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

Learning to Extract Action Descriptions from Narrative Text

This paper focuses on the mapping of natural language sentences in written stories to a structured knowledge representation. This process yields an exponential explosion of instance combinations since each sentence may contain a set of ambiguous terms, each one giving place to a set of instance candidates. The selection of the best combination of instances is a structured classification problem that yields a highdemanding combinatorial optimization problem which, in this paper, is approached by a novel and efficient formulation of a genetic algorithm, which is able to exploit the conditional independence among variables, while improving the parallel scalability. The automatic rating of the resulting set of instance combinations, i.e. possible text interpretations, demands an exhaustive exploitation of the state-of-the-art resources in natural language processing to feed the system with pieces of evidence to be fused by the proposed framework. In this sense, a mapping framework able to reason with uncertainty, to integrate supervision, and evidence from external sources, was adopted. To improve the generalization capacity while learning from a limited amount of annotated data, a new constrained learning algorithm for Bayesian networks is introduced. This algorithm bounds the search space through a set of constraints which encode information on mutually exclusive values. The mapping of natural language utterances to a structured knowledge representation is important in the context of game construction, e.g. in an RPG setting, as it alleviates the manual knowledge acquisition bottleneck. The effectiveness of the proposed algorithm is evaluated on a set of three stories, yielding nine experiments. Our mapping framework yields performance gains in predicting the most likely structured representations of sentences when compared with a baseline algorithm

CDˆ2CR:Co-reference resolution across documents and domains

Cross-document co-reference resolution (CDCR) is the task of identifying and linking mentions to entities and concepts across many text documents. Current state-of-the-art models for this task assume that all documents are of the same type (e.g. news articles) or fall under the same theme. However, it is also desirable to perform CDCR across different domains (type or theme). A particular use case we focus on in this paper is the resolution of entities mentioned across scientific work and newspaper articles that discuss them. Identifying the same entities and corresponding concepts in both scientific articles and news can help scientists understand how their work is represented in mainstream media. We propose a new task and English language dataset for cross-document cross-domain co-reference resolution (CD$^2$CR). The task aims to identify links between entities across heterogeneous document types. We show that in this cross-domain, cross-document setting, existing CDCR models do not perform well and we provide a baseline model that outperforms current state-of-the-art CDCR models on CD$^2$CR. Our data set, annotation tool and guidelines as well as our model for cross-document cross-domain co-reference are all supplied as open access open source resources.Comment: 9 pages, 5 figures, accepted at EACL 202

A modular, open-source information extraction framework for identifying clinical concepts and processes of care in clinical narratives

In this thesis, a synthesis is presented of the knowledge models required by clinical informa- tion systems that provide decision support for longitudinal processes of care. Qualitative research techniques and thematic analysis are novelly applied to a systematic review of the literature on the challenges in implementing such systems, leading to the development of an original conceptual framework. The thesis demonstrates how these process-oriented systems make use of a knowledge base derived from workflow models and clinical guidelines, and argues that one of the major barriers to implementation is the need to extract explicit and implicit information from diverse resources in order to construct the knowledge base. Moreover, concepts in both the knowledge base and in the electronic health record (EHR) must be mapped to a common ontological model. However, the majority of clinical guideline information remains in text form, and much of the useful clinical information residing in the EHR resides in the free text fields of progress notes and laboratory reports. In this thesis, it is shown how natural language processing and information extraction techniques provide a means to identify and formalise the knowledge components required by the knowledge base. Original contributions are made in the development of lexico-syntactic patterns and the use of external domain knowledge resources to tackle a variety of information extraction tasks in the clinical domain, such as recognition of clinical concepts, events, temporal relations, term disambiguation and abbreviation expansion. Methods are developed for adapting existing tools and resources in the biomedical domain to the processing of clinical texts, and approaches to improving the scalability of these tools are proposed and evalu- ated. These tools and techniques are then combined in the creation of a novel approach to identifying processes of care in the clinical narrative. It is demonstrated that resolution of coreferential and anaphoric relations as narratively and temporally ordered chains provides a means to extract linked narrative events and processes of care from clinical notes. Coreference performance in discharge summaries and progress notes is largely dependent on correct identification of protagonist chains (patient, clinician, family relation), pronominal resolution, and string matching that takes account of experiencer, temporal, spatial, and anatomical context; whereas for laboratory reports additional, external domain knowledge is required. The types of external knowledge and their effects on system performance are identified and evaluated. Results are compared against existing systems for solving these tasks and are found to improve on them, or to approach the performance of recently reported, state-of-the- art systems. Software artefacts developed in this research have been made available as open-source components within the General Architecture for Text Engineering framework

Clinical text data in machine learning: Systematic review

Background: Clinical narratives represent the main form of communication within healthcare providing a personalized account of patient history and assessments, offering rich information for clinical decision making. Natural language processing (NLP) has repeatedly demonstrated its feasibility to unlock evidence buried in clinical narratives. Machine learning can facilitate rapid development of NLP tools by leveraging large amounts of text data. Objective: The main aim of this study is to provide systematic evidence on the properties of text data used to train machine learning approaches to clinical NLP. We also investigate the types of NLP tasks that have been supported by machine learning and how they can be applied in clinical practice. Methods: Our methodology was based on the guidelines for performing systematic reviews. In August 2018, we used PubMed, a multi-faceted interface, to perform a literature search against MEDLINE. We identified a total of 110 relevant studies and extracted information about the text data used to support machine learning, the NLP tasks supported and their clinical applications. The data properties considered included their size, provenance, collection methods, annotation and any relevant statistics. Results: The vast majority of datasets used to train machine learning models included only hundreds or thousands of documents. Only 10 studies used tens of thousands of documents with a handful of studies utilizing more. Relatively small datasets were utilized for training even when much larger datasets were available. The main reason for such poor data utilization is the annotation bottleneck faced by supervised machine learning algorithms. Active learning was explored to iteratively sample a subset of data for manual annotation as a strategy for minimizing the annotation effort while maximizing predictive performance of the model. Supervised learning was successfully used where clinical codes integrated with free text notes into electronic health records were utilized as class labels. Similarly, distant supervision was used to utilize an existing knowledge base to automatically annotate raw text. Where manual annotation was unavoidable, crowdsourcing was explored, but it remains unsuitable due to sensitive nature of data considered. Beside the small volume, training data were typically sourced from a small number of institutions, thus offering no hard evidence about the transferability of machine learning models. The vast majority of studies focused on the task of text classification. Most commonly, the classification results were used to support phenotyping, prognosis, care improvement, resource management and surveillance. Conclusions: We identified the data annotation bottleneck as one of the key obstacles to machine learning approaches in clinical NLP. Active learning and distant supervision were explored as a way of saving the annotation efforts. Future research in this field would benefit from alternatives such as data augmentation and transfer learning, or unsupervised learning, which does not require data annotation