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.

A pattern database (PDB) is a heuristic function implemented as a lookup table that stores the lengths of optimal solutions for subproblem instances. Standard PDBs have a distinct entry in the table for each subproblem instance. In this paper we investigate compressing PDBs by merging several entries into one, thereby allowing the use of PDBs that exceed available memory in their uncompressed form. We introduce a number of methods for determining which entries to merge and discuss their relative merits. These vary from domain-independent approaches that allow any set of entries in the PDB to be merged, to more intelligent methods that take into account the structure of the problem. The choice of the best compression method is based on domain-dependent attributes. We present experimental results on a number of combinatorial problems, including the four-peg Towers of Hanoi problem, the sliding-tile puzzles, and the Top-Spin puzzle. For the Towers of Hanoi, we show that the search time can be reduced by up to three orders of magnitude by using compressed PDBs compared to uncompressed PDBs of the same size. More modest improvements were observed for the other domains.

Data mining allows the exploration of sequences of phenomena, whereas one usually tends to focus on isolated phenomena or on the relation between two phenomena. It offers invaluable tools for theoretical analyses and exploration of the structure of sentences, texts, dialogues, and speech. We report here the results of an attempt at using it for inspecting sequences of verbs from French accounts of road accidents. This analysis comes from an original approach of unsupervised training allowing the discovery of the structure of sequential data. The entries of the analyzer were only made of the verbs appearing in the sentences. It provided a classification of the links between two successive verbs into four distinct clusters, allowing thus text segmentation. We give here an interpretation of these clusters by comparing the statistical distribution of independent semantic annotations.

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.

Wikipedia provides a semantic network for computing semantic relatedness in a more structured fashion than a search engine and with more coverage than WordNet. We present experiments on using Wikipedia for computing semantic relatedness and compare it to WordNet on various benchmarking datasets. Existing relatedness measures perform better using Wikipedia than a baseline given by Google counts, and we show that Wikipedia outperforms WordNet on some datasets. We also address the question whether and how Wikipedia can be integrated into NLP applications as a knowledge base. Including Wikipedia improves the performance of a machine learning based coreference resolution system, indicating that it represents a valuable resource for NLP applications. Finally, we show that our method can be easily used for languages other than English by computing semantic relatedness for a German dataset.

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.

This paper describes experiments on identifying the language of a single name in isolation or in a document written in a different language. A new corpus has been compiled and made available, matching names against languages. This corpus is used in a series of experiments measuring the performance of general language models and names-only language models on the language identification task. Conclusions are drawn from the comparison between using general language models and names-only language models and between identifying the language of isolated names and the language of very short document fragments. Future research directions are outlined.

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.

We present a new local approximation algorithm for computing Maximum a Posteriori (MAP) and log-partition function for arbitrary exponential family distribution represented by a finite-valued pair-wise Markov random field (MRF), say $G$. Our algorithm is based on decomposition of $G$ into {\em appropriately} chosen small components; then computing estimates locally in each of these components and then producing a {\em good} global solution. We show that if the underlying graph $G$ either excludes some finite-sized graph as its minor (e.g. Planar graph) or has low doubling dimension (e.g. any graph with {\em geometry}), then our algorithm will produce solution for both questions within {\em arbitrary accuracy}. We present a message-passing implementation of our algorithm for MAP computation using self-avoiding walk of graph. In order to evaluate the computational cost of this implementation, we derive novel tight bounds on the size of self-avoiding walk tree for arbitrary graph. As a consequence of our algorithmic result, we show that the normalized log-partition function (also known as free-energy) for a class of {\em regular} MRFs will converge to a limit, that is computable to an arbitrary accuracy.