Methods of Disambiguating and De-anonymizing Authorship in Large Scale Operational Data

Operational data from software development, social networks and other domains are often contaminated with incorrect or missing values. Examples include misspelled or changed names, multiple emails belonging to the same person and user profiles that vary in different systems. Such digital traces are extensively used in research and practice to study collaborating communities of various kinds. To achieve a realistic representation of the networks that represent these communities, accurate identities are essential. In this work, we aim to identify, model, and correct identity errors in data from open-source software repositories, which include more than 23M developer IDs and nearly 1B Git commits (developer activity records). Our investigation into the nature and prevalence of identity errors in software activity data reveals that they are different and occur at much higher rates than other domains. Existing techniques relying on string comparisons can only disambiguate Synonyms, but not Homonyms, which are common in software activity traces. Therefore, we introduce measures of behavioral fingerprinting to improve the accuracy of Synonym resolution, and to disambiguate Homonyms. Fingerprints are constructed from the traces of developers’ activities, such as, the style of writing in commit messages, the patterns in files modified and projects participated in by developers, and the patterns related to the timing of the developers’ activity. Furthermore, to address the lack of training data necessary for the supervised learning approaches that are used in disambiguation, we design a specific active learning procedure that minimizes the manual effort necessary to create training data in the domain of developer identity matching. We extensively evaluate the proposed approach, using over 16,000 OpenStack developers in 1200 projects, against commercial and most recent research approaches, and further on recent research on a much larger sample of over 2,000,000 IDs. Results demonstrate that our method is significantly better than both the recent research and commercial methods. We also conduct experiments to demonstrate that such erroneous data have significant impact on developer networks. We hope that the proposed approach will expedite research progress in the domain of software engineering, especially in applications for which graphs of social networks are critical

Evaluating a European knowledge hub on climate change in agriculture:Are we building a better connected community?

In order to maintain food security and sustainability of production under climate change, interdisciplinary and international collaboration in research is essential. In the EU, knowledge hubs are important funding instruments for the development of an interconnected European Research Area. Here, network analysis was used to assess whether the pilot knowledge hub MACSUR has affected interdisciplinary collaboration, using co-authorship of peer reviewed articles as a measure of collaboration. The broad community of all authors identified as active in the field of agriculture and climate change was increasingly well connected over the period studied. Between knowledge hub members, changes in network parameters suggest an increase in collaborative interaction beyond that expected due to network growth, and greater than that found in the broader community. Given that interdisciplinary networks often take several years to have an impact on research outputs, these changes within the relatively new MACSUR community provide evidence that the knowledge hub structure has been effective in stimulating collaboration. However, analysis showed that knowledge hub partners were initially well-connected, suggesting that the initiative may have gathered together researchers with particular resources or inclinations towards collaborative working. Long term, consistent funding and ongoing reflection to improve networking structures may be necessary to sustain the early positive signs from MACSUR, to extend its success to a wider community of researchers, or to repeat it in less connected fields of science. Tackling complex challenges such as climate change will require research structures that can effectively support and utilise the diversity of talents beyond the already well-connected core of scientists at major research institutes. But network research shows that this core, well-connected group are vital brokers in achieving wider integration

Learning Embeddings for Academic Papers

Academic papers contain both text and citation links. Representing such data is crucial for many downstream tasks, such as classification, disambiguation, duplicates detection, recommendation and influence prediction. The success of Skip-gram with Negative Sampling model (hereafter SGNS) has inspired many algorithms to learn embeddings for words, documents, and networks. However, there is limited research on learning the representation of linked documents such as academic papers. This dissertation first studies the norm convergence issue in SGNS and propose to use an L2 regularization to fix the problem. Our experiments show that our method improves SGNS and its variants on different types of data. We observe improvements upto 17.47% for word embeddings, 1.85% for document embeddings, and 46.41% for network embeddings. To learn the embeddings for academic papers, we propose several neural network based algorithms that can learn high-quality embeddings from different types of data. The algorithms we proposed are N2V (network2vector) for networks, D2V (document2vector) for documents, and P2V (paper2vector) for academic papers. Experiments show that our models outperform traditional algorithms and the state-of-the-art neural network methods on various datasets under different machine learning tasks. With the high quality embeddings, we design and present four applications on real-world datasets, i.e., academic paper and author search engines, author name disambiguation, and paper influence prediction

Knowledge-Driven Methods for Geographic Information Extraction in the Biomedical Domain

abstract: Accounting for over a third of all emerging and re-emerging infections, viruses represent a major public health threat, which researchers and epidemiologists across the world have been attempting to contain for decades. Recently, genomics-based surveillance of viruses through methods such as virus phylogeography has grown into a popular tool for infectious disease monitoring. When conducting such surveillance studies, researchers need to manually retrieve geographic metadata denoting the location of infected host (LOIH) of viruses from public sequence databases such as GenBank and any publication related to their study. The large volume of semi-structured and unstructured information that must be reviewed for this task, along with the ambiguity of geographic locations, make it especially challenging. Prior work has demonstrated that the majority of GenBank records lack sufficient geographic granularity concerning the LOIH of viruses. As a result, reviewing full-text publications is often necessary for conducting in-depth analysis of virus migration, which can be a very time-consuming process. Moreover, integrating geographic metadata pertaining to the LOIH of viruses from different sources, including different fields in GenBank records as well as full-text publications, and normalizing the integrated metadata to unique identifiers for subsequent analysis, are also challenging tasks, often requiring expert domain knowledge. Therefore, automated information extraction (IE) methods could help significantly accelerate this process, positively impacting public health research. However, very few research studies have attempted the use of IE methods in this domain. This work explores the use of novel knowledge-driven geographic IE heuristics for extracting, integrating, and normalizing the LOIH of viruses based on information available in GenBank and related publications; when evaluated on manually annotated test sets, the methods were found to have a high accuracy and shown to be adequate for addressing this challenging problem. It also presents GeoBoost, a pioneering software system for georeferencing GenBank records, as well as a large-scale database containing over two million virus GenBank records georeferenced using the algorithms introduced here. The methods, database and software developed here could help support diverse public health domains focusing on sequence-informed virus surveillance, thereby enhancing existing platforms for controlling and containing disease outbreaks.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201

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

Tag disambiguation based on social network information

Within 20 years the Web has grown from a tool for scientists at CERN into a global information space. While returning to its roots as a read/write tool, its entering a more social and participatory phase. Hence a new, improved version called the Social Web where users are responsible for generating and sharing content on the global information space, they are also accountable for replicating the information. This collaborative activity can be observed in two of the most widely practised Social Web services such as social network sites and social tagging systems. Users annotate their interests and inclinations with free form keywords while they share them with their social connections. Although these keywords (tag) assist information organization and retrieval, theysuffer from polysemy.In this study we employ the effectiveness of social network sites to address the issue of ambiguity in social tagging. Moreover, we also propose that homophily in social network sites can be a useful aspect is disambiguating tags. We have extracted the ‘Likes’ of 20 Facebook users and employ them in disambiguation tags on Flickr. Classifiers are generated on the retrieved clusters from Flickr using K-Nearest-Neighbour algorithm and then their degree of similarity is calculated with user keywords. As tag disambiguation techniques lack gold standards for evaluation, we asked the users to indicate the contexts and used them as ground truth while examining the results. We analyse the performance of our approach by quantitative methods and report successful results. Our proposed method is able classify images with an accuracy of 6 out of 10 (on average). Qualitative analysis reveal some factors that affect the findings, and if addressed can produce more precise results

Biomedical Information Extraction Pipelines for Public Health in the Age of Deep Learning

abstract: Unstructured texts containing biomedical information from sources such as electronic health records, scientific literature, discussion forums, and social media offer an opportunity to extract information for a wide range of applications in biomedical informatics. Building scalable and efficient pipelines for natural language processing and extraction of biomedical information plays an important role in the implementation and adoption of applications in areas such as public health. Advancements in machine learning and deep learning techniques have enabled rapid development of such pipelines. This dissertation presents entity extraction pipelines for two public health applications: virus phylogeography and pharmacovigilance. For virus phylogeography, geographical locations are extracted from biomedical scientific texts for metadata enrichment in the GenBank database containing 2.9 million virus nucleotide sequences. For pharmacovigilance, tools are developed to extract adverse drug reactions from social media posts to open avenues for post-market drug surveillance from non-traditional sources. Across these pipelines, high variance is observed in extraction performance among the entities of interest while using state-of-the-art neural network architectures. To explain the variation, linguistic measures are proposed to serve as indicators for entity extraction performance and to provide deeper insight into the domain complexity and the challenges associated with entity extraction. For both the phylogeography and pharmacovigilance pipelines presented in this work the annotated datasets and applications are open source and freely available to the public to foster further research in public health.Dissertation/ThesisDoctoral Dissertation Biomedical Informatics 201

Towards Name Disambiguation: Relational, Streaming, and Privacy-Preserving Text Data

In the real world, our DNA is unique but many people share names. This phenomenon often causes erroneous aggregation of documents of multiple persons who are namesakes of one another. Such mistakes deteriorate the performance of document retrieval, web search, and more seriously, cause improper attribution of credit or blame in digital forensics. To resolve this issue, the name disambiguation task 1 is designed to partition the documents associated with a name reference such that each partition contains documents pertaining to a unique real-life person. Existing algorithms for this task mainly suffer from the following drawbacks. First, the majority of existing solutions substantially rely on feature engineering, such as biographical feature extraction, or construction of auxiliary features from Wikipedia. However, for many scenarios, such features may be costly to obtain or unavailable in privacy sensitive domains. Instead we solve the name disambiguation task in restricted setting by leveraging only the relational data in the form of anonymized graphs. Second, most of the existing works for this task operate in a batch mode, where all records to be disambiguated are initially available to the algorithm. However, more realistic settings require that the name disambiguation task should be performed in an online streaming fashion in order to identify records of new ambiguous entities having no preexisting records. Finally, we investigate the potential disclosure risk of textual features used in name disambiguation and propose several algorithms to tackle the task in a privacy-aware scenario. In summary, in this dissertation, we present a number of novel approaches to address name disambiguation tasks from the above three aspects independently, namely relational, streaming, and privacy preserving textual data