2011 Conference Abstracts: Annual Undergraduate Research Conference at the Interface of Biology and Mathematics

Abstract book for the Third Annual Undergraduate Research Conference at the Interface of Biology and Mathematics Date: October 21-22, 2011Plenary speaker: J. Carl Panetta, Department of Pharmaceutical Sciences, St. Jude Children\u27s Research HospitalFeatured Speaker: John Jungck, Mead Chair of the Sciences and Professor of Biology, Beloit Colleg

Big data analytics in computational biology and bioinformatics

Big data analytics in computational biology and bioinformatics refers to an array of operations including biological pattern discovery, classification, prediction, inference, clustering as well as data mining in the cloud, among others. This dissertation addresses big data analytics by investigating two important operations, namely pattern discovery and network inference. The dissertation starts by focusing on biological pattern discovery at a genomic scale. Research reveals that the secondary structure in non-coding RNA (ncRNA) is more conserved during evolution than its primary nucleotide sequence. Using a covariance model approach, the stems and loops of an ncRNA secondary structure are represented as a statistical image against which an entire genome can be efficiently scanned for matching patterns. The covariance model approach is then further extended, in combination with a structural clustering algorithm and a random forests classifier, to perform genome-wide search for similarities in ncRNA tertiary structures. The dissertation then presents methods for gene network inference. Vast bodies of genomic data containing gene and protein expression patterns are now available for analysis. One challenge is to apply efficient methodologies to uncover more knowledge about the cellular functions. Very little is known concerning how genes regulate cellular activities. A gene regulatory network (GRN) can be represented by a directed graph in which each node is a gene and each edge or link is a regulatory effect that one gene has on another gene. By evaluating gene expression patterns, researchers perform in silico data analyses in systems biology, in particular GRN inference, where the “reverse engineering” is involved in predicting how a system works by looking at the system output alone. Many algorithmic and statistical approaches have been developed to computationally reverse engineer biological systems. However, there are no known bioin-formatics tools capable of performing perfect GRN inference. Here, extensive experiments are conducted to evaluate and compare recent bioinformatics tools for inferring GRNs from time-series gene expression data. Standard performance metrics for these tools based on both simulated and real data sets are generally low, suggesting that further efforts are needed to develop more reliable GRN inference tools. It is also observed that using multiple tools together can help identify true regulatory interactions between genes, a finding consistent with those reported in the literature. Finally, the dissertation discusses and presents a framework for parallelizing GRN inference methods using Apache Hadoop in a cloud environment

Evaluating the Impact of Defeasible Argumentation as a Modelling Technique for Reasoning under Uncertainty

Limited work exists for the comparison across distinct knowledge-based approaches in Artificial Intelligence (AI) for non-monotonic reasoning, and in particular for the examination of their inferential and explanatory capacity. Non-monotonicity, or defeasibility, allows the retraction of a conclusion in the light of new information. It is a similar pattern to human reasoning, which draws conclusions in the absence of information, but allows them to be corrected once new pieces of evidence arise. Thus, this thesis focuses on a comparison of three approaches in AI for implementation of non-monotonic reasoning models of inference, namely: expert systems, fuzzy reasoning and defeasible argumentation. Three applications from the fields of decision-making in healthcare and knowledge representation and reasoning were selected from real-world contexts for evaluation: human mental workload modelling, computational trust modelling, and mortality occurrence modelling with biomarkers. The link between these applications comes from their presumptively non-monotonic nature. They present incomplete, ambiguous and retractable pieces of evidence. Hence, reasoning applied to them is likely suitable for being modelled by non-monotonic reasoning systems. An experiment was performed by exploiting six deductive knowledge bases produced with the aid of domain experts. These were coded into models built upon the selected reasoning approaches and were subsequently elicited with real-world data. The numerical inferences produced by these models were analysed according to common metrics of evaluation for each field of application. For the examination of explanatory capacity, properties such as understandability, extensibility, and post-hoc interpretability were meticulously described and qualitatively compared. Findings suggest that the variance of the inferences produced by expert systems and fuzzy reasoning models was higher, highlighting poor stability. In contrast, the variance of argument-based models was lower, showing a superior stability of its inferences across different system configurations. In addition, when compared in a context with large amounts of conflicting information, defeasible argumentation exhibited a stronger potential for conflict resolution, while presenting robust inferences. An in-depth discussion of the explanatory capacity showed how defeasible argumentation can lead to the construction of non-monotonic models with appealing properties of explainability, compared to those built with expert systems and fuzzy reasoning. The originality of this research lies in the quantification of the impact of defeasible argumentation. It illustrates the construction of an extensive number of non-monotonic reasoning models through a modular design. In addition, it exemplifies how these models can be exploited for performing non-monotonic reasoning and producing quantitative inferences in real-world applications. It contributes to the field of non-monotonic reasoning by situating defeasible argumentation among similar approaches through a novel empirical comparison

Computer Aided Verification

This open access two-volume set LNCS 10980 and 10981 constitutes the refereed proceedings of the 30th International Conference on Computer Aided Verification, CAV 2018, held in Oxford, UK, in July 2018. The 52 full and 13 tool papers presented together with 3 invited papers and 2 tutorials were carefully reviewed and selected from 215 submissions. The papers cover a wide range of topics and techniques, from algorithmic and logical foundations of verification to practical applications in distributed, networked, cyber-physical, and autonomous systems. They are organized in topical sections on model checking, program analysis using polyhedra, synthesis, learning, runtime verification, hybrid and timed systems, tools, probabilistic systems, static analysis, theory and security, SAT, SMT and decisions procedures, concurrency, and CPS, hardware, industrial applications

Domain-specific languages for modeling and simulation

Simulation models and simulation experiments are increasingly complex. One way to handle this complexity is developing software languages tailored to specific application domains, so-called domain-specific languages (DSLs). This thesis explores the potential of employing DSLs in modeling and simulation. We study different DSL design and implementation techniques and illustrate their benefits for expressing simulation models as well as simulation experiments with several examples.Simulationsmodelle und -experimente werden immer komplexer. Eine Möglichkeit, dieser Komplexität zu begegnen, ist, auf bestimmte Anwendungsgebiete spezialisierte Softwaresprachen, sogenannte domänenspezifische Sprachen (\emph{DSLs, domain-specific languages}), zu entwickeln. Die vorliegende Arbeit untersucht, wie DSLs in der Modellierung und Simulation eingesetzt werden können. Wir betrachten verschiedene Techniken für Entwicklung und Implementierung von DSLs und illustrieren ihren Nutzen für das Ausdrücken von Simulationsmodellen und -experimenten anhand einiger Beispiele