Software Requirements Classification Using Word Embeddings and Convolutional Neural Networks

Software requirements classification, the practice of categorizing requirements by their type or purpose, can improve organization and transparency in the requirements engineering process and thus promote requirement fulfillment and software project completion. Requirements classification automation is a prominent area of research as automation can alleviate the tediousness of manual labeling and loosen its necessity for domain-expertise. This thesis explores the application of deep learning techniques on software requirements classification, specifically the use of word embeddings for document representation when training a convolutional neural network (CNN). As past research endeavors mainly utilize information retrieval and traditional machine learning techniques, we entertain the potential of deep learning on this particular task. With the support of learning libraries such as TensorFlow and Scikit-Learn and word embedding models such as word2vec and fastText, we build a Python system that trains and validates configurations of Naïve Bayes and CNN requirements classifiers. Applying our system to a suite of experiments on two well-studied requirements datasets, we recreate or establish the Naïve Bayes baselines and evaluate the impact of CNNs equipped with word embeddings trained from scratch versus word embeddings pre-trained on Big Data

Transforming user data into user value by novel mining techniques for extraction of web content, structure and usage patterns. The Development and Evaluation of New Web Mining Methods that enhance Information Retrieval and improve the Understanding of User¿s Web Behavior in Websites and Social Blogs.

The rapid growth of the World Wide Web in the last decade makes it the largest publicly accessible data source in the world, which has become one of the most significant and influential information revolution of modern times. The influence of the Web has impacted almost every aspect of humans' life, activities and fields, causing paradigm shifts and transformational changes in business, governance, and education. Moreover, the rapid evolution of Web 2.0 and the Social Web in the past few years, such as social blogs and friendship networking sites, has dramatically transformed the Web from a raw environment for information consumption to a dynamic and rich platform for information production and sharing worldwide. However, this growth and transformation of the Web has resulted in an uncontrollable explosion and abundance of the textual contents, creating a serious challenge for any user to find and retrieve the relevant information that he truly seeks to find on the Web. The process of finding a relevant Web page in a website easily and efficiently has become very difficult to achieve. This has created many challenges for researchers to develop new mining techniques in order to improve the user experience on the Web, as well as for organizations to understand the true informational interests and needs of their customers in order to improve their targeted services accordingly by providing the products, services and information that truly match the requirements of every online customer. With these challenges in mind, Web mining aims to extract hidden patterns and discover useful knowledge from Web page contents, Web hyperlinks, and Web usage logs. Based on the primary kinds of Web data used in the mining process, Web mining tasks can be categorized into three main types: Web content mining, which extracts knowledge from Web page contents using text mining techniques, Web structure mining, which extracts patterns from the hyperlinks that represent the structure of the website, and Web usage mining, which mines user's Web navigational patterns from Web server logs that record the Web page access made by every user, representing the interactional activities between the users and the Web pages in a website. The main goal of this thesis is to contribute toward addressing the challenges that have been resulted from the information explosion and overload on the Web, by proposing and developing novel Web mining-based approaches. Toward achieving this goal, the thesis presents, analyzes, and evaluates three major contributions. First, the development of an integrated Web structure and usage mining approach that recommends a collection of hyperlinks for the surfers of a website to be placed at the homepage of that website. Second, the development of an integrated Web content and usage mining approach to improve the understanding of the user's Web behavior and discover the user group interests in a website. Third, the development of a supervised classification model based on recent Social Web concepts, such as Tag Clouds, in order to improve the retrieval of relevant articles and posts from Web social blogs

ENHANCING IMAGE FINDABILITY THROUGH A DUAL-PERSPECTIVE NAVIGATION FRAMEWORK

This dissertation focuses on investigating whether users will locate desired images more efficiently and effectively when they are provided with information descriptors from both experts and the general public. This study develops a way to support image finding through a human-computer interface by providing subject headings and social tags about the image collection and preserving the information scent (Pirolli, 2007) during the image search experience. In order to improve search performance most proposed solutions integrating experts’ annotations and social tags focus on how to utilize controlled vocabularies to structure folksonomies which are taxonomies created by multiple users (Peters, 2009). However, these solutions merely map terms from one domain into the other without considering the inherent differences between the two. In addition, many websites reflect the benefits of using both descriptors by applying a multiple interface approach (McGrenere, Baecker, & Booth, 2002), but this type of navigational support only allows users to access one information source at a time. By contrast, this study is to develop an approach to integrate these two features to facilitate finding resources without changing their nature or forcing users to choose one means or the other. Driven by the concept of information scent, the main contribution of this dissertation is to conduct an experiment to explore whether the images can be found more efficiently and effectively when multiple access routes with two information descriptors are provided to users in the dual-perspective navigation framework. This framework has proven to be more effective and efficient than the subject heading-only and tag-only interfaces for exploratory tasks in this study. This finding can assist interface designers who struggle with determining what information is best to help users and facilitate the searching tasks. Although this study explicitly focuses on image search, the result may be applicable to wide variety of other domains. The lack of textual content in image systems makes them particularly hard to locate using traditional search methods. While the role of professionals in describing items in a collection of images, the role of the crowd in assigning social tags augments this professional effort in a cost effective manner

Still a Lot to Lose: The Role of Controlled Vocabulary in Keyword Searching

In their 2005 study, Gross and Taylor found that more than a third of records retrieved by keyword searches would be lost without subject headings. A review of the literature since then shows that numerous studies, in various disciplines, have found that a quarter to a third of records returned in a keyword search would be lost without controlled vocabulary. Other writers, though, have continued to suggest that controlled vocabulary be discontinued. Addressing criticisms of the Gross/Taylor study, this study replicates the search process in the same online catalog, but after the addition of automated enriched metadata such as tables of contents and summaries. The proportion of results that would be lost remains high

Web knowledge bases

Knowledge is key to natural language understanding. References to specific people, places and things in text are crucial to resolving ambiguity and extracting meaning. Knowledge Bases (KBs) codify this information for automated systems — enabling applications such as entity-based search and question answering. This thesis explores the idea that sites on the web may act as a KB, even if that is not their primary intent. Dedicated kbs like Wikipedia are a rich source of entity information, but are built and maintained at an ongoing cost in human effort. As a result, they are generally limited in terms of the breadth and depth of knowledge they index about entities. Web knowledge bases offer a distributed solution to the problem of aggregating entity knowledge. Social networks aggregate content about people, news sites describe events with tags for organizations and locations, and a diverse assortment of web directories aggregate statistics and summaries for long-tail entities notable within niche movie, musical and sporting domains. We aim to develop the potential of these resources for both web-centric entity Information Extraction (IE) and structured KB population. We first investigate the problem of Named Entity Linking (NEL), where systems must resolve ambiguous mentions of entities in text to their corresponding node in a structured KB. We demonstrate that entity disambiguation models derived from inbound web links to Wikipedia are able to complement and in some cases completely replace the role of resources typically derived from the KB. Building on this work, we observe that any page on the web which reliably disambiguates inbound web links may act as an aggregation point for entity knowledge. To uncover these resources, we formalize the task of Web Knowledge Base Discovery (KBD) and develop a system to automatically infer the existence of KB-like endpoints on the web. While extending our framework to multiple KBs increases the breadth of available entity knowledge, we must still consolidate references to the same entity across different web KBs. We investigate this task of Cross-KB Coreference Resolution (KB-Coref) and develop models for efficiently clustering coreferent endpoints across web-scale document collections. Finally, assessing the gap between unstructured web knowledge resources and those of a typical KB, we develop a neural machine translation approach which transforms entity knowledge between unstructured textual mentions and traditional KB structures. The web has great potential as a source of entity knowledge. In this thesis we aim to first discover, distill and finally transform this knowledge into forms which will ultimately be useful in downstream language understanding tasks

Development of a recommendation system for scientific literature based on deep learning

Dissertação de mestrado em BioinformaticsThe previous few decades have seen an enormous volume of articles from the scientific commu nity on the most diverse biomedical topics, making it extremely challenging for researchers to find relevant information. Methods like Machine Learning (ML) and Deep Learning (DL) have been used to create tools that can speed up this process. In that context, this work focuses on examining the performance of different ML and DL techniques when classifying biomedical documents, mainly regarding their relevance to given topics. To evaluate the different techniques, the dataset from the BioCreative VI Track 4 challenge was used. The objective of the challenge was to identify documents related to protein-protein interactions altered by mutations, a topic extremely important in precision medicine. Protein-protein interactions play a crucial role in the cellular mechanisms of all living organisms, and mutations in these interaction sites could be indicative of diseases. To handle the data to be used in training, some text processing methods were implemented in the Omnia package from OmniumAI, the host company of this work. Several preprocessing and feature extraction methods were implemented, such as removing stopwords and TF-IDF, which may be used in other case studies. They can be used either with generic text or biomedical text. These methods, in conjunction with ML pipelines already developed by the Omnia team, allowed the training of several traditional ML models. We were able to achieve a small improvement on performance, compared to the challenge baseline, when applying these traditional ML models on the same dataset. Regarding DL, testing with a CNN model, it was clear that the BioWordVec pre-trained embedding achieved the best performance of all pre-trained embeddings. Additionally, we explored the application of more complex DL models. These models achieved a better performance than the best challenge submission. BioLinkBERT managed an improvement of 0.4 percent points on precision, 4.9 percent points on recall, and 2.2 percent points on F1.As décadas anteriores assistiram a um enorme aumento no volume de artigos da comunidade científica sobre os mais diversos tópicos biomédicos, tornando extremamente difícil para os investigadores encontrar informação relevante. Métodos como Aprendizagem Máquina (AM) e Aprendizagem Profunda (AP) tem sido utilizados para criar ferramentas que podem acelerar este processo. Neste contexto, este trabalho centra-se na avaliação do desempenho de diferentes técnicas de AM e AP na classificação de documentos biomédicos, principalmente no que diz respeito à sua relevância para determinados tópicos. Para avaliar as diferentes técnicas, foi utilizado o conjunto de dados do desafio BioCreative VI Track 4. O objectivo do desafio era identificar documentos relacionados com as interações proteína-proteína alteradas por mutações, um tópico extremamente importante na medicina de precisão. As interacções proteína-proteína desempenham um papel crucial nos mecanismos celulares de todos os organismos vivos, e as mutações nestes locais de interacção podem ser indicativas de doenças. Para tratar os dados a utilizar no treino, alguns métodos de processamento de texto foram implementados no pacote Omnia da OmniumAI, a empresa anfitriã deste trabalho. Foram implementados vários métodos de pré-processamento e extracção de características, tais como a remoção de palavras irrelevantes e TF-IDF, que podem ser utilizados em outros casos de estudos, tanto com texto genérico quer com texto biomédico. Estes métodos, em conjunto com as pipelines de AM já desenvolvidas pela equipa da Omnia, permitiram o treino de vários modelos tradicionais de AM. Conseguimos alcançar uma pequena melhoria no desempenho, em comparação com a linha de referência do desafio, ao aplicar estes modelos tradicionais de AM no mesmo conjunto de dados. Relativamente a AP, testando com um modelo CNN, ficou claro que o embedding pré-treinado BioWordVec alcançou o melhor desempenho de todos os embeddings pré-treinados. Adicionalmente, exploramos a aplicação de modelos de AP mais complexos. Estes modelos alcançaram um melhor desempenho do que a melhor submissão do desafio. BioLinkBERT conseguiu uma melhoria de 0,4 pontos percentuais na precisão, 4,9 pontos percentuais no recall, e 2,2 pontos percentuais em F1

Document analysis by means of data mining techniques

The huge amount of textual data produced everyday by scientists, journalists and Web users, allows investigating many different aspects of information stored in the published documents. Data mining and information retrieval techniques are exploited to manage and extract information from huge amount of unstructured textual data. Text mining also known as text data mining is the processing of extracting high quality information (focusing relevance, novelty and interestingness) from text by identifying patterns etc. Text mining typically involves the process of structuring input text by means of parsing and other linguistic features or sometimes by removing extra data and then finding patterns from structured data. Patterns are then evaluated at last and interpretation of output is performed to accomplish the desired task. Recently, text mining has got attention in several fields such as in security (involves analysis of Internet news), for commercial (for search and indexing purposes) and in academic departments (such as answering query). Beyond searching the documents consisting the words given in a user query, text mining may provide direct answer to user by semantic web for content based (content meaning and its context). It can also act as intelligence analyst and can also be used in some email spam filters for filtering out unwanted material. Text mining usually includes tasks such as clustering, categorization, sentiment analysis, entity recognition, entity relation modeling and document summarization. In particular, summarization approaches are suitable for identifying relevant sentences that describe the main concepts presented in a document dataset. Furthermore, the knowledge existed in the most informative sentences can be employed to improve the understanding of user and/or community interests. Different approaches have been proposed to extract summaries from unstructured text documents. Some of them are based on the statistical analysis of linguistic features by means of supervised machine learning or data mining methods, such as Hidden Markov models, neural networks and Naive Bayes methods. An appealing research field is the extraction of summaries tailored to the major user interests. In this context, the problem of extracting useful information according to domain knowledge related to the user interests is a challenging task. The main topics have been to study and design of novel data representations and data mining algorithms useful for managing and extracting knowledge from unstructured documents. This thesis describes an effort to investigate the application of data mining approaches, firmly established in the subject of transactional data (e.g., frequent itemset mining), to textual documents. Frequent itemset mining is a widely exploratory technique to discover hidden correlations that frequently occur in the source data. Although its application to transactional data is well-established, the usage of frequent itemsets in textual document summarization has never been investigated so far. A work is carried on exploiting frequent itemsets for the purpose of multi-document summarization so a novel multi-document summarizer, namely ItemSum (Itemset-based Summarizer) is presented, that is based on an itemset-based model, i.e., a framework comprise of frequent itemsets, taken out from the document collection. Highly representative and not redundant sentences are selected for generating summary by considering both sentence coverage, with respect to a sentence relevance score, based on tf-idf statistics, and a concise and highly informative itemset-based model. To evaluate the ItemSum performance a suite of experiments on a collection of news articles has been performed. Obtained results show that ItemSum significantly outperforms mostly used previous summarizers in terms of precision, recall, and F-measure. We also validated our approach against a large number of approaches on the DUC’04 document collection. Performance comparisons, in terms of precision, recall, and F-measure, have been performed by means of the ROUGE toolkit. In most cases, ItemSum significantly outperforms the considered competitors. Furthermore, the impact of both the main algorithm parameters and the adopted model coverage strategy on the summarization performance are investigated as well. In some cases, the soundness and readability of the generated summaries are unsatisfactory, because the summaries do not cover in an effective way all the semantically relevant data facets. A step beyond towards the generation of more accurate summaries has been made by semantics-based summarizers. Such approaches combine the use of general-purpose summarization strategies with ad-hoc linguistic analysis. The key idea is to also consider the semantics behind the document content to overcome the limitations of general-purpose strategies in differentiating between sentences based on their actual meaning and context. Most of the previously proposed approaches perform the semantics-based analysis as a preprocessing step that precedes the main summarization process. Therefore, the generated summaries could not entirely reflect the actual meaning and context of the key document sentences. In contrast, we aim at tightly integrating the ontology-based document analysis into the summarization process in order to take the semantic meaning of the document content into account during the sentence evaluation and selection processes. With this in mind, we propose a new multi-document summarizer, namely Yago-based Summarizer, that integrates an established ontology-based entity recognition and disambiguation step. Named Entity Recognition from Yago ontology is being used for the task of text summarization. The Named Entity Recognition (NER) task is concerned with marking occurrences of a specific object being mentioned. These mentions are then classified into a set of predefined categories. Standard categories include “person”, “location”, “geo-political organization”, “facility”, “organization”, and “time”. The use of NER in text summarization improved the summarization process by increasing the rank of informative sentences. To demonstrate the effectiveness of the proposed approach, we compared its performance on the DUC’04 benchmark document collections with that of a large number of state-of-the-art summarizers. Furthermore, we also performed a qualitative evaluation of the soundness and readability of the generated summaries and a comparison with the results that were produced by the most effective summarizers. A parallel effort has been devoted to integrating semantics-based models and the knowledge acquired from social networks into a document summarization model named as SociONewSum. The effort addresses the sentence-based generic multi-document summarization problem, which can be formulated as follows: given a collection of news articles ranging over the same topic, the goal is to extract a concise yet informative summary, which consists of most salient document sentences. An established ontological model has been used to improve summarization performance by integrating a textual entity recognition and disambiguation step. Furthermore, the analysis of the user-generated content coming from Twitter has been exploited to discover current social trends and improve the appealing of the generated summaries. An experimental evaluation of the SociONewSum performance was conducted on real English-written news article collections and Twitter posts. The achieved results demonstrate the effectiveness of the proposed summarizer, in terms of different ROUGE scores, compared to state-of-the-art open source summarizers as well as to a baseline version of the SociONewSum summarizer that does not perform any UGC analysis. Furthermore, the readability of the generated summaries has also been analyzed

BlogForever D2.6: Data Extraction Methodology

This report outlines an inquiry into the area of web data extraction, conducted within the context of blog preservation. The report reviews theoretical advances and practical developments for implementing data extraction. The inquiry is extended through an experiment that demonstrates the effectiveness and feasibility of implementing some of the suggested approaches. More specifically, the report discusses an approach based on unsupervised machine learning that employs the RSS feeds and HTML representations of blogs. It outlines the possibilities of extracting semantics available in blogs and demonstrates the benefits of exploiting available standards such as microformats and microdata. The report proceeds to propose a methodology for extracting and processing blog data to further inform the design and development of the BlogForever platform

SUPPORT EFFECTIVE DISCOVERY MANAGEMENT IN VISUAL ANALYTICS

Visual analytics promises to supply analysts with the means necessary to ana- lyze complex datasets and make effective decisions in a timely manner. Although significant progress has been made towards effective data exploration in existing vi- sual analytics systems, few of them provide systematic solutions for managing the vast amounts of discoveries generated in data exploration processes. Analysts have to use off line tools to manually annotate, browse, retrieve, organize, and connect their discoveries. In addition, they have no convenient access to the important discoveries captured by collaborators. As a consequence, the lack of effective discovery manage- ment approaches severely hinders the analysts from utilizing the discoveries to make effective decisions. In response to this challenge, this dissertation aims to support effective discov- ery management in visual analytics. It contributes a general discovery manage- ment framework which achieves its effectiveness surrounding the concept of patterns, namely the results of users’ low-level analytic tasks. Patterns permit construction of discoveries together with users’ mental models and evaluation. Different from the mental models, the categories of patterns that can be discovered from data are pre- dictable and application-independent. In addition, the same set of information is often used to annotate patterns in the same category. Therefore, visual analytics sys- tems can semi-automatically annotate patterns in a formalized format by predicting what should be recorded for patterns in popular categories. Using the formalized an- notations, the framework also enhances the automation and efficiency of a variety of discovery management activities such as discovery browsing, retrieval, organization, association, and sharing. The framework seamlessly integrates them with the visual interactive explorations to support effective decision making. Guided by the discovery management framework, our second contribution lies in proposing a variety of novel discovery management techniques for facilitating the discovery management activities. The proposed techniques and framework are im- plemented in a prototype system, ManyInsights, to facilitate discovery management in multidimensional data exploration. To evaluate the prototype system, two long- term case studies are presented. They investigated how the discovery management techniques worked together to benefit exploratory data analysis and collaborative analysis. The studies allowed us to understand the advantages, the limitations, and design implications of ManyInsights and its underlying framework