Maria Rosaria Del Sorbo

Genomic comparison using Data Mining techniques based on a possibilistic fuzzy sets model

Current copiousness of genomic information stored in biological databases [Mar Albà, M., Lee, M., Pearl, D., Shepherd, F.M.G., Martin, A.J., Orengo, N., Kellam, C.A., 2001. P. VIDA: a virus database system for the organisation of virus genome open reading frames. Nuleic Acids Res. 133-136] makes ultimately feasible the proposal for an application of knowledge management aimed to discover general rules in subcellular phenomena. The goal of this work is primarily to discover relationships between genes by microarray analysis. The tools exploited come from clustering techniques and are mainly based on Knowledge Discovery in Databases (KDD) concepts [Fayyad, U., Piatetsky-Shapiro, G., Smyth, P., 1996. From data mining to knowledge discovery in databases. AI Magazine 17(3), 37-54]. Starting from a data set, each element can be represented by a characteristic matrix, which sums up all data attributes. In this case data mining is oriented to perform a Pattern Recognition of related sequences, hidden in databases [Hand, D.J., Nicholas, A., 2005. Heard finding groups in gene expression data. J. Biomed. Biotechnol. 215-225]. Following a bottom up approach, the next refinement is to compare retrieved data to gather similar features, by dedicated clustering algorithms [Kaufman, L., Rousseeuw, P.J., 1990. Finding groups in data. An Introduction to Cluster Analysis. John Wiley & Sons, New York; Forman, G., Zhang, B., 2000. Distributed Data clustering can be efficient and exact HP. Laboratories Palo Alto HPL-2000, p. 158], driven by fuzzy logic, allowing us to perceive by intuition a common denominator for various genomic families and to anticipate likely future developments.

A Logic-based Clustering Approach for Cooperative Traffic Control Systems

Cooperative traffic control-systems have helped in the last years to extend the electronic horizon of vehicles in such a way that drivers can be informed quite in advance about any unexpected event occurring along a road. In this area, Vehicular Ad Hoc Networks (VANETs) perform information exchanges between vehicles by exploiting decentralized structures, where each vehicle is equipped with On Board Units (OBU) that allow to broadcast signals. In this paper, we revisit this communication framework by using a centralized approach, i.e., we consider a central unit for the data processing. This approach, on the one hand, facilitates the clustering process, thus obtaining the mitigation of the “broadcast storm” phenomenon (typically affecting VANETs); on the other hand, it allows the collection, management, and storage of the most relevant data concerning roads. Along the paper we evaluate the benefits of using our model, as well as we discuss on a smartphone integration.

CoTracks: A New Lossy Compression Schema for Tracking Logs Data Based on Multiparametric Segmentation

A massive diffusion of positioning devices and services, transmitting and producing spatio-temporal data, raised space complexity problems and pulled the research focus toward efficient and specific algorithms to compress these huge amount of stored or flowing data. Co Tracks algorithm has been projected for a lossy compression of GPS data, exploiting analogies between all their spatio-temporal features. The original contribution of this algorithm is the consideration of the altitude of the track, an elaboration of 3D data and a dynamic vision of the moving point, because the speed, tightly linked to the time, is supposed to be one of the significant parameters in the uniformity search. Minimum Bounding Box has been the tool employed to group data points and to generate the key points of the approximated trajectory. The compression ratio, resulting also after a further Huffman coding, appears attractively high, suggesting new interesting developments of this new technique.

SoCar: A Social Car2Car Framework to Refine Routes Information Based on Road Events and GPS

GPS-based applications make travelling easier, supplying information about routes, such as real-time traffic, Estimated Time of Arrival, faster or cheaper path. These applications exploit digital maps supplied by specific companies, often updated also thanks to user-submitted data. The aim of this work is to show an event driven system for territory mapping and monitoring, using multi-hop wireless networks, relying on C2X communication and on VANETs in general. The idea is to keep road maps up to date automatically and autonomously, exploiting a collaborative communication of events in social networking style, without the need for a centralized communication system. Moreover, it is possible to enhance standard map data introducing two more layers: an events layer, automatically built by the events detected by SoCar clients, characterized by a short life span, and a prevision area layer, derived from events layer statistics, where data point are clustered in proper spatial neighborhood. Both these layers contribute to choose the most convenient route, the events layer for the short term and the prevision area layer for the long term.

Assessing co-regulation of directly linked genes in biological networks using microarray time series analysis.

Differential expression of genes detected with the analysis of high throughput genomic experiments is a commonly used intermediate step for the identification of signaling pathways involved in the response to different biological conditions. The impact analysis was the first approach for the analysis of signaling pathways involved in a certain biological process that was able to take into account not only the magnitude of the expression change of the genes but also the topology of signaling pathways including the type of each interactions between the genes. In the impact analysis, signaling pathways are represented as weighted directed graphs with genes as nodes and the interactions between genes as edges. Edges weights are represented by a β factor, the regulatory efficiency, which is assumed to be equal to 1 in inductive interactions between genes and equal to -1 in repressive interactions. This study presents a similarity analysis between gene expression time series aimed to find correspondences with the regulatory efficiency, i.e. the β factor as found in a widely used pathway database. Here, we focused on correlations among genes directly connected in signaling pathways, assuming that the expression variations of upstream genes impact immediately downstream genes in a short time interval and without significant influences by the interactions with other genes. Time series were processed using three different similarity metrics. The first metric is based on the bit string matching; the second one is a specific application of the Dynamic Time Warping to detect similarities even in presence of stretching and delays; the third one is a quantitative comparative analysis resulting by an evaluation of frequency domain representation of time series: the similarity metric is the correlation between dominant spectral components. These three approaches are tested on real data and pathways, and a comparison is performed using Information Retrieval benchmark tools, indicating the frequency approach as the best similarity metric among the three, for its ability to detect the correlation based on the correspondence of the most significant frequency components.

M-DGPS: An Algorithm for the Post-Processing of Geodetic Tracks Based on Multiple DGPS

GPS measurements are often affected by errors. This is mainly due to the fact that GPS signals need to pass through the atmospheric layers and this gives rise to unpredictable delays. In this paper we introduce M-DGPS, a novel algorithm to post-processing correct geodetic tracks by means of data coming from multiple DGPS stations. The main idea of M-DGPS is to use a set of DGPS stations as Voronoi generators to define the area of influence of a station. The algorithm uses the error of each available station, in a weighted manner, to estimate the error of the point to be corrected. We apply M-DGPS over the RINEX data files of the GPS stations of the Neapolitan Volcanoes Continuous GPS (NeVoCGPS) network of Vesuvius Observatory to build an error dataset. We show that close stations are affected by similar errors. The correction ratio of the proposed M-DGPS, better than the DGPS standard approach, appears attractively good, suggesting interesting developments of this technique.

A SCHEME OF STRATEGIES FOR REAL-TIME WEB COLLABORATION BASED ON AJAX/COMET TECHNIQUES FOR LIVE RIA

Proposta di strategie per il real-time client/server e comunicazioni client/client assistite da server per una gestione innovativa della collaborazione multiutente. Le strategie proposte sono basate su Ajax e Comet senza installazione di plug-ins aggiunti

Analysis and Comparison of Information Theory‐based Distances for Genomic Strings

Genomic string comparison via alignment are widely applied for mining and retrieval of information in biological databases. In some situation, the effectiveness of such alignment based comparison is still unclear, e.g., for sequences with non‐uniform length and with significant shuffling of identical substrings. An alternative approach is the one based on information theory distances. Biological data information content is stored in very long strings of only four characters. In last ten years, several entropic measures have been proposed for genomic string analysis. Notwithstanding their individual merit and experimental validation, to the nest of our knowledge, there is no direct comparison of these different metrics. We shall present four of the most representative alignment‐free distance measures, based on mutual information. Each one has a different origin and expression. Our comparison involves a sort of arrangement, to reduce different concepts to a unique formalism, so as it has been possible to co...