Many important software systems, including communication protocols and concurrent and distributed algorithms generate infinite state-spaces. Model-checking which is the most prominent algorithmic technique for the verification of concurrent systems is restricted to the analysis of finite-state models. Algorithmic analysis of infinite-state models is complicated--most interesting properties are undecidable for sufficiently expressive classes of infinite-state models. In this thesis, we focus on the development of algorithmic analysis techniques for two important classes of infinite-state models: FIFO Systems and Parameterized Systems. FIFO systems consisting of a set of finite-state machines that communicate via unbounded, perfect, FIFO channels arise naturally in the analysis of distributed protocols. We study the problem of computing the set of reachable states of a FIFO system composed of piecewise components. This problem is closely related to calculating the set of all possible channel contents, i.e. the limit language. We present new algorithms for calculating the limit language of a system with a single communication channel and important subclasses of multi-channel systems. We also discuss the complexity of these algorithms. Furthermore, we present a procedure that translates a piecewise FIFO system to an abridged structure, representing an expressive abstraction of the system. We show that we can analyze the infinite computations of the more concrete model by analyzing the computations of the finite, abridged model. Parameterized systems are a common model of computation for concurrent systems consisting of an arbitrary number of homogenous processes. We study the reachability problem in parameterized systems of infinite-state processes. We describe a framework that combines Abstract Interpretation with a backward-reachability algorithm. Our key idea is to create an abstract domain in which each element (a) represents the lower bound on the number of processes at a control location and (b) employs a numeric abstract domain to capture arithmetic relations among variables of the processes. We also provide an extrapolation operator for the domain to guarantee sound termination of the backward-reachability algorithm.

We can visualize a graph by producing a geometric representation of the graph in which each node is represented by a single point on the plane, and each edge is represented by a curve that connects its two endpoints. Directed graphs are often used to model hierarchical structures; in order to visualize the hierarchy represented by such a graph, it is desirable that a drawing of the graph reflects this hierarchy. This can be achieved by drawing all the edges in the graph such that they all point in an upwards direction. A graph that has a drawing in which all edges point in an upwards direction and in which no edges cross is known as an upward planar graph. Unfortunately, testing if a graph is upward planar is NP-complete. Parameterized complexity is a technique used to find efficient algorithms for hard problems, and in particular, NP-complete problems. The main idea is that the complexity of an algorithm can be constrained, for the most part, to a parameter that describes some aspect of the problem. If the parameter is fixed, the algorithm will run in polynomial time. In this thesis, we investigate contracting an edge in an upward planar graph that has a specified embedding, and show that we can determine whether or not the resulting embedding is upward planar given the orientation of the clockwise and counterclockwise neighbours of the given edge. Using this result, we then show that under certain conditions, we can join two upward planar graphs at a vertex and obtain a new upward planar graph. These two results expand on work done by Hutton and Lubiw. Finally, we show that a biconnected graph has at most <i>k</i>!8^<i>k</i>-1 planar embeddings, where <i>k</i> is the number of triconnected components. By using an algorithm by Bertolazzi et al. that tests whether a given embedding is upward planar, we obtain a parameterized algorithm, where the parameter is the number of triconnected components, for testing the upward planarity of a biconnected graph. This algorithm runs in <i>O</i>(<i>k</i>!8^<i>k</i><i>n</i>³) time.

Many important software systems, including communication protocols and concurrent and distributed algorithms generate infinite state-spaces. Model-checking which is the most prominent algorithmic technique for the verification of concurrent systems is restricted to the analysis of finite-state models. Algorithmic analysis of infinite-state models is complicated--most interesting properties are undecidable for sufficiently expressive classes of infinite-state models. In this thesis, we focus on the development of algorithmic analysis techniques for two important classes of infinite-state models: FIFO Systems and Parameterized Systems. FIFO systems consisting of a set of finite-state machines that communicate via unbounded, perfect, FIFO channels arise naturally in the analysis of distributed protocols. We study the problem of computing the set of reachable states of a FIFO system composed of piecewise components. This problem is closely related to calculating the set of all possible channel contents, i.e. the limit language. We present new algorithms for calculating the limit language of a system with a single communication channel and important subclasses of multi-channel systems. We also discuss the complexity of these algorithms. Furthermore, we present a procedure that translates a piecewise FIFO system to an abridged structure, representing an expressive abstraction of the system. We show that we can analyze the infinite computations of the more concrete model by analyzing the computations of the finite, abridged model. Parameterized systems are a common model of computation for concurrent systems consisting of an arbitrary number of homogenous processes. We study the reachability problem in parameterized systems of infinite-state processes. We describe a framework that combines Abstract Interpretation with a backward-reachability algorithm. Our key idea is to create an abstract domain in which each element (a) represents the lower bound on the number of processes at a control location and (b) employs a numeric abstract domain to capture arithmetic relations among variables of the processes. We also provide an extrapolation operator for the domain to guarantee sound termination of the backward-reachability algorithm.

Parameterized NP-hard problems are NP-hard problems that are associated with special variables called parameters. One example of the problem is to find simple paths of length k in a graph, where the integer k is the parameter. We call this problem the p-path problem. The p-path problem is the parameterized version of the well-known NP-complete problem - the longest simple path problem. There are two main reasons why we study parameterized NP-hard problems. First, many application problems are naturally associated with certain parameters. Hence we need to solve these parameterized NP-hard problems. Second, if parameters take only small values, we can take advantage of these parameters to design very effective algorithms. If a parameterized NP-hard problem can be solved by an algorithm of running time in form of f(k)nO(1), where k is the parameter, f(k) is independent of n, and n is the input size of the problem instance, we say that this parameterized NP-hard problem is fixed parameter tractable (FPT). If a problem is FPT and the parameter takes only small values, the problem can be solved efficiently (it can be solved almost in polynomial time). In this dissertation, first, we introduce several techniques that can be used to design efficient algorithms for parameterized NP-hard problems. These techniques include branch and bound, divide and conquer, color coding and dynamic programming, iterative compression, iterative expansion and kernelization. Then we present our results about how to use these techniques to solve parameterized NP-hard problems, such as the p-path problem and the pd-feedback vertex set problem. Especially, we designed the first algorithm of running time in form of f(k)nO(1) for the pd-feedback vertex set problem. Thus solved an outstanding open problem, i.e. if the pd-feedback vertex set problem is FPT. Finally, we will introduce how to use parameterized algorithm techniques to solve the signaling pathway problem and the motif finding problem from bioinformatics.

We provide a unifying projection-based framework for structure-preserving interpolatory model reduction of parameterized linear dynamical systems, i.e., systems having a structured dependence on parameters that we wish to retain in the reduced-order model. The parameter dependence may be linear or nonlinear and is retained in the reduced-order model. Moreover, we are able to give conditions under which the gradient and Hessian of the system response with respect to the system parameters is matched in the reduced-order model. We provide a systematic approach built on established interpolatory $\mathcal{H}_2$ optimal model reduction methods that will produce parameterized reduced-order models having high fidelity throughout a parameter range of interest. For single input/single output systems with parameters in the input/output maps, we provide reduced-order models that are \emph{optimal} with respect to an $\mathcal{H}_2\otimes\mathcal{L}_2$ joint error measure. The capabilities of these approaches are illustrated by several numerical examples from technical applications.

In recent years, there has been much advancement in the area of verification of infinite-state systems. A system can have an infinite state-space due to unbounded data structures such as counters, clocks, stacks, queues, etc. It may also be infinite-state due to parameterization, i.e., the possibility of having an arbitrary number of components in the system. For parameterized systems, we are interested in checking correctness of all the instances in one verification step. In this thesis, we consider systems which contain both sources of infiniteness, namely: (a) real-valued clocks and (b) parameterization. More precisely, we consider two models: (a) the timed Petri net (TPN) model, which is an extension of the classical Petri net model; and (b) the timed network (TN) model in which an arbitrary number of timed automata run in parallel. We consider verification of safety properties for timed Petri nets using forward analysis. Since forward analysis is necessarily incomplete, we provide a semi-algorithm augmented with an acceleration technique in order to make it terminate more often on practical examples. Then we consider a number of problems which are generalisations of the corresponding ones for timed automata and Petri nets. For instance, we consider zenoness where we check the existence of an infinite computation with a finite duration. We also consider two variants of boundedness problem: syntactic boundedness in which both live and dead tokens are considered and semantic boundedness where only live tokens are considered. We show that the former problem is decidable while the latter is not. Finally, we show undecidability of LTL model checking both for dense and discrete timed Petri nets. Next we consider timed networks. We show undecidability of safety properties in case each component is equipped with two or more clocks. This result contrasts previous decidability result for the case where each component has a single clock. Also ,we show that the problem is decidable when clocks range over the discrete time domain. This decidability result holds when the processes have any finite number of clocks. Furthermore, we outline the border between decidability and undecidability of safety for TNs by considering several syntactic and semantic variants.

In this thesis we propose general and simple methods for automatic verification of parameterized systems. These are systems consisting of an arbitrary number of identical processes or components. The number of processes defines the size of the system. A parameterized system may be regarded as an infinite family of instances, namely one for each size. The aim is to perform a parameterized verification, i.e. to verify that behaviors produced by all instances, regardless of their size, comply with some safety or liveness property. In this work, we describe three approaches to parameterized verification. First, we extend the Regular Model Checking framework to systems where components are organized in tree-like structures. For such systems, we give a methodology for computing the set of reachable configurations (used to verify safety properties) and the transitive closure (used to verify liveness properties). Next, we introduce a methodology allowing the verification of safety properties for a large class of parameterized systems. We focus on systems where components are organized in linear arrays and manipulate variables or arrays of variables ranging over bounded or numerical domains. We perform backwards reachability analysis on a uniform over-approximation of the parameterized system at hand. Finally, we suggest a new approach that enables us to reduce the verification of termination under weak fairness conditions to a reachability analysis for systems with simple commutativity properties. The idea is that reachability calculations (associated with safety) are usually less expensive then termination (associated with liveness). This idea can also be used for other transition systems and not only those induced by parameterized systems.

Both the maximum agreement forest problem and the multicut on trees problem are NP-hard, thus cannot be solved efficiently if P /=NP. The maximum agreement forest problem was motivated in the study of evolution trees in bioinformatics, in which we are given two leaf-labeled trees and are asked to find a maximum forest that is a subgraph of both trees. The multicuton trees problem has applications in networks, in which we are given a forest and a set of pairs of termianls and are asked to find a cut that separates all pairs of terminals. We develop combinatorial and algorithmic techniques that lead to improved parameterized algorithms, approximation algorithms, and kernelization algorithms for these problems. For the maximum agreement forest problem, we proceed from the bottommost level of trees and extend solutions to whole trees. With this technique, we show that the maxi- mum agreement forest problem is fixed-parameterized tractable in general trees, resolving an open problem in this area. We also provide the first constant ratio approximation algorithm for the problem in general trees. For the multicut on trees problem, we take a new look at the problem through the eyes of vertex cover problem. This connection allows us to develop an kernelization algorithm for the problem, which gives an upper bound of O(k3) on the kernel size, significantly improving the previous best upper bound O(k6). We further exploit this connection to give a parameterized algorithm for the problem that runs in time O∗ (1.62k), thus improving the previous best algorithm of running time O∗ (2k). In the protein complex prediction problem, which comes directly from the study of bioinformatics, we are given a protein-protein interaction network, and are asked to find dense regions in this graph. We formulate this problem as a graph clustering problem and develop an algorithm to refine the results for identifying protein complexes. We test our algorithm on yeast protein- protein interaction networks, and we show that our algorithm is able to identify complexes more accurately than other existing algorithms.

Les décompositions de graphes, lorsqu’elles sont de petite largeur, sont souvent utilisées pour résoudre plus efficacement des problèmes étant difficiles dans le cas de graphes quelconques. Dans ce travail de thèse, nous nous intéressons aux limites liées à ces décompositions, et à la construction d’obstructions certifiant leur grande largeur. Dans une première partie, nous donnons un algorithme généralisant et unifiant la construction d’obstructions pour différentes largeurs de graphes, en temps XP lorsque paramétré par la largeur considérée. Nous obtenons en particulier le premier algorithme permettant de construire efficacement une obstruction à la largeur arborescente en temps O(ntw+4). La seconde partie de notre travail porte sur l’étude du problème ENSEMBLE [σ, ρ]-DOMINANT, une généralisation des problèmes de domination sur les graphes et caractérisée par deux ensembles d’entiers σ et ρ. Les diverses études de ce problème apparaissant dans la littérature concernent uniquement les cas ou le problème est FPT, lorsque paramétré par la largeur arborescente. Nous montrons que ce problème ne l’est pas toujours, et que pour certains cas d’ensembles σ et ρ, il devient W[1]-difficile lorsque paramétré par la largeur arborescente. Dans la dernière partie, nous étudions la complexité d’un nouveau problème de coloration appelé k-COLORATION ADDITIVE, combinant théorie des graphes et théorie des nombres. Nous montrons que ce nouveau problème est NP-complet pour tout k ≥ 4 fixé, tandis qu’il peut être résolu en temps polynomial sur les arbres pour k quelconque et non fixé. / Graphs decompositions of small width are usually used to solve efficiently problems which are difficult in general. In this thesis, we focus on some limits of these decompositions, and the construction of some obstructions certifying a large width. First, we give a generic algorithm unifying obstructions’ construction for several graph widths, in XP time when parameterized by the considered width. In particular, it gives the first algorithm computing efficiently an obstruction to tree-width in time O(ntw+4). Secondly, we study the parameterized complexity of [σ, ρ]-DOMINATING SET, a generalization of some domination problems characterized by two sets of integers σ and ρ. All known studies focused only on cases where this problem is FPT when parameterized by tree-width. In this work, we show that there are some cases where the problem is no longer FPT, and become W[1]-hard instead. Finally, we study the computational complexity of a new coloration problem, named k-ADDITIVE COLORING, which combines both graph theory and number theory. We show that this new problem is NP-complete for any fixed number k ≥ 4, while it can be solved in polynomial time on trees for any k.

This study investigates the global stiffness of a timer frame structure under wind loading using the finite element method by creating parameterized script files. Of key interest was the accuracy of the global stiffness determined from an adaptive 3D beam model in comparison to a 2D beam model and, the stiffness of a 3D beam model when subjected to different types of bracing in the presence of internal bracing provided by a lift shaft structure. Investigation of contact forces on the surfaces between the fastener and the timber at the connection was carried out and a design check for the specified bolts shear capacity done with respect to Eurocode 5. A 3D adaptive connection was created for a 2D frame model and the stiffness of the structure was studied. A comparison of the maximum displacement of the structure in the x direction, under the same wind loading, spring stiffness and boundary conditions, with a 2D beam structure without the adaptive connection initially showed a difference in the displacement. This implied that the rotational stiffness in the beam model was greater than that of the adaptive connection created. Therefore after altering the rotational stiffness of the beam model to achieve similar displacement as in the adaptive model, the rotational stiffness of the created connection was found to be 33.4 · 106Nm. The study also determined the contact forces generated at the surfaces between the fasteners and the timber using the finite element method to integrate over the surfaces and calculate the forces. The results were generated using the History Output in the step module. The only disadvantage of acquiring the contact forces was that, the contact surface simulation caused larger run times for the model to complete the time step. For the adaptive model it took 18 hours to complete each step. Further investigation into the stiffness of a 3D frame structure was conducted. The model of the 3D structure was created by a parameterized script which makes it easy to change input variables such as number of internal walls, geometry in x-z-plane, number of storeys, cross-sectional dimensions, material properties number of diagonals and location of diagonals. A variety of models with different conditions was analyzed. This showed that stiffness has a major impact on the magnitude of reaction forces and displacements.