Structural Analysis of Boolean Equation Systems

We analyse the problem of solving Boolean equation systems through the use of structure graphs. The latter are obtained through an elegant set of Plotkin-style deduction rules. Our main contribution is that we show that equation systems with bisimilar structure graphs have the same solution. We show that our work conservatively extends earlier work, conducted by Keiren and Willemse, in which dependency graphs were used to analyse a subclass of Boolean equation systems, viz., equation systems in standard recursive form. We illustrate our approach by a small example, demonstrating the effect of simplifying an equation system through minimisation of its structure graph

Modelling & analysis of hybrid dynamic systems using a bond graph approach

Hybrid models are those containing continuous and discontinuous behaviour. In constructing dynamic systems models, it is frequently desirable to abstract rapidly changing, highly nonlinear behaviour to a discontinuity. Bond graphs lend themselves to systems modelling by being multi-disciplinary and reflecting the physics of the system. One advantage is that they can produce a mathematical model in a form that simulates quickly and efficiently. Hybrid bond graphs are a logical development which could further improve speed and efficiency. A range of hybrid bond graph forms have been proposed which are suitable for either simulation or further analysis, but not both. None have reached common usage. A Hybrid bond graph method is proposed here which is suitable for simulation as well as providing engineering insight through analysis. This new method features a distinction between structural and parametric switching. The controlled junction is used for the former, and gives rise to dynamic causality. A controlled element is developed for the latter. Dynamic causality is unconstrained so as to aid insight, and a new notation is proposed. The junction structure matrix for the hybrid bond graph features Boolean terms to reflect the controlled junctions in the graph structure. This hybrid JSM is used to generate a mixed-Boolean state equation. When storage elements are in dynamic causality, the resulting system equation is implicit. The focus of this thesis is the exploitation of the model. The implicit form enables application of matrix-rank criteria from control theory, and control properties can be seen in the structure and causal assignment. An impulsive mode may occur when storage elements are in dynamic causality, but otherwise there are no energy losses associated with commutation because this method dictates the way discontinuities are abstracted. The main contribution is therefore a Hybrid Bond Graph which reflects the physics of commutating systems and offers engineering insight through the choice of controlled elements and dynamic causality. It generates a unique, implicit, mixed-Boolean system equation, describing all modes of operation. This form is suitable for both simulation and analysis

Construction and analysis of causally dynamic hybrid bond graphs

Engineering systems are frequently abstracted to models with discontinuous behaviour (such as a switch or contact), and a hybrid model is one which contains continuous and discontinuous behaviours. Bond graphs are an established physical modelling method, but there are several methods for constructing switched or ‘hybrid’ bond graphs, developed for either qualitative ‘structural’ analysis or efficient numerical simulation of engineering systems. This article proposes a general hybrid bond graph suitable for both. The controlled junction is adopted as an intuitive way of modelling a discontinuity in the model structure. This element gives rise to ‘dynamic causality’ that is facilitated by a new bond graph notation. From this model, the junction structure and state equations are derived and compared to those obtained by existing methods. The proposed model includes all possible modes of operation and can be represented by a single set of equations. The controlled junctions manifest as Boolean variables in the matrices of coefficients. The method is more compact and intuitive than existing methods and dispenses with the need to derive various modes of operation from a given reference representation. Hence, a method has been developed, which can reach common usage and form a platform for further study

Analysis of Boolean Equation Systems through Structure Graphs

We analyse the problem of solving Boolean equation systems through the use of structure graphs. The latter are obtained through an elegant set of Plotkin-style deduction rules. Our main contribution is that we show that equation systems with bisimilar structure graphs have the same solution. We show that our work conservatively extends earlier work, conducted by Keiren and Willemse, in which dependency graphs were used to analyse a subclass of Boolean equation systems, viz., equation systems in standard recursive form. We illustrate our approach by a small example, demonstrating the effect of simplifying an equation system through minimisation of its structure graph

Exploiting Query Structure and Document Structure to Improve Document Retrieval Effectiveness

In this paper we present a systematic analysis of document retrieval using unstructured and structured queries within the score region algebra (SRA) structured retrieval framework. The behavior of di®erent retrieval models, namely Boolean, tf.idf, GPX, language models, and Okapi, is tested using the transparent SRA framework in our three-level structured retrieval system called TIJAH. The retrieval models are implemented along four elementary retrieval aspects: element and term selection, element score computation, score combination, and score propagation. The analysis is performed on a numerous experiments evaluated on TREC and CLEF collections, using manually generated unstructured and structured queries. Unstructured queries range from the short title queries to long title + description + narrative queries. For generating structured queries we exploit the knowledge of the document structure and the content used to semantically describe or classify documents. We show that such structured information can be utilized in retrieval engines to give more precise answers to user queries then when using unstructured queries

Relative Stability of Network States in Boolean Network Models of Gene Regulation in Development

Progress in cell type reprogramming has revived the interest in Waddington's concept of the epigenetic landscape. Recently researchers developed the quasi-potential theory to represent the Waddington's landscape. The Quasi-potential U(x), derived from interactions in the gene regulatory network (GRN) of a cell, quantifies the relative stability of network states, which determine the effort required for state transitions in a multi-stable dynamical system. However, quasi-potential landscapes, originally developed for continuous systems, are not suitable for discrete-valued networks which are important tools to study complex systems. In this paper, we provide a framework to quantify the landscape for discrete Boolean networks (BNs). We apply our framework to study pancreas cell differentiation where an ensemble of BN models is considered based on the structure of a minimal GRN for pancreas development. We impose biologically motivated structural constraints (corresponding to specific type of Boolean functions) and dynamical constraints (corresponding to stable attractor states) to limit the space of BN models for pancreas development. In addition, we enforce a novel functional constraint corresponding to the relative ordering of attractor states in BN models to restrict the space of BN models to the biological relevant class. We find that BNs with canalyzing/sign-compatible Boolean functions best capture the dynamics of pancreas cell differentiation. This framework can also determine the genes' influence on cell state transitions, and thus can facilitate the rational design of cell reprogramming protocols.Comment: 24 pages, 6 figures, 1 tabl