abstract: This is a study of scientific realism, and of the extent to which it is undermined by objections that have been raised by advocates of various forms of antirealism. I seek to develop and present a version of scientific realism that improves on past formulations, and then to show that standard antirealist arguments against it do not succeed. In this paper, I will first present my formulation of scientific realism, which conceives of theories as model-based and as fundamentally non-linguistic. I advocate an epistemic position that accords with indirect realism, and I review and assess the threat posed by theses of underdetermination. Next, I review and discuss three important views: the antirealist constructivist view of Thomas Kuhn, the realist view of Norwood Hanson, and the antirealist constructive empiricist view of Bas van Fraassen. I find merits and flaws in all three views. In the course of those discussions, I develop the theme that antirealists' arguments generally depend on assumptions that are open to question, especially from the perspective of the version of realism I advocate. I further argue that these antirealist views are undermined by their own tacit appeals to realism. / Dissertation/Thesis / Ph.D. Philosophy 2013

The complexity of biological systems constitute a significant problem for the development of biological models. This inspired the creation of a few Computational Scientific Discovery systems that attempt to address this problem in the context of metabolomics through the use of computers and automation. These systems have important limitations, however, like limited revision and experiment design abilities and the inability to revise refuted models. The goal of this project was to address some of these limitations. The system developed for this project, "Huginn", was based on the use of Abductive Logic Programming to automate crucial development tasks, like experiment design, testing consistency of models with experimental results and revision of refuted models. The main questions of this project were (1) whether the proposed system can successfully develop Metabolic Network Models and (2) whether it can do it better than its predecessors. To answer these questions we tested Huginn in a simulated environment. Its task was to relearn the structures of disrupted fragments of a state-of-the-art model of yeast metabolism. The results of the simulations show that Huginn can relearn the structure of metabolic models, and that it can do it better than previous systems thanks to the specific features introduced in it. Furthermore, we show how the design of extended crucial experiments can be automated using Answer Set Programming for the first time.

Several real world tasks involve data that is uncertain and relational in nature. Traditional approaches like first-order logic and probabilistic models either deal with structured data or uncertainty, but not both. To address these limitations, statistical relational learning (SRL), a new area in machine learning integrating both first-order logic and probabilistic graphical models, has emerged in the recent past. The advantage of SRL models is that they can handle both uncertainty and structured/relational data. As a result, they are widely used in domains like social network analysis, biological data analysis, and natural language processing. Bayesian Logic Programs (BLPs), which integrate both first-order logic and Bayesian net- works are a powerful SRL formalism developed in the recent past. In this dissertation, we develop approaches using BLPs to solve two real world tasks – plan recognition and machine reading. Plan recognition is the task of predicting an agent’s top-level plans based on its observed actions. It is an abductive reasoning task that involves inferring cause from effect. In the first part of the dissertation, we develop an approach to abductive plan recognition using BLPs. Since BLPs employ logical deduction to construct the networks, they cannot be used effectively for abductive plan recognition as is. Therefore, we extend BLPs to use logical abduction to construct Bayesian networks and call the resulting model Bayesian Abductive Logic Programs (BALPs). In the second part of the dissertation, we apply BLPs to the task of machine reading, which involves automatic extraction of knowledge from natural language text. Most information extraction (IE) systems identify facts that are explicitly stated in text. However, much of the information conveyed in text must be inferred from what is explicitly stated since easily inferable facts are rarely mentioned. Human readers naturally use common sense knowledge and “read between the lines” to infer such implicit information from the explicitly stated facts. Since IE systems do not have access to common sense knowledge, they cannot perform deeper reasoning to infer implicitly stated facts. Here, we first develop an approach using BLPs to infer implicitly stated facts from natural language text. It involves learning uncertain common sense knowledge in the form of probabilistic first-order rules by mining a large corpus of automatically extracted facts using an existing rule learner. These rules are then used to derive additional facts from extracted information using BLP inference. We then develop an online rule learner that handles the concise, incomplete nature of natural-language text and learns first-order rules from noisy IE extractions. Finally, we develop a novel approach to calculate the weights of the rules using a curated lexical ontology like WordNet. Both tasks described above involve inference and learning from partially observed or incomplete data. In plan recognition, the underlying cause or the top-level plan that resulted in the observed actions is not known or observed. Further, only a subset of the executed actions can be observed by the plan recognition system resulting in partially observed data. Similarly, in machine reading, since some information is implicitly stated, they are rarely observed in the data. In this dissertation, we demonstrate the efficacy of BLPs for inference and learning from incomplete data. Experimental comparison on various benchmark data sets on both tasks demonstrate the superior performance of BLPs over state-of-the-art methods. / text