D6.3 – Semantic Content Annotation Support

The Semantic Annotation component is a software application that provides support for automated text classification, a process grounded in a cohesion-centered representation of discourse that facilitates topic extraction. The component enables the semantic meta-annotation of text resources, including automated classification, thus facilitating information retrieval within the RAGE ecosystem. It is available in the ReaderBench framework (http://readerbench.com/) which integrates advanced Natural Language Processing (NLP) techniques. The component makes use of Cohesion Network Analysis (CNA) in order to ensure an in-depth representation of discourse, useful for mining keywords and performing automated text categorization. Our component automatically classifies documents into the categories provided by the ACM Computing Classification System (http://dl.acm.org/ccs_flat.cfm), but also into the categories from a high level serious games categorization provisionally developed by RAGE. English and French languages are already covered by the provided web service, whereas the entire framework can be extended in order to support additional languages.

Protein-protein interactions classification from text via local learning with class priors

Text classification is essential for narrowing down the number of documents relevant to a particular topic for further pursual, especially when searching through large biomedical databases. Protein-protein interactions are an example of such a topic with databases being devoted specifically to them. This paper proposed a semi-supervised learning algorithm via local learning with class priors (LL-CP) for biomedical text classification where unlabeled data points are classified in a vector space based on their proximity to labeled nodes. The algorithm has been evaluated on a corpus of biomedical documents to identify abstracts containing information about protein-protein interactions with promising results. Experimental results show that LL-CP outperforms the traditional semisupervised learning algorithms such as SVMand it also performs better than local learning without incorporating class priors.

Use of Medical Subject Headings (MeSH) in Portuguese for categorizing web-based healthcare content

Introduction: Internet users are increasingly using the worldwide web to search for information relating to their health. This situation makes it necessary to create specialized tools capable of supporting users in their searches. Objective: To apply and compare strategies that were developed to investigate the use of the Portuguese version of Medical Subject Headings (MeSH) for constructing an automated classifier for Brazilian Portuguese-language web-based content within or outside of the field of healthcare, focusing on the lay public. Methods: 3658 Brazilian web pages were used to train the classifier and 606 Brazilian web pages were used to validate it. The strategies proposed were constructed using content-based vector methods for text classification, such that Naive Bayes was used for the task of classifying vector patterns with characteristics obtained through the proposed strategies. Results: A strategy named InDeCS was developed specifically to adapt MeSH for the problem that was put forward. This approach achieved better accuracy for this pattern classification task (0.94 sensitivity, specificity and area under the ROC curve). Conclusions: Because of the significant results achieved by InDeCS, this tool has been successfully applied to the Brazilian healthcare search portal known as Busca Saude. Furthermore, it could be shown that MeSH presents important results when used for the task of classifying web-based content focusing on the lay public. It was also possible to show from this study that MeSH was able to map out mutable non-deterministic characteristics of the web. (c) 2010 Elsevier Inc. All rights reserved.

A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network.

BACKGROUND: The nuclear receptors are a large family of eukaryotic transcription factors that constitute major pharmacological targets. They exert their combinatorial control through homotypic heterodimerisation. Elucidation of this dimerisation network is vital in order to understand the complex dynamics and potential cross-talk involved. RESULTS: Phylogeny, protein-protein interactions, protein-DNA interactions and gene expression data have been integrated to provide a comprehensive and up-to-date description of the topology and properties of the nuclear receptor interaction network in humans. We discriminate between DNA-binding and non-DNA-binding dimers, and provide a comprehensive interaction map, that identifies potential cross-talk between the various pathways of nuclear receptors. CONCLUSION: We infer that the topology of this network is hub-based, and much more connected than previously thought. The hub-based topology of the network and the wide tissue expression pattern of NRs create a highly competitive environment for the common heterodimerising partners. Furthermore, a significant number of negative feedback loops is present, with the hub protein SHP [NR0B2] playing a major role. We also compare the evolution, topology and properties of the nuclear receptor network with the hub-based dimerisation network of the bHLH transcription factors in order to identify both unique themes and ubiquitous properties in gene regulation. In terms of methodology, we conclude that such a comprehensive picture can only be assembled by semi-automated text-mining, manual curation and integration of data from various sources.

classification and content based retrieval of digital mammograms and placental sonograms

Image processing has been a challenging and multidisciplinary research area since decades with continuing improvements in its various branches especially Medical Imaging. The healthcare industry was very much benefited with the advances in Image Processing techniques for the efficient management of large volumes of clinical data. The popularity and growth of Image Processing field attracts researchers from many disciplines including Computer Science and Medical Science due to its applicability to the real world. In the meantime, Computer Science is becoming an important driving force for the further development of Medical Sciences. The objective of this study is to make use of the basic concepts in Medical Image Processing and develop methods and tools for clinicians’ assistance. This work is motivated from clinical applications of digital mammograms and placental sonograms, and uses real medical images for proposing a method intended to assist radiologists in the diagnostic process. The study consists of two domains of Pattern recognition, Classification and Content Based Retrieval. Mammogram images of breast cancer patients and placental images are used for this study. Cancer is a disaster to human race. The accuracy in characterizing images using simplified user friendly Computer Aided Diagnosis techniques helps radiologists in detecting cancers at an early stage. Breast cancer which accounts for the major cause of cancer death in women can be fully cured if detected at an early stage. Studies relating to placental characteristics and abnormalities are important in foetal monitoring. The diagnostic variability in sonographic examination of placenta can be overlooked by detailed placental texture analysis by focusing on placental grading. The work aims on early breast cancer detection and placental maturity analysis. This dissertation is a stepping stone in combing various application domains of healthcare and technology.

FEATURE SELECTION AND COMPARISON OF TWO NAÏVE BAYES CLASSIFICATION METHODS IN THE CONTEXT OF SPAM FILTERING

Treating e-mail filtering as a binary text classification problem, researchers have applied several statistical learning algorithms to email corpora with promising results. This paper examines the performance of a Naive Bayes classifier using different approaches to feature selection and tokenization on different email corpora

Metodi di previsione di indici di borsa con tecniche di text & opinion mining applicate a twitter

Il problema relativo alla predizione, la ricerca di pattern predittivi all‘interno dei dati, è stato studiato ampiamente. Molte metodologie robuste ed efficienti sono state sviluppate, procedimenti che si basano sull‘analisi di informazioni numeriche strutturate. Quella testuale, d‘altro canto, è una tipologia di informazione fortemente destrutturata. Quindi, una immediata conclusione, porterebbe a pensare che per l‘analisi predittiva su dati testuali sia necessario sviluppare metodi completamente diversi da quelli ben noti dalle tecniche di data mining. Un problema di predizione può essere risolto utilizzando invece gli stessi metodi : dati testuali e documenti possono essere trasformati in valori numerici, considerando per esempio l‘assenza o la presenza di termini, rendendo di fatto possibile una utilizzazione efficiente delle tecniche già sviluppate. Il text mining abilita la congiunzione di concetti da campi di applicazione estremamente eterogenei. Con l‘immensa quantità di dati testuali presenti, basti pensare, sul World Wide Web, ed in continua crescita a causa dell‘utilizzo pervasivo di smartphones e computers, i campi di applicazione delle analisi di tipo testuale divengono innumerevoli. L‘avvento e la diffusione dei social networks e della pratica di micro blogging abilita le persone alla condivisione di opinioni e stati d‘animo, creando un corpus testuale di dimensioni incalcolabili aggiornato giornalmente. Le nuove tecniche di Sentiment Analysis, o Opinion Mining, si occupano di analizzare lo stato emotivo o la tipologia di opinione espressa all‘interno di un documento testuale. Esse sono discipline attraverso le quali, per esempio, estrarre indicatori dello stato d‘animo di un individuo, oppure di un insieme di individui, creando una rappresentazione dello stato emotivo sociale. L‘andamento dello stato emotivo sociale può condizionare macroscopicamente l‘evolvere di eventi globali? Studi in campo di Economia e Finanza Comportamentale assicurano un legame fra stato emotivo, capacità nel prendere decisioni ed indicatori economici. Grazie alle tecniche disponibili ed alla mole di dati testuali continuamente aggiornati riguardanti lo stato d‘animo di milioni di individui diviene possibile analizzare tali correlazioni. In questo studio viene costruito un sistema per la previsione delle variazioni di indici di borsa, basandosi su dati testuali estratti dalla piattaforma di microblogging Twitter, sotto forma di tweets pubblici; tale sistema include tecniche di miglioramento della previsione basate sullo studio di similarità dei testi, categorizzandone il contributo effettivo alla previsione.

Content Classification of Multimedia Documents using Partitions of Low-Level Features

Audio-visual documents obtained from German TV news are classified according to the IPTC topic categorization scheme. To this end usual text classification techniques are adapted to speech, video, and non-speech audio. For each of the three modalities word analogues are generated: sequences of syllables for speech, “video words” based on low level color features (color moments, color correlogram and color wavelet), and “audio words” based on low-level spectral features (spectral envelope and spectral flatness) for non-speech audio. Such audio and video words provide a means to represent the different modalities in a uniform way. The frequencies of the word analogues represent audio-visual documents: the standard bag-of-words approach. Support vector machines are used for supervised classification in a 1 vs. n setting. Classification based on speech outperforms all other single modalities. Combining speech with non-speech audio improves classification. Classification is further improved by supplementing speech and non-speech audio with video words. Optimal F-scores range between 62% and 94% corresponding to 50% - 84% above chance. The optimal combination of modalities depends on the category to be recognized. The construction of audio and video words from low-level features provide a good basis for the integration of speech, non-speech audio and video.

Application of Text Summarization techniques to the Geographical Information Retrieval task

Automatic Text Summarization has been shown to be useful for Natural Language Processing tasks such as Question Answering or Text Classification and other related fields of computer science such as Information Retrieval. Since Geographical Information Retrieval can be considered as an extension of the Information Retrieval field, the generation of summaries could be integrated into these systems by acting as an intermediate stage, with the purpose of reducing the document length. In this manner, the access time for information searching will be improved, while at the same time relevant documents will be also retrieved. Therefore, in this paper we propose the generation of two types of summaries (generic and geographical) applying several compression rates in order to evaluate their effectiveness in the Geographical Information Retrieval task. The evaluation has been carried out using GeoCLEF as evaluation framework and following an Information Retrieval perspective without considering the geo-reranking phase commonly used in these systems. Although single-document summarization has not performed well in general, the slight improvements obtained for some types of the proposed summaries, particularly for those based on geographical information, made us believe that the integration of Text Summarization with Geographical Information Retrieval may be beneficial, and consequently, the experimental set-up developed in this research work serves as a basis for further investigations in this field.

Untangling a Web of Lies: Exploring Automated Detection of Deception in Computer-Mediated Communication

Safeguarding organizations against opportunism and severe deception in computer-mediated communication (CMC) presents a major challenge to CIOs and IT managers. New insights into linguistic cues of deception derive from the speech acts innate to CMC. Applying automated text analysis to archival email exchanges in a CMC system as part of a reward program, we assess the ability of word use (micro-level), message development (macro-level), and intertextual exchange cues (meta-level) to detect severe deception by business partners. We empirically assess the predictive ability of our framework using an ordinal multilevel regression model. Results indicate that deceivers minimize the use of referencing and self-deprecation but include more superfluous descriptions and flattery. Deceitful channel partners also over structure their arguments and rapidly mimic the linguistic style of the account manager across dyadic e-mail exchanges. Thanks to its diagnostic value, the proposed framework can support firms’ decision-making and guide compliance monitoring system development.

Automated Discovery of Social Networks in Online Learning Communities

As a way to gain greater insights into the operation of online communities, this dissertation applies automated text mining techniques to text-based communication to identify, describe and evaluate underlying social networks among online community members. The main thrust of the study is to automate the discovery of social ties that form between community members, using only the digital footprints left behind in their online forum postings. Currently, one of the most common but time consuming methods for discovering social ties between people is to ask questions about their perceived social ties. However, such a survey is difficult to collect due to the high investment in time associated with data collection and the sensitive nature of the types of questions that may be asked. To overcome these limitations, the dissertation presents a new, content-based method for automated discovery of social networks from threaded discussions, referred to as ‘name network’. As a case study, the proposed automated method is evaluated in the context of online learning communities. The results suggest that the proposed ‘name network’ method for collecting social network data is a viable alternative to costly and time-consuming collection of users’ data using surveys. The study also demonstrates how social networks produced by the ‘name network’ method can be used to study online classes and to look for evidence of collaborative learning in online learning communities. For example, educators can use name networks as a real time diagnostic tool to identify students who might need additional help or students who may provide such help to others. Future research will evaluate the usefulness of the ‘name network’ method in other types of online communities.

Learning techniques for automatic email message tagging

A organização automática de mensagens de correio electrónico é um desafio actual na área da aprendizagem automática. O número excessivo de mensagens afecta cada vez mais utilizadores, especialmente os que usam o correio electrónico como ferramenta de comunicação e trabalho. Esta tese aborda o problema da organização automática de mensagens de correio electrónico propondo uma solução que tem como objectivo a etiquetagem automática de mensagens. A etiquetagem automática é feita com recurso às pastas de correio electrónico anteriormente criadas pelos utilizadores, tratando-as como etiquetas, e à sugestão de múltiplas etiquetas para cada mensagem (top-N). São estudadas várias técnicas de aprendizagem e os vários campos que compõe uma mensagem de correio electrónico são analisados de forma a determinar a sua adequação como elementos de classificação. O foco deste trabalho recai sobre os campos textuais (o assunto e o corpo das mensagens), estudando-se diferentes formas de representação, selecção de características e algoritmos de classificação. É ainda efectuada a avaliação dos campos de participantes através de algoritmos de classificação que os representam usando o modelo vectorial ou como um grafo. Os vários campos são combinados para classificação utilizando a técnica de combinação de classificadores Votação por Maioria. Os testes são efectuados com um subconjunto de mensagens de correio electrónico da Enron e um conjunto de dados privados disponibilizados pelo Institute for Systems and Technologies of Information, Control and Communication (INSTICC). Estes conjuntos são analisados de forma a perceber as características dos dados. A avaliação do sistema é realizada através da percentagem de acerto dos classificadores. Os resultados obtidos apresentam melhorias significativas em comparação com os trabalhos relacionados.

Modelo de representação de texto mais adequado à classificação

Mestrado em Engenharia Informática

An unsupervised approach to feature discretization and selection

Many learning problems require handling high dimensional datasets with a relatively small number of instances. Learning algorithms are thus confronted with the curse of dimensionality, and need to address it in order to be effective. Examples of these types of data include the bag-of-words representation in text classification problems and gene expression data for tumor detection/classification. Usually, among the high number of features characterizing the instances, many may be irrelevant (or even detrimental) for the learning tasks. It is thus clear that there is a need for adequate techniques for feature representation, reduction, and selection, to improve both the classification accuracy and the memory requirements. In this paper, we propose combined unsupervised feature discretization and feature selection techniques, suitable for medium and high-dimensional datasets. The experimental results on several standard datasets, with both sparse and dense features, show the efficiency of the proposed techniques as well as improvements over previous related techniques.