BioCloud Search EnGene: Surfing Biological Data on the Cloud

The massive production and spread of biomedical data around the web introduces new challenges related to identify computational approaches for providing quality search and browsing of web resources. This papers presents BioCloud Search EnGene (BSE), a cloud application that facilitates searching and integration of the many layers of biological information offered by public large-scale genomic repositories. Grounding on the concept of dataspace, BSE is built on top of a cloud platform that severely curtails issues associated with scalability and performance. Like popular online gene portals, BSE adopts a gene-centric approach: researchers can find their information of interest by means of a simple “Google-like” query interface that accepts standard gene identification as keywords. We present BSE architecture and functionality and discuss how our strategies contribute to successfully tackle big data problems in querying gene-based web resources. BSE is publically available at: http://biocloud-unica.appspot.com/

Image mining: issues, frameworks and techniques

[Abstract]: Advances in image acquisition and storage technology have led to tremendous growth in significantly large and detailed image databases. These images, if analyzed, can reveal useful information to the human users. Image mining deals with the extraction of implicit knowledge, image data relationship, or other patterns not explicitly stored in the images. Image mining is more than just an extension of data mining to image domain. It is an interdisciplinary endeavor that draws upon expertise in computer vision, image processing, image retrieval, data mining, machine learning, database, and artificial intelligence. Despite the development of many applications and algorithms in the individual research fields cited above, research in image mining is still in its infancy. In this paper, we will examine the research issues in image mining, current developments in image mining, particularly, image mining frameworks, state-of-the-art techniques and systems. We will also identify some future research directions for image mining at the end of this paper

When Things Matter: A Data-Centric View of the Internet of Things

With the recent advances in radio-frequency identification (RFID), low-cost wireless sensor devices, and Web technologies, the Internet of Things (IoT) approach has gained momentum in connecting everyday objects to the Internet and facilitating machine-to-human and machine-to-machine communication with the physical world. While IoT offers the capability to connect and integrate both digital and physical entities, enabling a whole new class of applications and services, several significant challenges need to be addressed before these applications and services can be fully realized. A fundamental challenge centers around managing IoT data, typically produced in dynamic and volatile environments, which is not only extremely large in scale and volume, but also noisy, and continuous. This article surveys the main techniques and state-of-the-art research efforts in IoT from data-centric perspectives, including data stream processing, data storage models, complex event processing, and searching in IoT. Open research issues for IoT data management are also discussed

Transparent Persistence with Java Data Objects

Flexible and performant Persistency Service is a necessary component of any HEP Software Framework. The building of a modular, non-intrusive and performant persistency component have been shown to be very difficult task. In the past, it was very often necessary to sacrifice modularity to achieve acceptable performance. This resulted in the strong dependency of the overall Frameworks on their Persistency subsystems. Recent development in software technology has made possible to build a Persistency Service which can be transparently used from other Frameworks. Such Service doesn't force a strong architectural constraints on the overall Framework Architecture, while satisfying high performance requirements. Java Data Object standard (JDO) has been already implemented for almost all major databases. It provides truly transparent persistency for any Java object (both internal and external). Objects in other languages can be handled via transparent proxies. Being only a thin layer on top of a used database, JDO doesn't introduce any significant performance degradation. Also Aspect-Oriented Programming (AOP) makes possible to treat persistency as an orthogonal Aspect of the Application Framework, without polluting it with persistence-specific concepts. All these techniques have been developed primarily (or only) for the Java environment. It is, however, possible to interface them transparently to Frameworks built in other languages, like for example C++. Fully functional prototypes of flexible and non-intrusive persistency modules have been build for several other packages, as for example FreeHEP AIDA and LCG Pool AttributeSet (package Indicium).Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003. PSN TUKT00

The relationship between IR and multimedia databases

Modern extensible database systems support multimedia data through ADTs. However, because of the problems with multimedia query formulation, this support is not sufficient.\ud \ud Multimedia querying requires an iterative search process involving many different representations of the objects in the database. The support that is needed is very similar to the processes in information retrieval.\ud \ud Based on this observation, we develop the miRRor architecture for multimedia query processing. We design a layered framework based on information retrieval techniques, to provide a usable query interface to the multimedia database.\ud \ud First, we introduce a concept layer to enable reasoning over low-level concepts in the database.\ud \ud Second, we add an evidential reasoning layer as an intermediate between the user and the concept layer.\ud \ud Third, we add the functionality to process the users' relevance feedback.\ud \ud We then adapt the inference network model from text retrieval to an evidential reasoning model for multimedia query processing.\ud \ud We conclude with an outline for implementation of miRRor on top of the Monet extensible database system

Creating a Relational Distributed Object Store

In and of itself, data storage has apparent business utility. But when we can convert data to information, the utility of stored data increases dramatically. It is the layering of relation atop the data mass that is the engine for such conversion. Frank relation amongst discrete objects sporadically ingested is rare, making the process of synthesizing such relation all the more challenging, but the challenge must be met if we are ever to see an equivalent business value for unstructured data as we already have with structured data. This paper describes a novel construct, referred to as a relational distributed object store (RDOS), that seeks to solve the twin problems of how to persistently and reliably store petabytes of unstructured data while simultaneously creating and persisting relations amongst billions of objects.Comment: 12 pages, 5 figure

Probabilistic Relational Model Benchmark Generation

The validation of any database mining methodology goes through an evaluation process where benchmarks availability is essential. In this paper, we aim to randomly generate relational database benchmarks that allow to check probabilistic dependencies among the attributes. We are particularly interested in Probabilistic Relational Models (PRMs), which extend Bayesian Networks (BNs) to a relational data mining context and enable effective and robust reasoning over relational data. Even though a panoply of works have focused, separately , on the generation of random Bayesian networks and relational databases, no work has been identified for PRMs on that track. This paper provides an algorithmic approach for generating random PRMs from scratch to fill this gap. The proposed method allows to generate PRMs as well as synthetic relational data from a randomly generated relational schema and a random set of probabilistic dependencies. This can be of interest not only for machine learning researchers to evaluate their proposals in a common framework, but also for databases designers to evaluate the effectiveness of the components of a database management system