A large class of systems of biological and technological relevance can be described as analog networks, that is, collections of dynamical devices interconnected by links of varying strength. Some examples of analog networks are genetic regulatory networks, metabolic networks, neural networks, analog electronic circuits, and control systems. Analog networks are typically complex systems which include nonlinear feedback loops and possess temporal dynamics at different time scales. Both the synthesis and reverse engineering of analog networks are recognized as knowledge-intensive activities, for which few systematic techniques exist. In this paper we will discuss the general relevance of the analog network concept and describe an evolutionary approach to the automatic synthesis and the reverse engineering of analog networks. The proposed approach is called analog genetic encoding (AGE) and realizes an implicit genetic encoding of analog networks. AGE permits the evolution of human-competitive solutions to real-world analog network design and identification problems. This is illustrated by some examples of application to the design of electronic circuits, control systems, learning neural architectures, and the reverse engineering of biological networks.

The normalized information distance is a universal distance measure for objects of all kinds. It is based on Kolmogorov complexity and thus uncomputable, but there are ways to utilize it. First, compression algorithms can be used to approximate the Kolmogorov complexity if the objects have a string representation. Second, for names and abstract concepts, page count statistics from the World Wide Web can be used. These practical realizations of the normalized information distance can then be applied to machine learning tasks, expecially clustering, to perform feature-free and parameter-free data mining. This chapter discusses the theoretical foundations of the normalized information distance and both practical realizations. It presents numerous examples of successful real-world applications based on these distance measures, ranging from bioinformatics to music clustering to machine translation.

Approximation of the optimal two-part MDL code for given data, through successive monotonically length-decreasing two-part MDL codes, has the following properties: (i) computation of each step may take arbitrarily long; (ii) we may not know when we reach the optimum, or whether we will reach the optimum at all; (iii) the sequence of models generated may not monotonically improve the goodness of fit; but (iv) the model associated with the optimum has (almost) the best goodness of fit. To express the practically interesting goodness of fit of individual models for individual data sets we have to rely on Kolmogorov complexity.

Semantic networks qualify the meaning of an edge relating any two vertices. Determining which vertices are most "central" in a semantic network is difficult because one relationship type may be deemed subjectively more important than another. For this reason, research into semantic network metrics has focused primarily on context-based rankings (i.e. user prescribed contexts). Moreover, many of the current semantic network metrics rank semantic associations (i.e. directed paths between two vertices) and not the vertices themselves. This article presents a framework for calculating semantically meaningful primary eigenvector-based metrics such as eigenvector centrality and PageRank in semantic networks using a modified version of the random walker model of Markov chain analysis. Random walkers, in the context of this article, are constrained by a grammar, where the grammar is a user defined data structure that determines the meaning of the final vertex ranking. The ideas in this article are presented within the context of the Resource Description Framework (RDF) of the Semantic Web initiative.

The purpose of this paper is to present a new approach to ecological model calibration -- an agent-based software. This agent works on three stages: 1- It builds a matrix that synthesizes the inter-variable relationships; 2- It analyses the steady-state sensitivity of different variables to different parameters; 3- It runs the model iteratively and measures model lack of fit, adequacy and reliability. Stage 3 continues until some convergence criteria are attained. At each iteration, the agent knows from stages 1 and 2, which parameters are most likely to produce the desired shift on predicted results.

Minimizing the rank of a matrix subject to constraints is a challenging problem that arises in many applications in control theory, machine learning, and discrete geometry. This class of optimization problems, known as rank minimization, is NP-HARD, and for most practical problems there are no efficient algorithms that yield exact solutions. A popular heuristic algorithm replaces the rank function with the nuclear norm--equal to the sum of the singular values--of the decision variable. In this paper, we provide a necessary and sufficient condition that quantifies when this heuristic successfully finds the minimum rank solution of a linear constraint set. We additionally provide a probability distribution over instances of the affine rank minimization problem such that instances sampled from this distribution satisfy our conditions for success with overwhelming probability provided the number of constraints is appropriately large. Finally, we give empirical evidence that these probabilistic bounds provide accurate predictions of the heuristic's performance in non-asymptotic scenarios.

The paper presents a study of local search heuristics in general and variable neighborhood search in particular for the resolution of an assignment problem studied in the practical work of universities. Here, students have to be assigned to scientific topics which are proposed and supported by members of staff. The problem involves the optimization under given preferences of students which may be expressed when applying for certain topics. It is possible to observe that variable neighborhood search leads to superior results for the tested problem instances. One instance is taken from an actual case, while others have been generated based on the real world data to support the analysis with a deeper analysis. An extension of the problem has been formulated by integrating a second objective function that simultaneously balances the workload of the members of staff while maximizing utility of the students. The algorithmic approach has been prototypically implemented in a computer system. One important aspect in this context is the application of the research work to problems of other scientific institutions, and therefore the provision of decision support functionalities.

In the current paper, we present an optimization system solving multi objective production scheduling problems (MOOPPS). The identification of Pareto optimal alternatives or at least a close approximation of them is possible by a set of implemented metaheuristics. Necessary control parameters can easily be adjusted by the decision maker as the whole software is fully menu driven. This allows the comparison of different metaheuristic algorithms for the considered problem instances. Results are visualized by a graphical user interface showing the distribution of solutions in outcome space as well as their corresponding Gantt chart representation. The identification of a most preferred solution from the set of efficient solutions is supported by a module based on the aspiration interactive method (AIM). The decision maker successively defines aspiration levels until a single solution is chosen. After successfully competing in the finals in Ronneby, Sweden, the MOOPPS software has been awarded the European Academic Software Award 2002 (http://www.bth.se/llab/easa_2002.nsf)

The article proposes a heuristic approximation approach to the bin packing problem under multiple objectives. In addition to the traditional objective of minimizing the number of bins, the heterogeneousness of the elements in each bin is minimized, leading to a biobjective formulation of the problem with a tradeoff between the number of bins and their heterogeneousness. An extension of the Best-Fit approximation algorithm is presented to solve the problem. Experimental investigations have been carried out on benchmark instances of different size, ranging from 100 to 1000 items. Encouraging results have been obtained, showing the applicability of the heuristic approach to the described problem.

The article presents a local search approach for the solution of timetabling problems in general, with a particular implementation for competition track 3 of the International Timetabling Competition 2007 (ITC 2007). The heuristic search procedure is based on Threshold Accepting to overcome local optima. A stochastic neighborhood is proposed and implemented, randomly removing and reassigning events from the current solution. The overall concept has been incrementally obtained from a series of experiments, which we describe in each (sub)section of the paper. In result, we successfully derived a potential candidate solution approach for the finals of track 3 of the ITC 2007.