Catálogo de publicaciones - libros

Microarray experiments help researches to construct the structure of gene regulatory networks, i.e., networks representing relationships among different genes. Filter and knowledge extraction processes are necessary in order to handle the huge amount of data produced by microarray technologies. We propose regression trees techniques as a method to identify gene networks. Regression trees are a very useful technique to estimate the numerical values for the target outputs. They are very often more precise than linear regression models because they can adjust different linear regressions to separate areas of the search space. In our approach, we generate a single regression tree for each genes from a set of genes, taking as input the remaining genes, to finally build a graph from all the relationships among output and input genes. In this paper, we will simplify the approach by setting an only seed, the gene ARN1, and building the graph around it. The final model might gives some clues to understand the dynamics, the regulation or the topology of the gene network from one (or several) seeds, since it gathers relevant genes with accurate connections. The performance of our approach is experimentally tested on the yeast Saccharomyces cerevisiae dataset (Rosetta compendium).

DNA sequence is an important determinant of the positioning, stability, and activity of nucleosome, yet the molecular basis of these remains elusive. Positioned nucleosomes are believed to play an important role in transcriptional regulation and for the organization of chromatin in cell nuclei. After completing the genome project of many organisms, sequence mining received considerable and increasing attention. Many works devoted a lot of effort to detect the periodicity in DNA sequences, namely, the DNA segments that wrap the Histone protein. In this paper, we describe and apply a dynamic periodicity detection algorithm to discover periodicity in DNA sequences. Our algorithm is based on suffix tree as the underlying data structure. The proposed approach considers the periodicity of alternative substrings, in addition to considering dynamic window to detect the periodicity of certain instances of substrings. We demonstrate the applicability and effectiveness of the proposed approach by reporting test results on three data sets.

We apply learning vector quantization to the analysis of tiling microarray data. As an example we consider the classification of genomic probes as intronic or exonic. Training is based on the current annotation of the genome. Relevance learning techniques are used to weight and select features according to their importance for the classification. Among other findings, the analysis suggests that correlations between the perfect match intensity of a particular probe and its neighbors are highly relevant for successful exon identification.

Much work has been done to identify species-specific proteins in sequenced genomes and hence to determine their function. We assumed that such proteins have specific physico-chemical properties that will discriminate them from proteins in other species. In this paper, we examine the validity of this assumption by comparing proteins and their properties from different bacterial species using Support Vector Machines (SVM). We show that by training on selected protein sequence properties, SVMs can successfully discriminate between proteins of different species. This finding takes us a step closer to inferring the functional characteristics of these proteins.

This work tries to go a step further in the development of methods based on automatic learning techniques to parse and interpret data relating to cognitive decline (CD). There have been studied the neuropsychological tests of 267 consultations made over 30 patients by the Alzheimer’s Patient Association of Gran Canaria in 2005. The Sanger neural network adaptation for missing values treatment has allowed making a Principal Components Analysis (PCA) on the successfully obtained data. The results show that the first three obtained principal components are able to extract information relating to functional, cognitive and instrumental sintomatology, respectively, from the test. By means of these techniques, it is possible to develop tools that allow physicians to quantify, view and make a better pursuit of the sintomatology associated to the cognitive decline processes, contributing to a better knowledge of these ones.

False sharing is a result of co-location of unrelated data in the same unit of memory coherency, and is one source of unnecessary overhead being of no help to keep the memory coherency in multiprocessor systems. Moreover, the damage caused by false sharing becomes large in proportion to the granularity of memory coherency. To reduce false sharing in page-based DSM systems, it is necessary to allocate unrelated data objects that have different access patterns into the separate shared pages. In this paper we propose , shortly . SCSTallocator expects that the data objects requested from the different call-sites may have different access patterns in the future. So SCSTallocator places each data object requested from the different call-sites into the separate shared pages, and consequently data objects that have the same call-site are likely to get together into the same shared pages. At the same time SCSTallocator places each data object that has different size into different shared pages to prohibit the different-sized objects from being allocated to the same shared page. We use execution-driven simulation of real parallel applications to evaluate the effectiveness of our SCSTallocator. Our observations show that our SCSTallocator outperforms the existing dynamic shared memory allocators. By combining the two existing allocation technique, we can reduce a considerable amount of false sharing misses.

In this paper, a hybrid social model of econometric model and social influence model is proposed to settle the problem in power resources management. And, a hybrid society simulation platform based on the proposed model, termed Residential Electric Power Consumption Multi-Agent Systems (RECMAS), is designed to simulate residential power consumption by multi-agent. RECMAS is composed of consumer agent, power supplier agent, and policy maker agent. It provides the policy makers with an additional tool to evaluate power price policies and public education campaigns in different scenarios. Through an influenced diffusion mechanism, RECMAS can simulate the factors affecting power consumption, and the ones associated with public education campaigns. The application of the method for simulating residential power consumption in China is presented.

In this paper a new type of interface agent will be presented. This agent is oriented to model systems for human based computation. This kind of computation, that we consider a logical extension of intelligent agent paradigm, emerges as valid approach for the resolution of complex problems.

Firstly an study of the state of the art of interface agents will be review. Next, human based computation will be defined and we will see how is necessary to extend the current typology of interface agents to model this new kind of computation. In addition, a new type of interface agent, oriented to model this type of computational system, will be presented. Finally, two of the most representative applications of human based computation will be specified using this new typology.

In multi-agent systems, complex and dynamic interactions often emerge among individual agents. The ability of each agent to learn adaptively is therefore important for them to survive in such changing environment. In this paper, we consider the effects of neighbourhood structure on the evolution of cooperative behaviour in the N-Player Iterated Prisoner’s Dilemma (NIPD). We simulate the NIPD as a bidding game on a two dimensional grid-world, where each agent has to bid against its neighbours based on a chosen game strategy. We conduct experiments with three different types of neighbourhood structures, namely the triangular neighbourhood structure, the rectangular neighbourhood structure and the random pairing structure. Our results show that cooperation does emerge under the triangular neighbourhood structure, but defection prevails under the rectangular neighbourhood structure as well as the random pairing structure.

The present work continues a longer research in the field of flexible transportation services and the design of an agent system devoted to the planning, scheduling and control of trips under such a domain. In particular, this paper focuses in the design and development of the interface agents present in the system by following an agent development methodology named PASSI. The interface agent devoted to interaction with the customers is explained in detail and its prototype is shown.