Development of novel software tools and methods for investigating the significance of overlapping transcription factor genomic interactions

Identifying overlapping DNA binding patterns of different transcription factors is a major objective of genomic studies, but existing methods to archive large numbers of datasets in a personalised database lack sophistication and utility. To address this need, various database systems were benchmarked and a tool BiSA (Binding Sites Analyser) was developed for archiving of genomic regions and easy identification of overlap with or proximity to other regions of interest. BiSA can also calculate statistical significance of overlapping regions and can also identify genes located near binding regions of interest or genomic features near a gene or locus of interest. BiSA was populated with >1000 datasets from previously published genomic studies describing transcription factor binding sites and histone modifications. Using BiSA, the relationships between binding sites for a range of transcription factors were analysed and a number of statistically significant relationships were identified. This included an extensive comparison of estrogen receptor alpha (ERα) and progesterone receptor (PR) in breast cancer cells, which revealed a statistically significant functional relationship at a subset of sites. In summary, the BiSA comprehensive knowledge base contains publicly available datasets describing transcription factor binding sites and epigenetic modification and provides an easy graphical interface to biologists for advanced analysis of genomic interactions

CHORUS Deliverable 2.2: Second report - identification of multi-disciplinary key issues for gap analysis toward EU multimedia search engines roadmap

After addressing the state-of-the-art during the first year of Chorus and establishing the existing landscape in multimedia search engines, we have identified and analyzed gaps within European research effort during our second year. In this period we focused on three directions, notably technological issues, user-centred issues and use-cases and socio- economic and legal aspects. These were assessed by two central studies: firstly, a concerted vision of functional breakdown of generic multimedia search engine, and secondly, a representative use-cases descriptions with the related discussion on requirement for technological challenges. Both studies have been carried out in cooperation and consultation with the community at large through EC concertation meetings (multimedia search engines cluster), several meetings with our Think-Tank, presentations in international conferences, and surveys addressed to EU projects coordinators as well as National initiatives coordinators. Based on the obtained feedback we identified two types of gaps, namely core technological gaps that involve research challenges, and “enablers”, which are not necessarily technical research challenges, but have impact on innovation progress. New socio-economic trends are presented as well as emerging legal challenges

Automatic Synchronization of Multi-User Photo Galleries

In this paper we address the issue of photo galleries synchronization, where pictures related to the same event are collected by different users. Existing solutions to address the problem are usually based on unrealistic assumptions, like time consistency across photo galleries, and often heavily rely on heuristics, limiting therefore the applicability to real-world scenarios. We propose a solution that achieves better generalization performance for the synchronization task compared to the available literature. The method is characterized by three stages: at first, deep convolutional neural network features are used to assess the visual similarity among the photos; then, pairs of similar photos are detected across different galleries and used to construct a graph; eventually, a probabilistic graphical model is used to estimate the temporal offset of each pair of galleries, by traversing the minimum spanning tree extracted from this graph. The experimental evaluation is conducted on four publicly available datasets covering different types of events, demonstrating the strength of our proposed method. A thorough discussion of the obtained results is provided for a critical assessment of the quality in synchronization.Comment: ACCEPTED to IEEE Transactions on Multimedi

Design and development of a generic spatial decision support system, based on artificial intelligence and multicriteria decision analysis

A new integrated and generic Spatial Decision Support System (SDSS) is presented based on a combination of Artificial Intelligence and Multicriteria Decision Analysis techniques. The approach proposed is developed to address commonly faced spatial decision problems of site selection, site ranking, impact assessment and spatial knowledge discovery under one system. The site selection module utilises a theme-based Analytical Hierarchy Process. Two novel site ranking techniques are introduced. The first is based on a systematic neighbourhood comparison of sites with respect to key datasets (criterions). The second utilises multivariate ordering capability of one-dimensional Self-Organizing Maps. The site impact assessment module utilises a new spatially enabled Rapid Impact Assessment Matrix. A spatial variant of General Regression Neural Networks is developed for Geographically Weighted Regression (GWR) and prediction analysis. The developed system is proposed as a useful modern tool that facilitates quantitative and evidence based decision making in multicriteria decision environment. The intended users of the system are decision makers in government organisations, in particular those involved in planning and development when taking into account socio-economic, environmental and public health related issues

Space models as a tool for sustainability development

Space Models are new space geometries that are created to emphasize the particularities of the geo-referenced data analysed. A Space Model integrates groups of regions that present similar behaviour attending to a specific characteristic. Each group represents a cluster aggregating regions that are similar regarding to the analysed characteristic, and regions in different clusters are as dissimilar as possible. This paper proposes the creation of Space Models, through the STICH (Space Models Identification Through Hierarchical Clustering) algorithm, as an alternative approach for data visualization, where the geometry of the maps is created from the data itself. Space Models are new space geometries that are created to emphasize the particularities of the analysed data, and integrate groups of regions that present similar behaviour attending to a specific characteristic. The achieved results are illustrated through a set of examples that are compared with conventional representations, showing that Space Models provide real added-value over conventional approaches, namely by facilitating the identification of peculiarities in the data.EPSILON Project, funded by the Information Society Technologies program from European Commission - IST-2001-32389