The field of metaheuristics for the application to combinatorial optimization problems is a rapidly growing field of research. This is due to the importance of combinatorial optimization problems for the scientific as well as the industrial world. We give a survey of the nowadays most important metaheuristics from a conceptual point of view. We outline the different components and concepts that are used in the different metaheuristics in order to analyze their similarities and differences. Two very important concepts in metaheuristics are intensification and diversification. These are the two forces that largely determine the behaviour of a metaheuristic. They are in some way contrary but also complementary to each other. We introduce a framework, that we call the I&D frame, in order to put different intensification and diversification components into relation with each other. Outlining the advantages and disadvantages of different metaheuristic approaches we conclude by pointing out the importance of hybridization of metaheuristics as well as the integration of metaheuristics and other methods for optimization.

Recently, there has been much interest in reverse engineering genetic networks from time series data. In this paper, we show that most of the proposed discrete time models — including the boolean network model [Kau93, SS96], the linear model of D’haeseleer et al. [DWFS99], and the nonlinear model of Weaver et al. [WWS99] — are all special cases of a general class of models called Dynamic Bayesian Networks (DBNs). The advantages of DBNs include the ability to model stochasticity, to incorporate prior knowledge, and to handle hidden variables and missing data in a principled way. This paper provides a review of techniques for learning DBNs. Keywords: Genetic networks, boolean networks, Bayesian networks, neural networks, reverse engineering, machine learning. 1

In order to cope with the large amounts of data that have become available in genomics, mathematical tools for the analysis of networks of interactions between genes, proteins, and other molecules are indispensable. We present a method for the qualitative simulation of genetic regulatory networks, based on a class of piecewise-linear (PL) differential equations that has been well-studied in mathematical biology. The simulation method is well-adapted to state-of-the-art measurement techniques in genomics, which often provide qualitative and coarsegrained descriptions of genetic regulatory networks. Given a qualitative model of a genetic regulatory network, consisting of a system of PL differential equations and inequality constraints on the parameter values, the method produces a graph of qualitative states and transitions between qualitative states, summarizing the qualitative dynamics of the system. The qualitative simulation method has been implemented in Java in the computer tool Genetic Network Analyzer.

Behavior-oriented AI is a scientific discipline that studies how behavior of agents emerges and becomes intelligent and adaptive. Success of the field is defined in terms of success in building physical agents that are capable of maximising their own self-preservation in interaction with a dynamically changing environment. The paper addresses this artificial life route towards artificial intelligence and reviews some of the results obtained so far. 1 Official reference: Steels, L. (1994) The artificial life roots of artificial intelligence. Artificial Life Journal, Vol 1,1. MIT Press, Cambridge. 1 Introduction For several decades, the field of Artificial Intelligence has been pursuing the study of intelligent behavior using the methodology of the artificial [104]. But the focus of this field, and hence the successes, have mostly been on higher order cognitive activities such as expert problem solving. The inspiration for AI theories has mostly come from logic and the cognitive...

Motivation: Bayesian networks have been applied to infer genetic regulatory interactions from microarray gene expression data. This inference problem is particularly hard in that interactions between hundreds of genes have to be learned from very small data sets, typically containing only a few dozen time points during a cell cycle. Most previous studies have assessed the inference results on real gene expression data by comparing predicted genetic regulatory interactions with those known from the biological literature. This approach is controversial due to the absence of known gold standards, which renders the estimation of the sensitivity and specificity, that is, the true and (complementary) false detection rate, unreliable and difficult. The objective of the present study is to test the viability of the Bayesian network paradigm in a realistic simulation study. First, gene expression data are simulated from a realistic biological network involving DNAs, mRNAs, inactive protein monomers and active protein dimers. Then, interaction networks are inferred from these data in a reverse engineering approach, using Bayesian networks and Bayesian learning with Markov chain Monte Carlo. Results: The simulation results are presented as receiver operator characteristics curves. This allows estimating the proportion of spurious gene interactions incurred for a specified target proportion of recovered true interactions. The findings demonstrate how the network inference performance varies with the training set size, the degree of inadequacy of prior assumptions, the experimental sampling strategy and the inclusion of further, sequence-based information.

One of the persistent themes in Artificial Life research is the use of co-evolutionary arms races in the development of specific and complex behaviors. However, other than Sims’s work on artificial robots, most of the work has attacked very simple games of prisoners dilemma or predator and prey. Following Tesauro’s work on TD-Gammon, we used a 4000 parameter feed-forward neural network to develop a competitive backgammon evaluation function. Play proceeds by a roll of the dice, application of the network to all legal moves, and choosing the move with the highest evaluation. However, no back-propagation, reinforcement

This paper describes an optimization-based algorithm for reconstructing a 3D model from a single, inaccurate, 2D edge-vertex graph. The graph, which serves as input for the reconstruction process, is obtained from an inaccurate freehand sketch of a 3D wireframe object. Compared with traditional reconstruction methods based on line labeling, the proposed approach is more tolerant of faults in handling both inaccurate vertex positioning and sketches with missing entities. Furthermore, the proposed reconstruction method supports a wide scope of general (manifold and non-manifold) objects containing flat and cylindrical faces. Sketches of wireframe models usually include enough information to reconstruct the complete body. The optimization algorithm is discussed, and examples from a working implementation are given.

Defining structure and detecting the emergence of complexity in nature are inherently subjective, though essential, scientific activities. Despite the difficulties, these problems can be analyzed in terms of how model-building observers infer from measurements the computational capabilities embedded in nonlinear processes. An observer’s notion of what is ordered, what is random, and what is complex in its environment depends directly on its computational resources: the amount of raw measurement data, of memory, and of time available for estimation and inference. The discovery of structure in an environment depends more critically and subtlely, though, on how those resources are organized. The descriptive power of the observer’s chosen (or implicit) computational model class, for example, can be an overwhelming determinant in finding regularity in data. This paper presents an overview of an inductive framework — hierarchical-machine reconstruction — in which the emergence of complexity is associated with the innovation of new computational model classes. Complexity metrics for detecting structure and quantifying emergence, along with an analysis of the constraints on the dynamics of innovation, are outlined. Illustrative examples are drawn from the onset of unpredictability in nonlinear systems, finitary nondeterministic processes, and

Our concepts of biology, evolution and complexity are constrained by having observed only a single instance of life, life on Earth. A truly comparative biology is needed to extend these concepts. Because we can not observe life on other planets, we are left with the alternative of creating artificial life forms on Earth. I will discuss the approach of inoculating evolution by natural selection into the medium of the digital computer. This is not a physical/chemical medium, it is a logical/informational medium. Thus these new instances of evolution are not subject to the same physical laws as organic evolution (e.g., the laws of thermodynamics), and therefore exist in what amounts to another universe, governed by the "physical laws" of the logic of the computer. This exercise gives us a broader perspective on what evolution is and what it does. An evolutionary approach to synthetic biology consists of inoculating the process of evolution by natural selection into an artificial medium. E...

The evolution of a population can be guided by phenotypic traits acquired by members of that population during their lifetime. This phenomenon, known as the Baldwin Effect, can speed the evolutionary process as traits that are initially acquired become genetically specified in later generations. This paper presents conditions under which this genetic assimilation can take place. As well as the benefits that lifetime adaptation can give a population, there may be a cost to be paid for that adaptive ability. It is the evolutionary trade-off between these costs and benefits that provides the selection pressure for acquired traits to become genetically specified. It is also noted that genotypic space, in which evolution operates, and phenotypic space, on which adaptive processes (such as learning) operate, are, in general, of a different nature. To guarantee an acquired characteristic can become genetically specified, then these spaces must have the property of neighbourhood correlation wh...