QBF with Soft Variables

QBF formulae are usually considered in prenex form, i.e. the quantifierblock is completely separated from the propositional part of the QBF.Among others, the semantics of the QBF is defined by the sequence ofthe variables within the prefix, where existentially quantifiedvariables depend on all universally quantified variables stated to theleft.In this paper we extend that classical definition and consider a newquantification type which we call soft variable. The idea is toallow a flexible position and quantifier type for these variables.Hence the type of quantifier of the soft variable can also bealtered. Based on this concept, we present an optimization problemseeking an optimal prefix as defined by user-given preferences. We statean algorithm based on MaxQBF, and present several applications – mainlyfrom verification area – which can be naturally translated into theoptimization problem for QBF with soft variables. We further implementeda prototype solver for this formalism, and compare our approach toprevious work, that differently from ours does not guarantee optimalityand completeness

Combining Boolean Networks and Ordinary Differential Equations for Analysis and Comparison of Gene Regulatory Networks

This thesis is concerned with different groups of qualitative models of gene regulatory networks. Four types of models will be considered: interaction graphs, Boolean networks, models based on differential equations and discrete abstractions of differential equations. We will investigate the relations between these modeling frameworks and how they can be used in the analysis of individual models. The focus lies on the mathematical analysis of these models. This thesis makes several contributions in relating these different modeling frameworks. The first approach concerns individual Boolean models and parametrized families of ordinary differential equations (ODEs). To construct ODE models systematically from Boolean models several automatic conversion algorithms have been proposed. In Chapter 2 several such closely related algorithms will be considered. It will be proven that certain invariant sets are preserved during the conversion from a Boolean network to a model based on ODEs. In the second approach the idea of abstracting the dynamics of individual models to relate structure and dynamics will be introduced. This approach will be applied to Boolean models and models based on differential equations. This allows to compare groups of models in these modeling frameworks which have the same structure. We demonstrate that this constitutes an approach to link the interaction graph to the dynamics of certain sets of Boolean networks and models based on differential equations. The abstracted dynamics – or more precisely the restrictions on the abstracted behavior – of such sets of Boolean networks or models based on differential equations will be represented as Boolean state transitions graphs themselves. We will show that these state transition graphs can be considered as asynchronous Boolean networks. Despite the rather theoretical question this thesis tries to answer there are many potential applications of the results. The results in Chapter 2 can be applied to network reduction of ODE models based on Hill kinetics. The results of the second approach in Chapter 4 can be applied to network inference and analysis of Boolean model sets. Furthermore, in the last chapter of this thesis several ideas for applications with respect to experiment design will be considered. This leads to the question how different asynchronous Boolean networks or different behaviours of a single asynchronous Boolean network can be distinguishedDiese Arbeit beschäftigt sich mit unterschiedlichen Typen von qualitativen Modellen genregulatorischer Netzwerke. Vier Typen von Modellen werden betrachtet: Interaktionsgraphen, Boolesche Netzwerke, Modelle, die auf Differentialgleichungen basieren und diskrete Abstraktionen von Differentialgleichungen. Wir werden mehr über die Beziehungen zwischen diesen Modellgruppen lernen und wie diese Beziehungen genutzt werden können, um einzelne Modelle zu analysieren. Der Schwerpunkt liegt hierbei auf der mathematischen Analyse dieser Modellgruppen. In dieser Hinsicht leistet diese Arbeit mehrere Beiträge. Zunächst betrachten wir Boolesche Netzwerke und parametrisierte Familien von gewöhnlichen Differentialgleichungen (ODEs). Um solche ODE-Modelle systematisch aus Booleschen Modellen abzuleiten, wurden in der Vergangenheit verschiedene automatische Konvertierungsalgorithmen vorgeschlagen. In Kapitel 2 werden einige dieser Algorithmen näher untersucht. Wir werden beweisen, dass bestimmte invariante Mengen bei der Konvertierung eines Booleschen Modells in ein ODE-Modell erhalten bleiben. Der zweite Ansatz, der in dieser Arbeit verfolgt wird, beschäftigt sich mit diskreten Abstraktionen der Dynamik von Modellen. Mit Hilfe dieser Abstraktionen ist es möglich, die Struktur – den Interaktionsgraphen – und die Dynamik der zugehörigen Modelle in Bezug zu setzen. Diese Methode wird sowohl auf Boolesche Modelle als auch auf ODE-Modelle angewandt. Gleichzeitig erlaubt dieser Ansatz Mengen von Modellen in unterschiedlichen Modellgruppen zu vergleichen, die dieselbe Struktur haben. Die abstrahierten Dynamiken (genauer die Einschränkungen der abstrahierten Dynamiken) der Booleschen Modellmengen oder ODE-Modellmengen können als Boolesche Zustandsübergangsgraphen repräsentiert werden. Wir werden zeigen, dass diese Zustandsübergangsgraphen wiederum selber als (asynchrone) Boolesche Netzwerke aufgefasst werden können. Trotz der theoretischen Ausgangsfrage werden in dieser Arbeit zahlreiche Anwendungen aufgezeigt. Die Ergebnisse aus Kapitel 2 können zur Modellreduktion benutzt werden, indem die Dynamik der ODE-Modelle auf den zu den Booleschen Netzwerken gehörigen “trap spaces” betrachtet wird. Die Resultate aus Kapitel 4 können zur Netzwerkinferenz oder zur Analyse von Modellmengen genutzt werden. Weiterhin werden im letzten Kapitel dieser Arbeit einige Anwendungsideen im Bezug auf Experimentdesign eingeführt. Dies führt zu der Fragestellung, wie verschiedene asynchrone Boolesche Netzwerke oder unterschiedliche Dynamiken, die mit einem einzelnen Modell vereinbar sind, unterschieden werden können

Modeling Packaged Heat Pumps in a Quasi-steady State Energy Simulation Program

The purpose of this study is to validate steady-state heat pump models implemented in EnergyPlus. The heat pump models include air-to-air, water-to-air heat and water-to-water. Part load models are used to adjust the models' full load outputs to part load conditions. New curve-fit heat pump models are proposed and compared to existing parameter estimation based models using experimental data. Uncertainties in the models are analyzed and quantified. A short study is also conducted on the compressor shell heat loss that is often neglected by the manufacturer. The EnergyPlus heat pump models agree with experimental data with an error of less than 12%. Most of the errors are attributed to the discrepancies between the catalog and the experimental measurement. The curve-fit models in EnergyPlus agree with detailed and parameter estimation based models within 6%. Curve-fit heat pump models also allow extrapolation beyond the catalog data without catastrophic error and require less computation time and are more robust than parameter estimation based models. The current drawback of curve-fit models is the inability to simulate the degradation effect of antifreeze on water source heat pump performance. The heat pump component models in EnergyPlus have been validated but the control algorithm and system interactions still require further validation with measured data.Mechanical & Aerospace Engineerin

On Combining 01X-Logic and QBF

We discuss how to combine 01X-logic and quantified boolean formulas (QBF) within a homogeneous SAT/QBF-framework in the context of bounded model checking of blackbox designs. The proposed combination allows a flexible handling of blackboxes w.r.t. computational resources. Preliminary results show the scalability of the approach