Distributed knowledge based clinical auto-coding system

Codification of free-text clinical narratives have long been recognised to be beneficial for secondary uses such as funding, insurance claim processing and research. In recent years, many researchers have studied the use of Natural Language Processing (NLP), related Machine Learning (ML) methods and techniques to resolve the problem of manual coding of clinical narratives. Most of the studies are focused on classification systems relevant to the U.S and there is a scarcity of studies relevant to Australian classification systems such as ICD- 10-AM and ACHI. Therefore, we aim to develop a knowledge-based clinical auto-coding system, that utilise appropriate NLP and ML techniques to assign ICD-10-AM and ACHI codes to clinical records, while adhering to both local coding standards (Australian Coding Standard) and international guidelines that get updated and validated continuously

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

Extreme multi-label deep neural classification of Spanish health records according to the International Classification of Diseases

111 p.Este trabajo trata sobre la minería de textos clínicos, un campo del Procesamiento del Lenguaje Natural aplicado al dominio biomédico. El objetivo es automatizar la tarea de codificación médica. Los registros electrónicos de salud (EHR) son documentos que contienen información clínica sobre la salud de unpaciente. Los diagnósticos y procedimientos médicos plasmados en la Historia Clínica Electrónica están codificados con respecto a la Clasificación Internacional de Enfermedades (CIE). De hecho, la CIE es la base para identificar estadísticas de salud internacionales y el estándar para informar enfermedades y condiciones de salud. Desde la perspectiva del aprendizaje automático, el objetivo es resolver un problema extremo de clasificación de texto de múltiples etiquetas, ya que a cada registro de salud se le asignan múltiples códigos ICD de un conjunto de más de 70 000 términos de diagnóstico. Una cantidad importante de recursos se dedican a la codificación médica, una laboriosa tarea que actualmente se realiza de forma manual. Los EHR son narraciones extensas, y los codificadores médicos revisan los registros escritos por los médicos y asignan los códigos ICD correspondientes. Los textos son técnicos ya que los médicos emplean una jerga médica especializada, aunque rica en abreviaturas, acrónimos y errores ortográficos, ya que los médicos documentan los registros mientras realizan la práctica clínica real. Paraabordar la clasificación automática de registros de salud, investigamos y desarrollamos un conjunto de técnicas de clasificación de texto de aprendizaje profundo

Explainable Prediction of Medical Codes from Clinical Text

Clinical notes are text documents that are created by clinicians for each patient encounter. They are typically accompanied by medical codes, which describe the diagnosis and treatment. Annotating these codes is labor intensive and error prone; furthermore, the connection between the codes and the text is not annotated, obscuring the reasons and details behind specific diagnoses and treatments. We present an attentional convolutional network that predicts medical codes from clinical text. Our method aggregates information across the document using a convolutional neural network, and uses an attention mechanism to select the most relevant segments for each of the thousands of possible codes. The method is accurate, achieving precision@8 of 0.71 and a Micro-F1 of 0.54, which are both better than the prior state of the art. Furthermore, through an interpretability evaluation by a physician, we show that the attention mechanism identifies meaningful explanations for each code assignmentComment: NAACL 201

Robust input representations for low-resource information extraction

Recent advances in the field of natural language processing were achieved with deep learning models. This led to a wide range of new research questions concerning the stability of such large-scale systems and their applicability beyond well-studied tasks and datasets, such as information extraction in non-standard domains and languages, in particular, in low-resource environments. In this work, we address these challenges and make important contributions across fields such as representation learning and transfer learning by proposing novel model architectures and training strategies to overcome existing limitations, including a lack of training resources, domain mismatches and language barriers. In particular, we propose solutions to close the domain gap between representation models by, e.g., domain-adaptive pre-training or our novel meta-embedding architecture for creating a joint representations of multiple embedding methods. Our broad set of experiments demonstrates state-of-the-art performance of our methods for various sequence tagging and classification tasks and highlight their robustness in challenging low-resource settings across languages and domains.Die jüngsten Fortschritte auf dem Gebiet der Verarbeitung natürlicher Sprache wurden mit Deep-Learning-Modellen erzielt. Dies führte zu einer Vielzahl neuer Forschungsfragen bezüglich der Stabilität solcher großen Systeme und ihrer Anwendbarkeit über gut untersuchte Aufgaben und Datensätze hinaus, wie z. B. die Informationsextraktion für Nicht-Standardsprachen, aber auch Textdomänen und Aufgaben, für die selbst im Englischen nur wenige Trainingsdaten zur Verfügung stehen. In dieser Arbeit gehen wir auf diese Herausforderungen ein und leisten wichtige Beiträge in Bereichen wie Repräsentationslernen und Transferlernen, indem wir neuartige Modellarchitekturen und Trainingsstrategien vorschlagen, um bestehende Beschränkungen zu überwinden, darunter fehlende Trainingsressourcen, ungesehene Domänen und Sprachbarrieren. Insbesondere schlagen wir Lösungen vor, um die Domänenlücke zwischen Repräsentationsmodellen zu schließen, z.B. durch domänenadaptives Vortrainieren oder unsere neuartige Meta-Embedding-Architektur zur Erstellung einer gemeinsamen Repräsentation mehrerer Embeddingmethoden. Unsere umfassende Evaluierung demonstriert die Leistungsfähigkeit unserer Methoden für verschiedene Klassifizierungsaufgaben auf Word und Satzebene und unterstreicht ihre Robustheit in anspruchsvollen, ressourcenarmen Umgebungen in verschiedenen Sprachen und Domänen

Children with mixed developmental language disorder have more insecure patterns of attachment.

Developmental Language disorders (DLD) are developmental disorders that can affect both expressive and receptive language. When severe and persistent, they are often associated with psychiatric comorbidities and poor social outcome. The development of language involves early parent-infant interactions. The quality of these interactions is reflected in the quality of the child's attachment patterns. We hypothesized that children with DLD are at greater risk of insecure attachment, making them more vulnerable to psychiatric comorbidities. Therefore, we investigated the patterns of attachment of children with expressive and mixed expressive- receptive DLD. Forty-six participants, from 4 years 6 months to 7 years 5 months old, 12 with expressive Specific Language Impairment (DLD), and 35 with mixed DLD, were recruited through our learning disorder clinic, and compared to 23 normally developing children aged 3 years and a half. The quality of attachment was measured using the Attachment Stories Completion Task (ASCT) developed by Bretherton. Children with developmental mixed language disorders were significantly less secure and more disorganized than normally developing children. Investigating the quality of attachment in children with DLD in the early stages could be important to adapt therapeutic strategies and to improve their social and psychiatric outcomes later in life