Data Reduction with Rough Sets

R. Jensen, Q. Shen, Data Reduction with Rough Sets, In: Encyclopedia of Data Warehousing and Mining - 2nd Edition, Vol. II, 2008.

VizMaps: A Bayesian Topic Modeling Based PubMed Search Interface

A common challenge that users of academic databases face is making sense of their query outputs for knowledge discovery. This is exacerbated by the size and growth of modern databases. PubMed, a central index of biomedical literature, contains over 25 million citations, and can output search results containing hundreds of thousands of citations. Under these conditions, efficient knowledge discovery requires a different data structure than a chronological list of articles. It requires a method of conveying what the important ideas are, where they are located, and how they are connected; a method of allowing users to see the underlying topical structure of their search. This paper presents VizMaps, a PubMed search interface that addresses some of these problems. Given search terms, our main backend pipeline extracts relevant words from the title and abstract, and clusters them into discovered topics using Bayesian topic models, in particular the Latent Dirichlet Allocation (LDA). It then outputs a visual, navigable map of the query results.

Representing and recognizing scenario patterns

This paper presents a formal method for representing and recognizing scenario patterns with rich internal temporal aspects. A scenario is presented as a collection of time-independent fluents, together with the corresponding temporal knowledge that can be relative and/or with absolute values. A graphical representation for temporal scenarios is introduced which supports consistence checking as for the temporal constraints. In terms of such a graphical representation, graph-matching algorithms/methodologies can be directly adopted for recognizing scenario patterns.

An ontological characterization of time-series and state-sequences for data mining

Time-series and sequences are important patterns in data mining. Based on an ontology of time-elements, this paper presents a formal characterization of time-series and state-sequences, where a state denotes a collection of data whose validation is dependent on time. While a time-series is formalized as a vector of time-elements temporally ordered one after another, a state-sequence is denoted as a list of states correspondingly ordered by a time-series. In general, a time-series and a state-sequence can be incomplete in various ways. This leads to the distinction between complete and incomplete time-series, and between complete and incomplete state-sequences, which allows the expression of both absolute and relative temporal knowledge in data mining.

Temporal pattern recognition in video clips detection

Temporal representation and reasoning plays an important role in Data Mining and Knowledge Discovery, particularly, in mining and recognizing patterns with rich temporal information. Based on a formal characterization of time-series and state-sequences, this paper presents the computational technique and algorithm for matching state-based temporal patterns. As a case study of real-life applications, zone-defense pattern recognition in basketball games is specially examined as an illustrating example. Experimental results demonstrate that it provides a formal and comprehensive temporal ontology for research and applications in video events detection.

GeneGrid: Architecture, Implementation and Application

The emergence of Grid computing technology has opened up an unprecedented opportunity for biologists to share and access data, resources and tools in an integrated environment leading to a greater chance of knowledge discovery. GeneGrid is a Grid computing framework that seamlessly integrates a myriad of heterogeneous resources spanning multiple administrative domains and locations. It provides scientists an integrated environment for the streamlined access of a number of bioinformatics programs and databases through a simple and intuitive interface. It acts as a virtual bioinformatics laboratory by allowing scientists to create, execute and manage workflows that represent bioinformatics experiments. A number of cooperating Grid services interact in an orchestrated manner to provide this functionality. This paper gives insight into the details of the architecture, components and implementation of GeneGrid.

Risk assessment of E-Commerce projects using evidential reasoning

The purpose of this study is to develop a decision making system to evaluate the risks in E-Commerce (EC) projects. Competitive software businesses have the critical task of assessing the risk in the software system development life cycle. This can be conducted on the basis of conventional probabilities, but limited appropriate information is available and so a complete set of probabilities is not available. In such problems, where the analysis is highly subjective and related to vague, incomplete, uncertain or inexact information, the Dempster-Shafer (DS) theory of evidence offers a potential advantage. We use a direct way of reasoning in a single step (i.e., extended DS theory) to develop a decision making system to evaluate the risk in EC projects. This consists of five stages 1) establishing knowledge base and setting rule strengths, 2) collecting evidence and data, 3) determining evidence and rule strength to a mass distribution for each rule; i.e., the first half of a single step reasoning process, 4) combining prior mass and different rules; i.e., the second half of the single step reasoning process, 5) finally, evaluating the belief interval for the best support decision of EC project. We test the system by using potential risk factors associated with EC development and the results indicate that the system is promising way of assisting an EC project manager in identifying potential risk factors and the corresponding project risks.

Introduction to Domain-Driven Data Mining Special Section

In the last decade, data mining has emerged as one of the most dynamic and lively areas in information technology. Although many algorithms and techniques for data mining have been proposed, they either focus on domain independent techniques or on very specific domain problems. A general requirement in bridging the gap between academia and business is to cater to general domain-related issues surrounding real-life applications, such as constraints, organizational factors, domain expert knowledge, domain adaption, and operational knowledge. Unfortunately, these either have not been addressed, or have not been sufficiently addressed, in current data mining research and development.Domain-Driven Data Mining (D3M) aims to develop general principles, methodologies, and techniques for modeling and merging comprehensive domain-related factors and synthesized ubiquitous intelligence surrounding problem domains with the data mining process, and discovering knowledge to support business decision-making. This paper aims to report original, cutting-edge, and state-of-the-art progress in D3M. It covers theoretical and applied contributions aiming to: 1) propose next-generation data mining frameworks and processes for actionable knowledge discovery, 2) investigate effective (automated, human and machine-centered and/or human-machined-co-operated) principles and approaches for acquiring, representing, modelling, and engaging ubiquitous intelligence in real-world data mining, and 3) develop workable and operational systems balancing technical significance and applications concerns, and converting and delivering actionable knowledge into operational applications rules to seamlessly engage application processes and systems.

Distributed Adaptive Learning Framework for Wide Area Monitoring of Power Systems Integrated with Distributed Generations

This paper presents a preliminary study of developing a novel distributed adaptive real-time learning framework for wide area monitoring of power systems integrated with distributed generations using synchrophasor technology. The framework comprises distributed agents (synchrophasors) for autonomous local condition monitoring and fault detection, and a central unit for generating global view for situation awareness and decision making. Key technologies that can be integrated into this hierarchical distributed learning scheme are discussed to enable real-time information extraction and knowledge discovery for decision making, without explicitly accumulating and storing all raw data by the central unit. Based on this, the configuration of a wide area monitoring system of power systems using synchrophasor technology, and the functionalities for locally installed open-phasor-measurement-units (OpenPMUs) and a central unit are presented. Initial results on anti-islanding protection using the proposed approach are given to illustrate the effectiveness.

AGWAN: A Generative Model for Labelled, Weighted Graphs

Real-world graphs or networks tend to exhibit a well-known set of properties, such as heavy-tailed degree distributions, clustering and community formation. Much effort has been directed into creating realistic and tractable models for unlabelled graphs, which has yielded insights into graph structure and evolution. Recently, attention has moved to creating models for labelled graphs: many real-world graphs are labelled with both discrete and numeric attributes. In this paper, we presentAgwan (Attribute Graphs: Weighted and Numeric), a generative model for random graphs with discrete labels and weighted edges. The model is easily generalised to edges labelled with an arbitrary number of numeric attributes. We include algorithms for fitting the parameters of the Agwanmodel to real-world graphs and for generating random graphs from the model. Using real-world directed and undirected graphs as input, we compare our approach to state-of-the-art random labelled graph generators and draw conclusions about the contribution of discrete vertex labels and edge weights to graph structure.

Detecting localized homogeneous anomalies over spatio-temporal data

The last decade has witnessed an unprecedented growth in availability of data having spatio-temporal characteristics. Given the scale and richness of such data, finding spatio-temporal patterns that demonstrate significantly different behavior from their neighbors could be of interest for various application scenarios such as – weather modeling, analyzing spread of disease outbreaks, monitoring traffic congestions, and so on. In this paper, we propose an automated approach of exploring and discovering such anomalous patterns irrespective of the underlying domain from which the data is recovered. Our approach differs significantly from traditional methods of spatial outlier detection, and employs two phases – i) discovering homogeneous regions, and ii) evaluating these regions as anomalies based on their statistical difference from a generalized neighborhood. We evaluate the quality of our approach and distinguish it from existing techniques via an extensive experimental evaluation.

Patient classification for intelligent wheelchair adaptation

A importância e preocupação dedicadas à autonomia e independência das pessoas idosas e dos pacientes que sofrem de algum tipo de deficiência tem vindo a aumentar significativamente ao longo das últimas décadas. As cadeiras de rodas inteligentes (CRI) são tecnologias que podem ajudar este tipo de população a aumentar a sua autonomia, sendo atualmente uma área de investigação bastante ativa. Contudo, a adaptação das CRIs a pacientes específicos e a realização de experiências com utilizadores reais são assuntos de estudo ainda muito pouco aprofundados. A cadeira de rodas inteligente, desenvolvida no âmbito do Projeto IntellWheels, é controlada a alto nível utilizando uma interface multimodal flexível, recorrendo a comandos de voz, expressões faciais, movimentos de cabeça e através de joystick. Este trabalho teve como finalidade a adaptação automática da CRI atendendo às características dos potenciais utilizadores. Foi desenvolvida uma metodologia capaz de criar um modelo do utilizador. A investigação foi baseada num sistema de recolha de dados que permite obter e armazenar dados de voz, expressões faciais, movimentos de cabeça e do corpo dos pacientes. A utilização da CRI pode ser efetuada em diferentes situações em ambiente real e simulado e um jogo sério foi desenvolvido permitindo especificar um conjunto de tarefas a ser realizado pelos utilizadores. Os dados foram analisados recorrendo a métodos de extração de conhecimento, de modo a obter o modelo dos utilizadores. Usando os resultados obtidos pelo sistema de classificação, foi criada uma metodologia que permite selecionar a melhor interface e linguagem de comando da cadeira para cada utilizador. A avaliação para validação da abordagem foi realizada no âmbito do Projeto FCT/RIPD/ADA/109636/2009 - "IntellWheels - Intelligent Wheelchair with Flexible Multimodal Interface". As experiências envolveram um vasto conjunto de indivíduos que sofrem de diversos níveis de deficiência, em estreita colaboração com a Escola Superior de Tecnologia de Saúde do Porto e a Associação do Porto de Paralisia Cerebral. Os dados recolhidos através das experiências de navegação na CRI foram acompanhados por questionários preenchidos pelos utilizadores. Estes dados foram analisados estatisticamente, a fim de provar a eficácia e usabilidade na adequação da interface da CRI ao utilizador. Os resultados mostraram, em ambiente simulado, um valor de usabilidade do sistema de 67, baseado na opinião de uma amostra de pacientes que apresentam os graus IV e V (os mais severos) de Paralisia Cerebral. Foi também demonstrado estatisticamente que a interface atribuída automaticamente pela ferramenta tem uma avaliação superior à sugerida pelos técnicos de Terapia Ocupacional, mostrando a possibilidade de atribuir automaticamente uma linguagem de comando adaptada a cada utilizador. Experiências realizadas com distintos modos de controlo revelaram a preferência dos utilizadores por um controlo compartilhado com um nível de ajuda associado ao nível de constrangimento do paciente. Em conclusão, este trabalho demonstra que é possível adaptar automaticamente uma CRI ao utilizador com claros benefícios a nível de usabilidade e segurança.

Mining biomedical information from scientific literature

The rapid evolution and proliferation of a world-wide computerized network, the Internet, resulted in an overwhelming and constantly growing amount of publicly available data and information, a fact that was also verified in biomedicine. However, the lack of structure of textual data inhibits its direct processing by computational solutions. Information extraction is the task of text mining that intends to automatically collect information from unstructured text data sources. The goal of the work described in this thesis was to build innovative solutions for biomedical information extraction from scientific literature, through the development of simple software artifacts for developers and biocurators, delivering more accurate, usable and faster results. We started by tackling named entity recognition - a crucial initial task - with the development of Gimli, a machine-learning-based solution that follows an incremental approach to optimize extracted linguistic characteristics for each concept type. Afterwards, Totum was built to harmonize concept names provided by heterogeneous systems, delivering a robust solution with improved performance results. Such approach takes advantage of heterogenous corpora to deliver cross-corpus harmonization that is not constrained to specific characteristics. Since previous solutions do not provide links to knowledge bases, Neji was built to streamline the development of complex and custom solutions for biomedical concept name recognition and normalization. This was achieved through a modular and flexible framework focused on speed and performance, integrating a large amount of processing modules optimized for the biomedical domain. To offer on-demand heterogenous biomedical concept identification, we developed BeCAS, a web application, service and widget. We also tackled relation mining by developing TrigNER, a machine-learning-based solution for biomedical event trigger recognition, which applies an automatic algorithm to obtain the best linguistic features and model parameters for each event type. Finally, in order to assist biocurators, Egas was developed to support rapid, interactive and real-time collaborative curation of biomedical documents, through manual and automatic in-line annotation of concepts and relations. Overall, the research work presented in this thesis contributed to a more accurate update of current biomedical knowledge bases, towards improved hypothesis generation and knowledge discovery.

Rede social académica

O processo de Bolonha apresenta directivas para a construção de um espaço europeu de ensino superior. A adopção destas directivas requer uma abordagem que favoreça, na prática, a mobilidade dos estudantes que têm dificuldades em compreenderem as oportunidades que lhes são oferecidas. Neste contexto, esta dissertação explora a hipótese de utilização de uma rede social para apoiar a mobilidade de estudantes no espaço europeu. No âmbito desta dissertação propõe-se um modelo de conhecimento para representar os membros de uma rede social vocacionada para apoiar cenários de mobilidade, designada por rede social académica. Este modelo foi obtido pela fusão da ontologia Academic Ontology to Support the Bologna Mobility Process com a ontologia Friend of a Friend Ontology. Para efeitos de avaliação experimental, foi criado um demonstrador numa rede social disponível publicamente na Internet que utiliza uma versão simplificada do modelo proposto. Os cenários usados nas experiências representam situações reais às quais foi aplicado um processo rudimentar de descoberta de conhecimento