GRAPH BASESD WORD SENSE DISAMBIGUATION FOR CLINICAL ABBREVIATIONS USING APACHE SPARK

Identification of the correct sense for an ambiguous word is one of the major challenges for language processing in all domains. Word Sense Disambiguation is the task of identifying the correct sense of an ambiguous word by referencing the surrounding context of the word. Similar to the narrative documents, clinical documents suffer from ambiguity issues that impact automatic extraction of correct sense from the document. In this project, we propose a graph-based solution based on an algorithm originally implemented by Osmar R. Zaine et al. for word sense disambiguation specifically focusing on clinical text. The algorithm makes use of proposed UMLS Metathesaurus as its source of knowledge. As an enhancement to the existing implementation of the algorithm, this project uses Apache Spark - A Big Data Technology for cluster based distributed processing and performance optimization

Interactive Machine Learning with Applications in Health Informatics

Recent years have witnessed unprecedented growth of health data, including millions of biomedical research publications, electronic health records, patient discussions on health forums and social media, fitness tracker trajectories, and genome sequences. Information retrieval and machine learning techniques are powerful tools to unlock invaluable knowledge in these data, yet they need to be guided by human experts. Unlike training machine learning models in other domains, labeling and analyzing health data requires highly specialized expertise, and the time of medical experts is extremely limited. How can we mine big health data with little expert effort? In this dissertation, I develop state-of-the-art interactive machine learning algorithms that bring together human intelligence and machine intelligence in health data mining tasks. By making efficient use of human expert's domain knowledge, we can achieve high-quality solutions with minimal manual effort. I first introduce a high-recall information retrieval framework that helps human users efficiently harvest not just one but as many relevant documents as possible from a searchable corpus. This is a common need in professional search scenarios such as medical search and literature review. Then I develop two interactive machine learning algorithms that leverage human expert's domain knowledge to combat the curse of "cold start" in active learning, with applications in clinical natural language processing. A consistent empirical observation is that the overall learning process can be reliably accelerated by a knowledge-driven "warm start", followed by machine-initiated active learning. As a theoretical contribution, I propose a general framework for interactive machine learning. Under this framework, a unified optimization objective explains many existing algorithms used in practice, and inspires the design of new algorithms.PHDComputer Science & EngineeringUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttps://deepblue.lib.umich.edu/bitstream/2027.42/147518/1/raywang_1.pd

Multi-domain clinical natural language processing with MedCAT: The Medical Concept Annotation Toolkit

Electronic health records (EHR) contain large volumes of unstructured text, requiring the application of information extraction (IE) technologies to enable clinical analysis. We present the open source Medical Concept Annotation Toolkit (MedCAT) that provides: (a) a novel self-supervised machine learning algorithm for extracting concepts using any concept vocabulary including UMLS/SNOMED-CT; (b) a feature-rich annotation interface for customizing and training IE models; and (c) integrations to the broader CogStack ecosystem for vendor-agnostic health system deployment. We show improved performance in extracting UMLS concepts from open datasets (F1:0.448-0.738 vs 0.429-0.650). Further real-world validation demonstrates SNOMED-CT extraction at 3 large London hospitals with self-supervised training over ∼8.8B words from ∼17M clinical records and further fine-tuning with ∼6K clinician annotated examples. We show strong transferability (F1 > 0.94) between hospitals, datasets and concept types indicating cross-domain EHR-agnostic utility for accelerated clinical and research use cases

Neural Graph Transfer Learning in Natural Language Processing Tasks

Natural language is essential in our daily lives as we rely on languages to communicate and exchange information. A fundamental goal for natural language processing (NLP) is to let the machine understand natural language to help or replace human experts to mine knowledge and complete tasks. Many NLP tasks deal with sequential data. For example, a sentence is considered as a sequence of works. Very recently, deep learning-based language models (i.e.,BERT \citep{devlin2018bert}) achieved significant improvement in many existing tasks, including text classification and natural language inference. However, not all tasks can be formulated using sequence models. Specifically, graph-structured data is also fundamental in NLP, including entity linking, entity classification, relation extraction, abstractive meaning representation, and knowledge graphs \citep{santoro2017simple,hamilton2017representation,kipf2016semi}. In this scenario, BERT-based pretrained models may not be suitable. Graph Convolutional Neural Network (GCN) \citep{kipf2016semi} is a deep neural network model designed for graphs. It has shown great potential in text classification, link prediction, question answering and so on. This dissertation presents novel graph models for NLP tasks, including text classification, prerequisite chain learning, and coreference resolution. We focus on different perspectives of graph convolutional network modeling: for text classification, a novel graph construction method is proposed which allows interpretability for the prediction; for prerequisite chain learning, we propose multiple aggregation functions that utilize neighbors for better information exchange; for coreference resolution, we study how graph pretraining can help when labeled data is limited. Moreover, an important branch is to apply pretrained language models for the mentioned tasks. So, this dissertation also focuses on the transfer learning method that generalizes pretrained models to other domains, including medical, cross-lingual, and web data. Finally, we propose a new task called unsupervised cross-domain prerequisite chain learning, and study novel graph-based methods to transfer knowledge over graphs

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

Deep learning for clinical texts in low-data regimes

Electronic health records contain a wealth of valuable information for improving healthcare. There are, however, challenges associated with clinical text that prevent computers from maximising the utility of such information. While deep learning (DL) has emerged as a practical paradigm for dealing with the complexities of natural language, applying this class of machine learning algorithms to clinical text raises several research questions. First, we tackled the problem of data sparsity by looking into the task of adverse event detection. As these events are rare, examples thereof are lacking. To compensate for data scarcity, we leveraged large pre-trained language models (LMs) in combination with formally represented medical knowledge. We demonstrated that such a combination exhibits remarkable generalisation abilities despite the low availability of data. Second, we focused on the omnipresence of short forms in clinical texts. This typically leads to out-of-vocabulary problems, which motivates unlocking the underlying words. The novelty of our approach lies in its capacity to learn how to automatically expand short forms without resorting to external resources. Third, we investigated data augmentation to address the issue of data scarcity at its core. To the best of our knowledge, we were one of the firsts to investigate population-based augmentation for scheduling text data augmentation. Interestingly, little improvement was seen in fine-tuning large pre-trained LMs with the augmented data. We suggest that, as LMs proved able to cope well with small datasets, the need for data augmentation was made redundant. We conclude that DL approaches to clinical text mining should be developed by fine-tuning large LMs. One area where such models may struggle is the use of clinical short forms. Our method to automating their expansion fixes this issue. Together, these two approaches provide a blueprint for successfully developing DL approaches to clinical text mining in low-data regimes