Network arrivals are often modeled as Poisson processes for analytic simplicity, even though a number of traffic studies have shown that packet interarrivals are not exponentially distributed. We evaluate 24 wide-area traces, investigating a number of wide-area TCP arrival processes (session and connection arrivals, FTP data connection arrivals within FTP sessions, and TELNET packet arrivals) to determine the error introduced by modeling them using Poisson processes. We find that user-initiated TCP session arrivals, such as remotelogin and file-transfer, are well-modeled as Poisson processes with fixed hourly rates, but that other connection arrivals deviate considerably from Poisson; that modeling TELNET packet interarrivals as exponential grievously underestimates the burstiness of TELNET traffic, but using the empirical Tcplib [Danzig et al, 1992] interarrivals preserves burstiness over many time scales; and that FTP data connection arrivals within FTP sessions come bunched into “connection bursts,” the largest of which are so large that they completely dominate FTP data traffic. Finally, we offer some results regarding how our findings relate to the possible self-similarity of widearea traffic.

In order to understand the functioning of organisms on the molecular level, we need to know which genes are expressed, when and where in the organism, and to which extent. The regulation of gene expression is achieved through genetic regulatory systems structured by networks of interactions between DNA, RNA, proteins, and small molecules. As most genetic regulatory networks of interest involve many components connected through interlocking positive and negative feedback loops, an intuitive understanding of their dynamics is hard to obtain. As a consequence, formal methods and computer tools for the modeling and simulation of genetic regulatory networks will be indispensable. This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations, ordinary and partial differential equations, qualitative differential equations, stochastic equations, and rule-based formalisms. In addition, the paper discusses how these formalisms have been used in the simulation of the behavior of actual regulatory systems. Key words: genetic regulatory networks, mathematical modeling, simulation, computational biology.

We review the recent fast progress in statistical physics of evolving networks. Interest has focused mainly on the structural properties of random complex networks in communications, biology, social sciences and economics. A number of giant artificial networks of such a kind came into existence recently. This opens a wide field for the study of their topology, evolution, and complex processes occurring in them. Such networks possess a rich set of scaling properties. A number of them are scale-free and show striking resilience against random breakdowns. In spite of large sizes of these networks, the distances between most their vertices are short — a feature known as the “smallworld” effect. We discuss how growing networks self-organize into scale-free structures and the role of the mechanism of preferential linking. We consider the topological and structural properties of evolving networks, and percolation in these networks. We present a number of models demonstrating the main features of evolving networks and discuss current approaches for their simulation and analytical study. Applications of the general results to particular networks in Nature are discussed. We demonstrate the generic connections of the network growth processes with the general problems

c biological data sets. The ability to adequately solve the inverse problem may enable in-depth analysis of complex dynamic systems in biology and other fields. Binary models of genetic networks Virtually all molecular and cellular signaling processes involve several inputs and outputs, forming a complex feedback network. The information for the construction and maintenance of this signaling system is stored in the genome. The DNA sequence codes for the structure and molecular dynamics of RNA and proteins, in turn determining biochemical recognition or signaling processes. The regulatory molecules that control the expression of genes are themselves the products of other genes. Effectively, genes turn each other on and off within a proximal genetic network of transcriptional regulators (Somogyi and Sniegoski, 1996). Furthermore, complex webs involving various intra- and extracellular signaling systems on the one hand depend on the expression of the genes that encode them, and on the

Motivation: Our goal is to construct a model for genetic regulatory networks such that the model class: (i ) incorporates rule-based dependencies between genes; (ii ) allows the systematic study of global network dynamics; (iii ) is able to cope with uncertainty, both in the data and the model selection; and (iv ) permits the quantification of the relative influence and sensitivity of genes in their interactions with other genes.

motivation: Advances in molecular biological, analytical and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using highthroughput gene expression assays, we are able to measure the output of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various aspects of clustering, ranging from distance measures to clustering algorithms and multiple-cluster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e. who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting and bioengineering.

Evolutionary computation has started to receive significant attention during the last decade, although the origins can be traced back to the late 1950s. This article surveys the history as well as the current state of this rapidly growing field. We describe the purpose, the general structure and the working principles of different approaches, including genetic algorithms (GA) (with links to genetic programming (GP) and classifier systems (CS)), evolution strategies (ES), and evolutionary programming (EP), by analysis and comparison of their most important constituents (i.e., representations, variation operators, reproduction and selection mechanism). Finally, we give a brief overview on the manifold of application domains, although this necessarily must remain incomplete.

We propose a theory of asset pricing based on heterogeneous agents who continually adapt their expectations to the market that these expectations aggregatively create. And we explore the implications of this theory computationally using our Santa Fe artificial stock market. Asset markets, we argue, have a recursive nature in that agents ’ expectations are formed on the basis of their anticipations of other agents ’ expectations, which precludes expectations being formed by deductive means. Instead traders continually hypothesize—continually explore—expectational models, buy or sell on the basis of those that perform best, and confirm or discard these according to their performance. Thus individual beliefs or expectations become endogenous to the market, and constantly compete within an ecology of others ’ beliefs or expectations. The ecology of beliefs co-evolves over time. Computer experiments with this endogenous-expectations market explain one of the more striking puzzles in finance: that market traders often believe in such concepts as technical trading, “market psychology, ” and bandwagon effects, while academic theorists believe in market efficiency and a lack of speculative opportunities. Both views, we show, are correct, but within different regimes. Within a regime where investors explore alternative expectational models at a low rate, the market settles into the rational-

A measure of search difficulty, fitness distance correlation (FDC), is introduced and examined in relation to genetic algorithm (GA) performance. In many cases, this correlation can be used to predict the performance of a GA on problems with known global maxima. It correctly classifies easy deceptive problems as easy and difficult non-deceptive problems as difficult, indicates when Gray coding will prove better than binary coding, and is consistent with the surprises encountered when GAs were used on the Tanese and royal road functions. The FDC measure is a consequence of an investigation into the connection between GAs and heuristic search. 1 INTRODUCTION A correspondence between evolutionary algorithms and heuristic state space search is developed in (Jones, 1995b). This is based on a model of fitness landscapes as directed, labeled graphs that are closely related to the state spaces employed in heuristic search. We examine one aspect of this correspondence, the relationship between...

Short abstract, isn't it? P.A.C.S. numbers 05.20, 02.50, 87.10 1 Introduction Large Numbers "...the optimal tour displayed (see Figure 6) is the possible unique tour having one arc fixed from among 10 655 tours that are possible among 318 points and have one arc fixed. Assuming that one could possibly enumerate 10 9 tours per second on a computer it would thus take roughly 10 639 years of computing to establish the optimality of this tour by exhaustive enumeration." This quote shows the real difficulty of a combinatorial optimization problem. The huge number of configurations is the primary difficulty when dealing with one of these problems. The quote belongs to M.W Padberg and M. Grotschel, Chap. 9., "Polyhedral computations", from the book The Traveling Salesman Problem: A Guided tour of Combinatorial Optimization [124]. It is interesting to compare the number of configurations of real-world problems in combinatorial optimization with those large numbers arising in Cosmol...