Tecniche di text mining per l'autoorganizzazione della conoscenza

L'elaborato ha come scopo l'analisi delle tecniche di Text Mining e la loro applicazione all'interno di processi per l'auto-organizzazione della conoscenza. La prima parte della tesi si concentra sul concetto del Text Mining. Viene fornita la sua definizione, i possibili campi di utilizzo, il processo di sviluppo che lo riguarda e vengono esposte le diverse tecniche di Text Mining. Si analizzano poi alcuni tools per il Text Mining e infine vengono presentati alcuni esempi pratici di utilizzo. Il macro-argomento che viene esposto successivamente riguarda TuCSoN, una infrastruttura per la coordinazione di processi: autonomi, distribuiti e intelligenti, come ad esempio gli agenti. Si descrivono innanzi tutto le entità sulle quali il modello si basa, vengono introdotte le metodologie di interazione fra di essi e successivamente, gli strumenti di programmazione che l'infrastruttura mette a disposizione. La tesi, in un secondo momento, presenta MoK, un modello di coordinazione basato sulla biochimica studiato per l'auto-organizzazione della conoscenza. Anche per MoK, come per TuCSoN, vengono introdotte le entità alla base del modello. Avvalendosi MoK dell'infrastruttura TuCSoN, viene mostrato come le entità del primo vengano mappate su quelle del secondo. A conclusione dell'argomento viene mostrata un'applicazione per l'auto-organizzazione di news che si avvale del modello. Il capitolo successivo si occupa di analizzare i possibili utilizzi delle tecniche di Text Mining all'interno di infrastrutture per l'auto-organizzazione, come MoK. Nell'elaborato vengono poi presentati gli esperimenti effettuati sfruttando tecniche di Text Mining. Tutti gli esperimenti svolti hanno come scopo la clusterizzazione di articoli scientifici in base al loro contenuto, vengono quindi analizzati i risultati ottenuti. L'elaborato di tesi si conclude mettendo in evidenza alcune considerazioni finali su quanto svolto.

Automatic information retrieval through text-mining

The dissertation presented for obtaining the Master’s Degree in Electrical Engineering and Computer Science, at Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Text mining e twitter : o poder das redes sociais num mercado competitivo

Actualmente, com a massificação da utilização das redes sociais, as empresas passam a sua mensagem nos seus canais de comunicação, mas os consumidores dão a sua opinião sobre ela. Argumentam, opinam, criticam (Nardi, Schiano, Gumbrecht, & Swartz, 2004). Positiva ou negativamente. Neste contexto o Text Mining surge como uma abordagem interessante para a resposta à necessidade de obter conhecimento a partir dos dados existentes. Neste trabalho utilizámos um algoritmo de Clustering hierárquico com o objectivo de descobrir temas distintos num conjunto de tweets obtidos ao longo de um determinado período de tempo para as empresas Burger King e McDonald’s. Com o intuito de compreender o sentimento associado a estes temas foi feita uma análise de sentimentos a cada tema encontrado, utilizando um algoritmo Bag-of-Words. Concluiu-se que o algoritmo de Clustering foi capaz de encontrar temas através do tweets obtidos, essencialmente ligados a produtos e serviços comercializados pelas empresas. O algoritmo de Sentiment Analysis atribuiu um sentimento a esses temas, permitindo compreender de entre os produtos/serviços identificados quais os que obtiveram uma polaridade positiva ou negativa, e deste modo sinalizar potencias situações problemáticas na estratégia das empresas, e situações positivas passíveis de identificação de decisões operacionais bem-sucedidas.

Preimplantation development regulatory pathway construction through a text-mining approach

Background: The integration of sequencing and gene interaction data and subsequent generation of pathways and networks contained in databases such as KEGG Pathway is essential for the comprehension of complex biological processes. We noticed the absence of a chart or pathway describing the well-studied preimplantation development stages; furthermore, not all genes involved in the process have entries in KEGG Orthology, important information for knowledge application with relation to other organisms. Results: In this work we sought to develop the regulatory pathway for the preimplantation development stage using text-mining tools such as Medline Ranker and PESCADOR to reveal biointeractions among the genes involved in this process. The genes present in the resulting pathway were also used as seeds for software developed by our group called SeedServer to create clusters of homologous genes. These homologues allowed the determination of the last common ancestor for each gene and revealed that the preimplantation development pathway consists of a conserved ancient core of genes with the addition of modern elements. Conclusions: The generation of regulatory pathways through text-mining tools allows the integration of data generated by several studies for a more complete visualization of complex biological processes. Using the genes in this pathway as “seeds” for the generation of clusters of homologues, the pathway can be visualized for other organisms. The clustering of homologous genes together with determination of the ancestry leads to a better understanding of the evolution of such process.

Descriptive Text Mining in ambito medico: applicazione della metodologia POIROT

Poiché la nostra conoscenza collettiva continua ad essere digitalizzata e memorizzata, diventa più difficile trovare e scoprire ciò che stiamo cercando. Abbiamo bisogno di nuovi strumenti computazionali per aiutare a organizzare, rintracciare e comprendere queste vaste quantità di informazioni. I modelli di linguaggio sono potenti strumenti che possono essere impiegati per estrarre conoscenza statisticamente significativa ed interpretabile tramite apprendimento non supervisionato, testuali o nel codice sorgente. L’obiettivo di questa tesi è impiegare una metodologia di descriptive text mining, denominata POIROT, per analizzare i rapporti medici del dataset Adverse Drug Reaction (ADE). Si vogliono stabilire delle correlazioni significative che permettano di comprendere le ragioni per cui un determinato rapporto medico fornisca o meno informazioni relative a effetti collaterali dovuti all’assunzione di determinati farmaci.

NovaIntell - projecto de text-Mining para a língua portuguesa numa empresa de Gestão de Informação e Conhecimento

Dissertação apresentada como requisito parcial para obtenção do grau de Mestre em Estatística e Gestão de Informação

Text Mining: análise de sentimentos na classificação de notícias

Trabalho de Projeto apresentado como requisito parcial para obtenção do grau de Mestre em Estatística e Gestão de Informação

Business intelligence in banking: A literature analysis from 2002 to 2013 using Text Mining and latent Dirichlet allocation

telligence applications for the banking industry. Searches were performed in relevant journals resulting in 219 articles published between 2002 and 2013. To analyze such a large number of manuscripts, text mining techniques were used in pursuit for relevant terms on both business intelligence and banking domains. Moreover, the latent Dirichlet allocation modeling was used in or- der to group articles in several relevant topics. The analysis was conducted using a dictionary of terms belonging to both banking and business intelli- gence domains. Such procedure allowed for the identification of relationships between terms and topics grouping articles, enabling to emerge hypotheses regarding research directions. To confirm such hypotheses, relevant articles were collected and scrutinized, allowing to validate the text mining proce- dure. The results show that credit in banking is clearly the main application trend, particularly predicting risk and thus supporting credit approval or de- nial. There is also a relevant interest in bankruptcy and fraud prediction. Customer retention seems to be associated, although weakly, with targeting, justifying bank offers to reduce churn. In addition, a large number of ar- ticles focused more on business intelligence techniques and its applications, using the banking industry just for evaluation, thus, not clearly acclaiming for benefits in the banking business. By identifying these current research topics, this study also highlights opportunities for future research.

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.

Text mining na análise de sentimentos em contextos de big data

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

Técnicas de Data e Text Mining Para Anotação de Um Arquivo Digital

O presente trabalho cujo Título é técnicas de Data e Text Mining para a anotação dum Arquivo Digital, tem como objectivo testar a viabilidade da utilização de técnicas de processamento automático de texto para a anotação das sessões dos debates parlamentares da Assembleia da República de Portugal. Ao longo do trabalho abordaram-se conceitos como tecnologias de descoberta do conhecimento (KDD), o processo da descoberta do conhecimento em texto, a caracterização das várias etapas do processamento de texto e a descrição de algumas ferramentas open souce para a mineração de texto. A metodologia utilizada baseou-se na experimentação de várias técnicas de processamento textual utilizando a open source R/tm. Apresentam-se, como resultados, a influência do pré-processamento, tamanho dos documentos e tamanhos dos corpora no resultado do processamento utilizando o algoritmo knnflex.

Application of text-mining for updating protein post-translational modification annotation in UniProtKB.

BACKGROUND: The annotation of protein post-translational modifications (PTMs) is an important task of UniProtKB curators and, with continuing improvements in experimental methodology, an ever greater number of articles are being published on this topic. To help curators cope with this growing body of information we have developed a system which extracts information from the scientific literature for the most frequently annotated PTMs in UniProtKB. RESULTS: The procedure uses a pattern-matching and rule-based approach to extract sentences with information on the type and site of modification. A ranked list of protein candidates for the modification is also provided. For PTM extraction, precision varies from 57% to 94%, and recall from 75% to 95%, according to the type of modification. The procedure was used to track new publications on PTMs and to recover potential supporting evidence for phosphorylation sites annotated based on the results of large scale proteomics experiments. CONCLUSIONS: The information retrieval and extraction method we have developed in this study forms the basis of a simple tool for the manual curation of protein post-translational modifications in UniProtKB/Swiss-Prot. Our work demonstrates that even simple text-mining tools can be effectively adapted for database curation tasks, providing that a thorough understanding of the working process and requirements are first obtained. This system can be accessed at http://eagl.unige.ch/PTM/.

Destination image of Girona: an online text-mining approach

The main objective of this Master Thesis is to discover more about Girona’s image as a tourism destination from different agents’ perspective and to study its differences on promotion or opinions. In order to meet this objective, three components of Girona’s destination image will be studied: attribute-based component, the holistic component, and the affective component. It is true that a lot of research has been done about tourism destination image, but it is less when we are talking about the destination of Girona. Some studies have already focused on Girona as a tourist destination, but they used a different type of sample and different methodological steps. This study is new among destination studies in the sense that it is based only on textual online data and it follows a methodology based on text-miming. Text-mining is a kind of methodology that allows people extract relevant information from texts. Also, after this information is extracted by this methodology, some statistical multivariate analyses are done with the aim of discovering more about Girona’s tourism image

A Dependency Parsing Approach to Biomedical Text Mining

Biomedical research is currently facing a new type of challenge: an excess of information, both in terms of raw data from experiments and in the number of scientific publications describing their results. Mirroring the focus on data mining techniques to address the issues of structured data, there has recently been great interest in the development and application of text mining techniques to make more effective use of the knowledge contained in biomedical scientific publications, accessible only in the form of natural human language. This thesis describes research done in the broader scope of projects aiming to develop methods, tools and techniques for text mining tasks in general and for the biomedical domain in particular. The work described here involves more specifically the goal of extracting information from statements concerning relations of biomedical entities, such as protein-protein interactions. The approach taken is one using full parsing—syntactic analysis of the entire structure of sentences—and machine learning, aiming to develop reliable methods that can further be generalized to apply also to other domains. The five papers at the core of this thesis describe research on a number of distinct but related topics in text mining. In the first of these studies, we assessed the applicability of two popular general English parsers to biomedical text mining and, finding their performance limited, identified several specific challenges to accurate parsing of domain text. In a follow-up study focusing on parsing issues related to specialized domain terminology, we evaluated three lexical adaptation methods. We found that the accurate resolution of unknown words can considerably improve parsing performance and introduced a domain-adapted parser that reduced the error rate of theoriginal by 10% while also roughly halving parsing time. To establish the relative merits of parsers that differ in the applied formalisms and the representation given to their syntactic analyses, we have also developed evaluation methodology, considering different approaches to establishing comparable dependency-based evaluation results. We introduced a methodology for creating highly accurate conversions between different parse representations, demonstrating the feasibility of unification of idiverse syntactic schemes under a shared, application-oriented representation. In addition to allowing formalism-neutral evaluation, we argue that such unification can also increase the value of parsers for domain text mining. As a further step in this direction, we analysed the characteristics of publicly available biomedical corpora annotated for protein-protein interactions and created tools for converting them into a shared form, thus contributing also to the unification of text mining resources. The introduced unified corpora allowed us to perform a task-oriented comparative evaluation of biomedical text mining corpora. This evaluation established clear limits on the comparability of results for text mining methods evaluated on different resources, prompting further efforts toward standardization. To support this and other research, we have also designed and annotated BioInfer, the first domain corpus of its size combining annotation of syntax and biomedical entities with a detailed annotation of their relationships. The corpus represents a major design and development effort of the research group, with manual annotation that identifies over 6000 entities, 2500 relationships and 28,000 syntactic dependencies in 1100 sentences. In addition to combining these key annotations for a single set of sentences, BioInfer was also the first domain resource to introduce a representation of entity relations that is supported by ontologies and able to capture complex, structured relationships. Part I of this thesis presents a summary of this research in the broader context of a text mining system, and Part II contains reprints of the five included publications.