An Automated Method to Enrich and Expand Consumer Health Vocabularies Using GloVe Word Embeddings

Clear language makes communication easier between any two parties. However, a layman may have difficulty communicating with a professional due to not understanding the specialized terms common to the domain. In healthcare, it is rare to find a layman knowledgeable in medical jargon, which can lead to poor understanding of their condition and/or treatment. To bridge this gap, several professional vocabularies and ontologies have been created to map laymen medical terms to professional medical terms and vice versa. Many of the presented vocabularies are built manually or semi-automatically requiring large investments of time and human effort and consequently the slow growth of these vocabularies. In this dissertation, we present an automatic method to enrich existing concepts in a medical ontology with additional laymen terms and also to expand the number of concepts in the ontology that do not have associated laymen terms. Our work has the benefit of being applicable to vocabularies in any domain. Our entirely automatic approach uses machine learning, specifically Global Vectors for Word Embeddings (GloVe), on a corpus collected from a social media healthcare platform to extend and enhance consumer health vocabularies. We improve these vocabularies by incorporating synonyms and hyponyms from the WordNet ontology. By performing iterative feedback using GloVe’s candidate terms, we can boost the number of word occurrences in the co-occurrence matrix allowing our approach to work with a smaller training corpus. Our novel algorithms and GloVe were evaluated using two laymen datasets from the National Library of Medicine (NLM), the Open-Access and Collaborative Consumer Health Vocabulary (OAC CHV) and the MedlinePlus Healthcare Vocabulary. For our first goal, enriching concepts, the results show that GloVe was able to find new laymen terms with an F-score of 48.44%. Our best algorithm enhanced the corpus with synonyms from WordNet, outperformed GloVe with an F-score relative improvement of 25%. For our second goal, expanding the number of concepts with related laymen’s terms, our synonym-enhanced GloVe outperformed GloVe with a relative F-score relative improvement of 63%. The results of the system were in general promising and can be applied not only to enrich and expand laymen vocabularies for medicine but any ontology for a domain, given an appropriate corpus for the domain. Our approach is applicable to narrow domains that may not have the huge training corpora typically used with word embedding approaches. In essence, by incorporating an external source of linguistic information, WordNet, and expanding the training corpus, we are getting more out of our training corpus. Our system can help building an application for patients where they can read their physician\u27s letters more understandably and clearly. Moreover, the output of this system can be used to improve the results of healthcare search engines, entity recognition systems, and many others

A Comparison of Word Embedding Techniques for Similarity Analysis

There have been a multitude of word embedding techniques developed that allow a computer to process natural language and compare the relationships between different words programmatically. In this paper, similarity analysis, or the testing of words for synonymic relations, is used to compare several of these techniques to see which performs the best. The techniques being compared all utilize the method of creating word vectors, reducing words down into a single vector of numerical values that denote how the word relates to other words that appear around it. In order to get a holistic comparison, multiple analyses were made, with the WOVe technique performing the best overall at producing both the most synonyms and the most accurate synonyms

UW-BHI at MEDIQA 2019: An Analysis of Representation Methods for Medical Natural Language Inference

Recent advances in distributed language modeling have led to large performance increases on a variety of natural language processing (NLP) tasks. However, it is not well understood how these methods may be augmented by knowledge-based approaches. This paper compares the performance and internal representation of an Enhanced Sequential Inference Model (ESIM) between three experimental conditions based on the representation method: Bidirectional Encoder Representations from Transformers (BERT), Embeddings of Semantic Predications (ESP), or Cui2Vec. The methods were evaluated on the Medical Natural Language Inference (MedNLI) subtask of the MEDIQA 2019 shared task. This task relied heavily on semantic understanding and thus served as a suitable evaluation set for the comparison of these representation methods

Content Enrichment of Digital Libraries: Methods, Technologies and Implementations

Parallel to the establishment of the concept of a "digital library", there have been rapid developments in the fields of semantic technologies, information retrieval and artificial intelligence. The idea is to use make use of these three fields to crosslink bibliographic data, i.e., library content, and to enrich it "intelligently" with additional, especially non-library, information. By linking the contents of a library, it is possible to offer users access to semantically similar contents of different digital libraries. For instance, a list of semantically similar publications from completely different subject areas and from different digital libraries can be made accessible. In addition, the user is able to see a wider profile about authors, enriched with information such as biographical details, name alternatives, images, job titles, institute affiliations, etc. This information comes from a wide variety of sources, most of which are not library sources. In order to make such scenarios a reality, this dissertation follows two approaches. The first approach is about crosslinking digital library content in order to offer semantically similar publications based on additional information for a publication. Hence, this approach uses publication-related metadata as a basis. The aligned terms between linked open data repositories/thesauri are considered as an important starting point by considering narrower, broader and related concepts through semantic data models such as SKOS. Information retrieval methods are applied to identify publications with high semantic similarity. For this purpose, approaches of vector space models and "word embedding" are applied and analyzed comparatively. The analyses are performed in digital libraries with different thematic focuses (e.g. economy and agriculture). Using machine learning techniques, metadata is enriched, e.g. with synonyms for content keywords, in order to further improve similarity calculations. To ensure quality, the proposed approaches will be analyzed comparatively with different metadata sets, which will be assessed by experts. Through the combination of different information retrieval methods, the quality of the results can be further improved. This is especially true when user interactions offer possibilities for adjusting the search properties. In the second approach, which this dissertation pursues, author-related data are harvested in order to generate a comprehensive author profile for a digital library. For this purpose, non-library sources, such as linked data repositories (e.g. WIKIDATA) and library sources, such as authority data, are used. If such different sources are used, the disambiguation of author names via the use of already existing persistent identifiers becomes necessary. To this end, we offer an algorithmic approach to disambiguate authors, which makes use of authority data such as the Virtual International Authority File (VIAF). Referring to computer sciences, the methodological value of this dissertation lies in the combination of semantic technologies with methods of information retrieval and artificial intelligence to increase the interoperability between digital libraries and between libraries with non-library sources. By positioning this dissertation as an application-oriented contribution to improve the interoperability, two major contributions are made in the context of digital libraries: (1) The retrieval of information from different Digital Libraries can be made possible via a single access. (2) Existing information about authors is collected from different sources and aggregated into one author profile.Parallel zur Etablierung des Konzepts einer „Digitalen Bibliothek“ gab es rasante Weiterentwicklungen in den Bereichen semantischer Technologien, Information Retrieval und künstliche Intelligenz. Die Idee ist es, mit ihrer Hilfe bibliographische Daten, also Inhalte von Bibliotheken, miteinander zu vernetzen und „intelligent“ mit zusätzlichen, insbesondere nicht-bibliothekarischen Informationen anzureichern. Durch die Verknüpfung von Inhalten einer Bibliothek wird es möglich, einen Zugang für Benutzer*innen anzubieten, über den semantisch ähnliche Inhalte unterschiedlicher Digitaler Bibliotheken zugänglich werden. Beispielsweise können hierüber ausgehend von einer bestimmten Publikation eine Liste semantisch ähnlicher Publikationen ggf. aus völlig unterschiedlichen Themenfeldern und aus verschiedenen digitalen Bibliotheken zugänglich gemacht werden. Darüber hinaus können sich Nutzer*innen ein breiteres Autoren-Profil anzeigen lassen, das mit Informationen wie biographischen Angaben, Namensalternativen, Bildern, Berufsbezeichnung, Instituts-Zugehörigkeiten usw. angereichert ist. Diese Informationen kommen aus unterschiedlichsten und in der Regel nicht-bibliothekarischen Quellen. Um derartige Szenarien Realität werden zu lassen, verfolgt diese Dissertation zwei Ansätze. Der erste Ansatz befasst sich mit der Vernetzung von Inhalten Digitaler Bibliotheken, um auf Basis zusätzlicher Informationen für eine Publikation semantisch ähnliche Publikationen anzubieten. Dieser Ansatz verwendet publikationsbezogene Metadaten als Grundlage. Die verknüpften Begriffe zwischen verlinkten offenen Datenrepositorien/Thesauri werden als wichtiger Angelpunkt betrachtet, indem Unterbegriffe, Oberbegriffe und verwandten Konzepte über semantische Datenmodelle, wie SKOS, berücksichtigt werden. Methoden des Information Retrieval werden angewandt, um v.a. Publikationen mit hoher semantischer Verwandtschaft zu identifizieren. Zu diesem Zweck werden Ansätze des Vektorraummodells und des „Word Embedding“ eingesetzt und vergleichend analysiert. Die Analysen werden in Digitalen Bibliotheken mit unterschiedlichen thematischen Schwerpunkten (z.B. Wirtschaft und Landwirtschaft) durchgeführt. Durch Techniken des maschinellen Lernens werden hierfür Metadaten angereichert, z.B. mit Synonymen für inhaltliche Schlagwörter, um so Ähnlichkeitsberechnungen weiter zu verbessern. Zur Sicherstellung der Qualität werden die beiden Ansätze mit verschiedenen Metadatensätzen vergleichend analysiert wobei die Beurteilung durch Expert*innen erfolgt. Durch die Verknüpfung verschiedener Methoden des Information Retrieval kann die Qualität der Ergebnisse weiter verbessert werden. Dies trifft insbesondere auch dann zu wenn Benutzerinteraktion Möglichkeiten zur Anpassung der Sucheigenschaften bieten. Im zweiten Ansatz, den diese Dissertation verfolgt, werden autorenbezogene Daten gesammelt, verbunden mit dem Ziel, ein umfassendes Autorenprofil für eine Digitale Bibliothek zu generieren. Für diesen Zweck kommen sowohl nicht-bibliothekarische Quellen, wie Linked Data-Repositorien (z.B. WIKIDATA) und als auch bibliothekarische Quellen, wie Normdatensysteme, zum Einsatz. Wenn solch unterschiedliche Quellen genutzt werden, wird die Disambiguierung von Autorennamen über die Nutzung bereits vorhandener persistenter Identifikatoren erforderlich. Hierfür bietet sich ein algorithmischer Ansatz für die Disambiguierung von Autoren an, der Normdaten, wie die des Virtual International Authority File (VIAF) nachnutzt. Mit Bezug zur Informatik liegt der methodische Wert dieser Dissertation in der Kombination von semantischen Technologien mit Verfahren des Information Retrievals und der künstlichen Intelligenz zur Erhöhung von Interoperabilität zwischen Digitalen Bibliotheken und zwischen Bibliotheken und nicht-bibliothekarischen Quellen. Mit der Positionierung dieser Dissertation als anwendungsorientierter Beitrag zur Verbesserung von Interoperabilität werden zwei wesentliche Beiträge im Kontext Digitaler Bibliotheken geleistet: (1) Die Recherche nach Informationen aus unterschiedlichen Digitalen Bibliotheken kann über einen Zugang ermöglicht werden. (2) Vorhandene Informationen über Autor*innen werden aus unterschiedlichsten Quellen eingesammelt und zu einem Autorenprofil aggregiert

Detection of Software Vulnerability Communication in Expert Social Media Channels: A Data-driven Approach

Conceptually, a vulnerability is: A flaw or weakness in a system’s design, implementation,or operation and management that could be exploited to violate the system’s security policy .Some of these flaws can go undetected and exploited for long periods of time after soft-ware release. Although some software providers are making efforts to avoid this situ-ation, inevitability, users are still exposed to vulnerabilities that allow criminal hackersto take advantage. These vulnerabilities are constantly discussed in specialised forumson social media. Therefore, from a cyber security standpoint, the information found inthese places can be used for countermeasures actions against malicious exploitation ofsoftware. However, manual inspection of the vast quantity of shared content in socialmedia is impractical. For this reason, in this thesis, we analyse the real applicability ofsupervised classification models to automatically detect software vulnerability com-munication in expert social media channels. We cover the following three principal aspects: Firstly, we investigate the applicability of classification models in a range of 5 differ-ent datasets collected from 3 Internet Domains: Dark Web, Deep Web and SurfaceWeb. Since supervised models require labelled data, we have provided a systematiclabelling process using multiple annotators to guarantee accurate labels to carry outexperiments. Using these datasets, we have investigated the classification models withdifferent combinations of learning-based algorithms and traditional features represen-tation. Also, by oversampling the positive instances, we have achieved an increaseof 5% in Positive Recall (on average) in these models. On top of that, we have appiiplied Feature Reduction, Feature Extraction and Feature Selection techniques, whichprovided a reduction on the dimensionality of these models without damaging the accuracy, thus, providing computationally efficient models. Furthermore, in addition to traditional features representation, we have investigated the performance of robust language models, such as Word Embedding (WEMB) andSentence Embedding (SEMB) on the accuracy of classification models. RegardingWEMB, our experiment has shown that this model trained with a small security-vocabulary dataset provides comparable results with WEMB trained in a very large general-vocabulary dataset. Regarding SEMB model, our experiment has shown thatits use overcomes WEMB model in detecting vulnerability communication, recording 8% of Avg. Class Accuracy and 74% of Positive Recall. In addition, we investigate twoDeep Learning algorithms as classifiers, text CNN (Convolutional Neural Network)and RNN (Recurrent Neural Network)-based algorithms, which have improved ourmodel, resulting in the best overall performance for our task