Language modelling for clinical natural language understanding and generation

One of the long-standing objectives of Artificial Intelligence (AI) is to design and develop algorithms for social good including tackling public health challenges. In the era of digitisation, with an unprecedented amount of healthcare data being captured in digital form, the analysis of the healthcare data at scale can lead to better research of diseases, better monitoring patient conditions and more importantly improving patient outcomes. However, many AI-based analytic algorithms rely solely on structured healthcare data such as bedside measurements and test results which only account for 20% of all healthcare data, whereas the remaining 80% of healthcare data is unstructured including textual data such as clinical notes and discharge summaries which is still underexplored. Conventional Natural Language Processing (NLP) algorithms that are designed for clinical applications rely on the shallow matching, templates and non-contextualised word embeddings which lead to limited understanding of contextual semantics. Though recent advances in NLP algorithms have demonstrated promising performance on a variety of NLP tasks in the general domain with contextualised language models, most of these generic NLP algorithms struggle at specific clinical NLP tasks which require biomedical knowledge and reasoning. Besides, there is limited research to study generative NLP algorithms to generate clinical reports and summaries automatically by considering salient clinical information. This thesis aims to design and develop novel NLP algorithms especially clinical-driven contextualised language models to understand textual healthcare data and generate clinical narratives which can potentially support clinicians, medical scientists and patients. The first contribution of this thesis focuses on capturing phenotypic information of patients from clinical notes which is important to profile patient situation and improve patient outcomes. The thesis proposes a novel self-supervised language model, named Phenotypic Intelligence Extraction (PIE), to annotate phenotypes from clinical notes with the detection of contextual synonyms and the enhancement to reason with numerical values. The second contribution is to demonstrate the utility and benefits of using phenotypic features of patients in clinical use cases by predicting patient outcomes in Intensive Care Units (ICU) and identifying patients at risk of specific diseases with better accuracy and model interpretability. The third contribution is to propose generative models to generate clinical narratives to automate and accelerate the process of report writing and summarisation by clinicians. This thesis first proposes a novel summarisation language model named PEGASUS which surpasses or is on par with the state-of-the-art performance on 12 downstream datasets including biomedical literature from PubMed. PEGASUS is further extended to generate medical scientific documents from input tabular data.Open Acces

Presuppositions in Context: Constructing Bridges

About the book: The First International and Interdisciplinary Conference on Modelling and Using Context, Rio de Janeiro, January 1997, gave rise to the present book, which contains a selection of the papers presented there, thoroughly refereed and revised. The treatment of contexts as bona fide objects of logical formalisation has gained wide acceptance, following the seminal impetus given by McCarthy in his Turing Award address. The field of natural language offers a particularly rich variety of examples and challenges to researchers concerned with the formal modelling of context, and several chapters in the volume deal with contextualisation in the setting of natural language. Others adopt a purely formal-logical viewpoint, seeking to develop general models of even wider applicability. The 12 chapters are organised in three groups: formalisation of contextual information in natural language understanding and generation, the application of context in mechanised reasoning domains, and novel non-classical logics for contextual application

Topic Modelling of Swedish Newspaper Articles about Coronavirus: a Case Study using Latent Dirichlet Allocation Method

Topic Modelling (TM) is from the research branches of natural language understanding (NLU) and natural language processing (NLP) that is to facilitate insightful analysis from large documents and datasets, such as a summarisation of main topics and the topic changes. This kind of discovery is getting more popular in real-life applications due to its impact on big data analytics. In this study, from the social-media and healthcare domain, we apply popular Latent Dirichlet Allocation (LDA) methods to model the topic changes in Swedish newspaper articles about Coronavirus. We describe the corpus we created including 6515 articles, methods applied, and statistics on topic changes over approximately 1 year and two months period of time from 17th January 2020 to 13th March 2021. We hope this work can be an asset for grounding applications of topic modelling and can be inspiring for similar case studies in an era with pandemics, to support socio-economic impact research as well as clinical and healthcare analytics. Our data and source code are openly available at https://github. com/poethan/Swed_Covid_TM Keywords: Latent Dirichlet Allocation (LDA); Topic Modelling; Coronavirus; Pandemics; Natural Language Understanding; BERT-topicComment: 14 pages, 14 figure

Jack the reader : a machine reading framework

Many Machine Reading and Natural Language Understanding tasks require reading supporting text in order to answer questions. For example, in Question Answering, the supporting text can be newswire orWikipedia articles; in Natural Language Inference, premises can be seen as the supporting text and hypotheses as questions. Providing a set of useful primitives operating in a single framework of related tasks would allow for expressive modelling, and easier model comparison and replication. To that end, we present Jack the Reader (JACK), a framework for Machine Reading that allows for quick model prototyping by component reuse, evaluation of new models on existing datasets as well as integrating new datasets and applying them on a growing set of implemented baseline models. JACK is currently supporting (but not limited to) three tasks: Question Answering, Natural Language Inference, and Link Prediction. It is developed with the aim of increasing research efficiency and code reuse

Multilingual Multi-Figurative Language Detection

Figures of speech help people express abstract concepts and evoke stronger emotions than literal expressions, thereby making texts more creative and engaging. Due to its pervasive and fundamental character, figurative language understanding has been addressed in Natural Language Processing, but it's highly understudied in a multilingual setting and when considering more than one figure of speech at the same time. To bridge this gap, we introduce multilingual multi-figurative language modelling, and provide a benchmark for sentence-level figurative language detection, covering three common figures of speech and seven languages. Specifically, we develop a framework for figurative language detection based on template-based prompt learning. In so doing, we unify multiple detection tasks that are interrelated across multiple figures of speech and languages, without requiring task- or language-specific modules. Experimental results show that our framework outperforms several strong baselines and may serve as a blueprint for the joint modelling of other interrelated tasks.Comment: Accepted to ACL 2023 (Findings

Multilingual Multi-Figurative Language Detection

Figures of speech help people express abstract concepts and evoke stronger emotions than literal expressions, thereby making texts more creative and engaging. Due to its pervasive and fundamental character, figurative language understanding has been addressed in Natural Language Processing, but it's highly understudied in a multilingual setting and when considering more than one figure of speech at the same time. To bridge this gap, we introduce multilingual multi-figurative language modelling, and provide a benchmark for sentence-level figurative language detection, covering three common figures of speech and seven languages. Specifically, we develop a framework for figurative language detection based on template-based prompt learning. In so doing, we unify multiple detection tasks that are interrelated across multiple figures of speech and languages, without requiring task- or language-specific modules. Experimental results show that our framework outperforms several strong baselines and may serve as a blueprint for the joint modelling of other interrelated tasks.</p

Biocharts: a visual formalism for complex biological systems

We address one of the central issues in devising languages, methods and tools for the modelling and analysis of complex biological systems, that of linking high-level (e.g. intercellular) information with lower-level (e.g. intracellular) information. Adequate ways of dealing with this issue are crucial for understanding biological networks and pathways, which typically contain huge amounts of data that continue to grow as our knowledge and understanding of a system increases. Trying to comprehend such data using the standard methods currently in use is often virtually impossible. We propose a two-tier compound visual language, which we call Biocharts, that is geared towards building fully executable models of biological systems. One of the main goals of our approach is to enable biologists to actively participate in the computational modelling effort, in a natural way. The high-level part of our language is a version of statecharts, which have been shown to be extremely successful in software and systems engineering. The statecharts can be combined with any appropriately well-defined language (preferably a diagrammatic one) for specifying the low-level dynamics of the pathways and networks. We illustrate the language and our general modelling approach using the well-studied process of bacterial chemotaxis

Enhancing natural language understanding using meaning representation and deep learning

Natural Language Understanding (NLU) is one of the complex tasks in artificial intelligence. Machine learning was introduced to address the complex and dynamic nature of natural language. Deep learning gained popularity within the NLU community due to its capability of learning features directly from data, as well as learning from the dynamic nature of natural language. Furthermore, deep learning has shown to be able to learn the hidden feature(s) automatically and outperform most of the other machine learning approaches for NLU. Deep learning models require natural language inputs to be converted to vectors (word embedding). Word2Vec and GloVe are word embeddings which are designed to capture the analogy context-based statistics and provide lexical relations on words. Using the context-based statistical approach does not capture the prior knowledge required to understand language combined with words. Although a deep learning model receives word embedding, language understanding requires Reasoning, Attention and Memory (RAM). RAM are key factors in understanding language. Current deep learning models focus either on reasoning, attention or memory. In order to properly understand a language however, all three factors of RAM should be considered. Also, a language normally has a long sequence. This long sequence creates dependencies which are required in order to understand a language. However, current deep learning models, which are developed to hold longer sequences, either forget or get affected by the vanishing or exploding gradient descent. In this thesis, these three main areas are of focus. A word embedding technique, which integrates analogy context-based statistical and semantic relationships, as well as extracts from a knowledge base to hold enhanced meaning representation, is introduced. Also, a Long Short-Term Reinforced Memory (LSTRM) network is introduced. This addresses RAM and is validated by testing on question answering data sets which require RAM. Finally, a Long Term Memory Network (LTM) is introduced to address language modelling. Good language modelling requires learning from long sequences. Therefore, this thesis demonstrates that integrating semantic knowledge and a knowledge base generates enhanced meaning and deep learning models that are capable of achieving RAM and long-term dependencies so as to improve the capability of NLU