Column-based databases: estudo exploratório no âmbito das bases de dados NoSQL

O aumento da quantidade de dados gerados que se tem verificado nos últimos anos e a que se tem vindo a dar o nome de Big Data levou a que a tecnologia relacional começasse a demonstrar algumas fragilidades no seu armazenamento e manuseamento o que levou ao aparecimento das bases de dados NoSQL. Estas estão divididas por quatro tipos distintos nomeadamente chave/valor, documentos, grafos e famílias de colunas. Este artigo é focado nas bases de dados do tipo column-based e nele serão analisados os dois sistemas deste tipo considerados mais relevantes: Cassandra e HBase.

Monitoring and analysis of queries in distributed databases

Dissertação de Mestrado em Engenharia Informática

Extracting kinetic information from literature with KineticRE

To better understand the dynamic behavior of metabolic networks in a wide variety of conditions, the field of Systems Biology has increased its interest in the use of kinetic models. The different databases, available these days, do not contain enough data regarding this topic. Given that a significant part of the relevant information for the development of such models is still wide spread in the literature, it becomes essential to develop specific and powerful text mining tools to collect these data. In this context, this work has as main objective the development of a text mining tool to extract, from scientific literature, kinetic parameters, their respective values and their relations with enzymes and metabolites. The approach proposed integrates the development of a novel plug-in over the text mining framework @Note2. In the end, the pipeline developed was validated with a case study on Kluyveromyces lactis, spanning the analysis and results of 20 full text documents.

Integrating data from heterogeneous DNA microarray platforms

DNA microarrays are one of the most used technologies for gene expression measurement. However, there are several distinct microarray platforms, from different manufacturers, each with its own measurement protocol, resulting in data that can hardly be compared or directly integrated. Data integration from multiple sources aims to improve the assertiveness of statistical tests, reducing the data dimensionality problem. The integration of heterogeneous DNA microarray platforms comprehends a set of tasks that range from the re-annotation of the features used on gene expression, to data normalization and batch effect elimination. In this work, a complete methodology for gene expression data integration and application is proposed, which comprehends a transcript-based re-annotation process and several methods for batch effect attenuation. The integrated data will be used to select the best feature set and learning algorithm for a brain tumor classification case study. The integration will consider data from heterogeneous Agilent and Affymetrix platforms, collected from public gene expression databases, such as The Cancer Genome Atlas and Gene Expression Omnibus.

Reconstructing transcriptional regulatory networks using data integration and text mining

Transcriptional Regulatory Networks (TRNs) are powerful tool for representing several interactions that occur within a cell. Recent studies have provided information to help researchers in the tasks of building and understanding these networks. One of the major sources of information to build TRNs is biomedical literature. However, due to the rapidly increasing number of scientific papers, it is quite difficult to analyse the large amount of papers that have been published about this subject. This fact has heightened the importance of Biomedical Text Mining approaches in this task. Also, owing to the lack of adequate standards, as the number of databases increases, several inconsistencies concerning gene and protein names and identifiers are common. In this work, we developed an integrated approach for the reconstruction of TRNs that retrieve the relevant information from important biological databases and insert it into a unique repository, named KREN. Also, we applied text mining techniques over this integrated repository to build TRNs. However, was necessary to create a dictionary of names and synonyms associated with these entities and also develop an approach that retrieves all the abstracts from the related scientific papers stored on PubMed, in order to create a corpora of data about genes. Furthermore, these tasks were integrated into @Note, a software system that allows to use some methods from the Biomedical Text Mining field, including an algorithms for Named Entity Recognition (NER), extraction of all relevant terms from publication abstracts, extraction relationships between biological entities (genes, proteins and transcription factors). And finally, extended this tool to allow the reconstruction Transcriptional Regulatory Networks through using scientific literature.

Column-based databases: estudo exploratório no âmbito das bases de dados NoSQL

Dissertação de mestrado integrado em Engenharia e Gestão de Sistemas de Informação

Document-based databases: estudo comparativo no âmbito das bases de dados NoSql

Dissertação de mestrado integrado em Engenharia e Gestão de Sistemas de Informação

Automatic visual detection of human behavior: a review from 2000 to 2014

Due to advances in information technology (e.g., digital video cameras, ubiquitous sensors), the automatic detection of human behaviors from video is a very recent research topic. In this paper, we perform a systematic and recent literature review on this topic, from 2000 to 2014, covering a selection of 193 papers that were searched from six major scientific publishers. The selected papers were classified into three main subjects: detection techniques, datasets and applications. The detection techniques were divided into four categories (initialization, tracking, pose estimation and recognition). The list of datasets includes eight examples (e.g., Hollywood action). Finally, several application areas were identified, including human detection, abnormal activity detection, action recognition, player modeling and pedestrian detection. Our analysis provides a road map to guide future research for designing automatic visual human behavior detection systems.

Comparison of single and multi-objective evolutionary algorithms for robust link-state routing

Traffic Engineering (TE) approaches are increasingly impor- tant in network management to allow an optimized configuration and resource allocation. In link-state routing, the task of setting appropriate weights to the links is both an important and a challenging optimization task. A number of different approaches has been put forward towards this aim, including the successful use of Evolutionary Algorithms (EAs). In this context, this work addresses the evaluation of three distinct EAs, a single and two multi-objective EAs, in two tasks related to weight setting optimization towards optimal intra-domain routing, knowing the network topology and aggregated traffic demands and seeking to mini- mize network congestion. In both tasks, the optimization considers sce- narios where there is a dynamic alteration in the state of the system, in the first considering changes in the traffic demand matrices and in the latter considering the possibility of link failures. The methods will, thus, need to simultaneously optimize for both conditions, the normal and the altered one, following a preventive TE approach towards robust configurations. Since this can be formulated as a bi-objective function, the use of multi-objective EAs, such as SPEA2 and NSGA-II, came nat- urally, being those compared to a single-objective EA. The results show a remarkable behavior of NSGA-II in all proposed tasks scaling well for harder instances, and thus presenting itself as the most promising option for TE in these scenarios.

Combining data mining and evolutionary computation for multi-criteria optimization of earthworks

Earthworks tasks aim at levelling the ground surface at a target construction area and precede any kind of structural construction (e.g., road and railway construction). It is comprised of sequential tasks, such as excavation, transportation, spreading and compaction, and it is strongly based on heavy mechanical equipment and repetitive processes. Under this context, it is essential to optimize the usage of all available resources under two key criteria: the costs and duration of earthwork projects. In this paper, we present an integrated system that uses two artificial intelligence based techniques: data mining and evolutionary multi-objective optimization. The former is used to build data-driven models capable of providing realistic estimates of resource productivity, while the latter is used to optimize resource allocation considering the two main earthwork objectives (duration and cost). Experiments held using real-world data, from a construction site, have shown that the proposed system is competitive when compared with current manual earthwork design.

Modern optimization in earthwork construction

Earthworks tasks are often regarded in transportation projects as some of the most demanding processes. In fact, sequential tasks such as excavation, transportation, spreading and compaction are strongly based on heavy mechanical equipment and repetitive processes, thus becoming as economically demanding as they are time-consuming. Moreover, actual construction requirements originate higher demands for productivity and safety in earthwork constructions. Given the percentual weight of costs and duration of earthworks in infrastructure construction, the optimal usage of every resource in these tasks is paramount. Considering the characteristics of an earthwork construction, it can be looked at as a production line based on resources (mechanical equipment) and dependency relations between sequential tasks, hence being susceptible to optimization. Up to the present, the steady development of Information Technology areas, such as databases, artificial intelligence and operations research, has resulted in the emergence of several technologies with potential application bearing that purpose in mind. Among these, modern optimization methods (also known as metaheuristics), such as evolutionary computation, have the potential to find high quality optimal solutions with a reasonable use of computational resources. In this context, this work describes an optimization algorithm for earthworks equipment allocation based on a modern optimization approach, which takes advantage of the concept that an earthwork construction can be regarded as a production line.

An integrated system for human action recognition from video using hidden Markov model

In this paper, we present an integrated system for real-time automatic detection of human actions from video. The proposed approach uses the boundary of humans as the main feature for recognizing actions. Background subtraction is performed using Gaussian mixture model. Then, features are extracted from silhouettes and Vector Quantization is used to map features into symbols (bag of words approach). Finally, actions are detected using the Hidden Markov Model. The proposed system was validated using a newly collected real- world dataset. The obtained results show that the system is capable of achieving robust human detection, in both indoor and outdoor environments. Moreover, promising classification results were achieved when detecting two basic human actions: walking and sitting.

Exploring chemical conversions in metabolic networks by tracing atoms transitions

Dissertação de mestrado em Bioinformática

7to77, A new database querying experience

Nowadays, the vulgarization of information and communication technologies has reached to a level that the majority of people spend a lot of time using software to do regular tasks, ranging from games and ordinary time and weather utilities to some more sophisticated ones, like retail or banking applications. This new way of life is supported by the Internet or by specific applications that changed the image people had about using information and communication technologies. All over the world, the first cycle of studies of educational systems also has been addressed with the justification that this encourages the development of children. Taking this into consideration, we design and develop a visual explorer system for relational databases that can be used by everyone, from “7 to 77”, in an intuitive and easy way, getting immediate results – a new database querying experience. Thus, in this paper we will expose the main characteristics and features of this visual database explorer, showing how it works and how it can be used to execute the most current data manipulation operations over a database.

Sistema de predição de avarias em máquinas de unidades fabris globalmente dispersas

Tese de Doutoramento Ramo Engenharia Industrial e de Sistemas