Many systems can be described in terms of networks of discrete elements and their various relationships to one another. A semantic network, or multi-relational network, is a directed labeled graph consisting of a heterogeneous set of entities connected by a heterogeneous set of relationships. Semantic networks serve as a promising general-purpose modeling substrate for complex systems. Various standardized formats and tools are now available to support practical, large-scale semantic network models. First, the Resource Description Framework (RDF) offers a standardized semantic network data model that can be further formalized by ontology modeling languages such as RDF Schema (RDFS) and the Web Ontology Language (OWL). Second, the recent introduction of highly performant triple-stores (i.e. semantic network databases) allows semantic network models on the order of $10^9$ edges to be efficiently stored and manipulated. RDF and its related technologies are currently used extensively in the domains of computer science, digital library science, and the biological sciences. This article will provide an introduction to RDF/RDFS/OWL and an examination of its suitability to model discrete element complex systems.

Previous work in social network analysis (SNA) has modeled the existence of links from one entity to another, but not the attributes such as language content or topics on those links. We present the Author-Recipient-Topic (ART) model for social network analysis, which learns topic distributions based on the direction-sensitive messages sent between entities. The model builds on Latent Dirichlet Allocation (LDA) and the Author-Topic (AT) model, adding the key attribute that distribution over topics is conditioned distinctly on both the sender and recipient---steering the discovery of topics according to the relationships between people. We give results on both the Enron email corpus and a researcher's email archive, providing evidence not only that clearly relevant topics are discovered, but that the ART model better predicts people's roles and gives lower perplexity on previously unseen messages. We also present the Role-Author-Recipient-Topic (RART) model, an extension to ART that explicitly represents people's roles.

The subcellular location of a protein can provide valuable information about its function. With the rapid increase of sequenced genomic data, the need for an automated and accurate tool to predict subcellular localization becomes increasingly important. Many efforts have been made to predict protein subcellular localization. This paper aims to merge the artificial neural networks and bioinformatics to predict the location of protein in yeast genome. We introduce a new subcellular prediction method based on a backpropagation neural network. The results show that the prediction within an error limit of 5 to 10 percentage can be achieved with the system.

Current methods of routing are based on network information in the form of routing tables, in which routing protocols determine how to update the tables according to the network changes. Despite the variability of data in routing tables, node addresses are constant. In this paper, we first introduce the new concept of variable addresses, which results in a novel framework to cope with routing problems using heuristic solutions. Then we propose a heuristic routing mechanism based on the application of genes for determination of network addresses in a variable address network and describe how this method flexibly solves different problems and induces new ideas in providing integral solutions for variety of problems. The case of ad-hoc networks is where simulation results are more supportive and original solutions have been proposed for issues like mobility.

Techniques for data-mining, latent semantic analysis, contextual search of databases, etc. have long ago been developed by computer scientists working on information retrieval (IR). Experimental scientists, from all disciplines, having to analyse large collections of raw experimental data (astronomical, physical, biological, etc.) have developed powerful methods for their statistical analysis and for clustering, categorising, and classifying objects. Finally, physicists have developed a theory of quantum measurement, unifying the logical, algebraic, and probabilistic aspects of queries into a single formalism. The purpose of this paper is twofold: first to show that when formulated at an abstract level, problems from IR, from statistical data analysis, and from physical measurement theories are very similar and hence can profitably be cross-fertilised, and, secondly, to propose a novel method of fuzzy hierarchical clustering, termed \textit{semantic distillation} -- strongly inspired from the theory of quantum measurement --, we developed to analyse raw data coming from various types of experiments on DNA arrays. We illustrate the method by analysing DNA arrays experiments and clustering the genes of the array according to their specificity.

Message passing algorithms have proved surprisingly successful in solving hard constraint satisfaction problems on sparse random graphs. In such applications, variables are fixed sequentially to satisfy the constraints. Message passing is run after each step. Its outcome provides an heuristic to make choices at next step. This approach has been referred to as `decimation,' with reference to analogous procedures in statistical physics. The behavior of decimation procedures is poorly understood. Here we consider a simple randomized decimation algorithm based on belief propagation (BP), and analyze its behavior on random k-satisfiability formulae. In particular, we propose a tree model for its analysis and we conjecture that it provides asymptotically exact predictions in the limit of large instances. This conjecture is confirmed by numerical simulations.

In this paper we present and evaluate a general framework for the design of truthful auctions for matching agents in a dynamic, two-sided market. A single commodity, such as a resource or a task, is bought and sold by multiple buyers and sellers that arrive and depart over time. Our algorithm, Chain, provides the first framework that allows a truthful dynamic double auction (DA) to be constructed from a truthful, single-period (i.e. static) double-auction rule. The pricing and matching method of the Chain construction is unique amongst dynamic-auction rules that adopt the same building block. We examine experimentally the allocative efficiency of Chain when instantiated on various single-period rules, including the canonical McAfee double-auction rule. For a baseline we also consider non-truthful double auctions populated with ``zero-intelligence plus"-style learning agents. Chain-based auctions perform well in comparison with other schemes, especially as arrival intensity falls and agent valuations become more volatile.

This paper describes a system capable of semi-automatically filling an XML template from free texts in the clinical domain (practice guidelines). The XML template includes semantic information not explicitly encoded in the text (pairs of conditions and actions/recommendations). Therefore, there is a need to compute the exact scope of conditions over text sequences expressing the required actions. We present in this paper the rules developed for this task. We show that the system yields good performance when applied to the analysis of French practice guidelines.

Real-time heuristic search methods are used by situated agents in applications that require the amount of planning per move to be independent of the problem size. Such agents plan only a few actions at a time in a local search space and avoid getting trapped in local minima by improving their heuristic function over time. We extend a wide class of real-time search algorithms with automatically-built state abstraction and prove completeness and convergence of the resulting family of algorithms. We then analyze the impact of abstraction in an extensive empirical study in real-time pathfinding. Abstraction is found to improve efficiency by providing better trading offs between planning time, learning speed and other negatively correlated performance measures.

Simulated annealing is a popular method for approaching the solution of a global optimization problem. Existing results on its performance apply to discrete combinatorial optimization where the optimization variables can assume only a finite set of possible values. We introduce a new general formulation of simulated annealing which allows one to guarantee finite-time performance in the optimization of functions of continuous variables. The results hold universally for any optimization problem on a bounded domain and establish a connection between simulated annealing and up-to-date theory of convergence of Markov chain Monte Carlo methods on continuous domains. This work is inspired by the concept of finite-time learning with known accuracy and confidence developed in statistical learning theory.