in the craft and deployment of ABM needed if ABM is to become an accepted part of mainstream science for policy or stakeholders. The conduct of ABM has, over the last decade, seen a transition from using abstracted representations of systems (supporting theory-led thought experiments) to more accessible representations derived empirically (to deliver more applied analysis). This has enhanced the perception of potential users of ABM outputs that the latter are salient and credible. Empirical ABM is not, however, a panacea, as it demands more computing and data resources, limiting applications to domains where data exist along with suitable environmental models where these are required. Further, empirical ABM is still facing serious questions of validation and the ontology used to describe the system in the first place. Using Geoffrey A. Moore’s Crossing the Chasm as a lens, we argue that the way ahead for ABM lies in identifying the niches in which it can best demonstrate its advantages, working with collaborators to demonstrate that it can deliver on its promises. This leads us to identify several areas where work is needed

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

Multi-Agent Systems

This Special Issue ""Multi-Agent Systems"" gathers original research articles reporting results on the steadily growing area of agent-oriented computing and multi-agent systems technologies. After more than 20 years of academic research on multi-agent systems (MASs), in fact, agent-oriented models and technologies have been promoted as the most suitable candidates for the design and development of distributed and intelligent applications in complex and dynamic environments. With respect to both their quality and range, the papers in this Special Issue already represent a meaningful sample of the most recent advancements in the field of agent-oriented models and technologies. In particular, the 17 contributions cover agent-based modeling and simulation, situated multi-agent systems, socio-technical multi-agent systems, and semantic technologies applied to multi-agent systems. In fact, it is surprising to witness how such a limited portion of MAS research already highlights the most relevant usage of agent-based models and technologies, as well as their most appreciated characteristics. We are thus confident that the readers of Applied Sciences will be able to appreciate the growing role that MASs will play in the design and development of the next generation of complex intelligent systems. This Special Issue has been converted into a yearly series, for which a new call for papers is already available at the Applied Sciences journal’s website: https://www.mdpi.com/journal/applsci/special_issues/Multi-Agent_Systems_2019

Proceedings, MSVSCC 2018

Proceedings of the 12th Annual Modeling, Simulation & Visualization Student Capstone Conference held on April 19, 2018 at VMASC in Suffolk, Virginia. 155 pp

Bioinspired metaheuristic algorithms for global optimization

This paper presents concise comparison study of newly developed bioinspired algorithms for global optimization problems. Three different metaheuristic techniques, namely Accelerated Particle Swarm Optimization (APSO), Firefly Algorithm (FA), and Grey Wolf Optimizer (GWO) are investigated and implemented in Matlab environment. These methods are compared on four unimodal and multimodal nonlinear functions in order to find global optimum values. Computational results indicate that GWO outperforms other intelligent techniques, and that all aforementioned algorithms can be successfully used for optimization of continuous functions