From Free Text to Clusters of Content in Health Records: An Unsupervised Graph Partitioning Approach

Electronic Healthcare records contain large volumes of unstructured data in different forms. Free text constitutes a large portion of such data, yet this source of richly detailed information often remains under-used in practice because of a lack of suitable methodologies to extract interpretable content in a timely manner. Here we apply network-theoretical tools to the analysis of free text in Hospital Patient Incident reports in the English National Health Service, to find clusters of reports in an unsupervised manner and at different levels of resolution based directly on the free text descriptions contained within them. To do so, we combine recently developed deep neural network text-embedding methodologies based on paragraph vectors with multi-scale Markov Stability community detection applied to a similarity graph of documents obtained from sparsified text vector similarities. We showcase the approach with the analysis of incident reports submitted in Imperial College Healthcare NHS Trust, London. The multiscale community structure reveals levels of meaning with different resolution in the topics of the dataset, as shown by relevant descriptive terms extracted from the groups of records, as well as by comparing a posteriori against hand-coded categories assigned by healthcare personnel. Our content communities exhibit good correspondence with well-defined hand-coded categories, yet our results also provide further medical detail in certain areas as well as revealing complementary descriptors of incidents beyond the external classification. We also discuss how the method can be used to monitor reports over time and across different healthcare providers, and to detect emerging trends that fall outside of pre-existing categories.Comment: 25 pages, 2 tables, 8 figures and 5 supplementary figure

A graph theoretical perspective for the unsupervised clustering of free text corpora

This thesis introduces a robust end to end topic discovery framework that extracts a set of coherent topics stemming intrinsically from document similarities. Some topic clustering methods can support embedded vectors instead of traditional Bag-of-Words (BoW) representation. Some can be free from the number of topics hyperparameter and some others can extract a multi-scale relation between topics. However, no topic clustering method supports all these properties together. This thesis focuses on this gap in the literature by designing a framework that supports any type of document-level features especially the embedded vectors. This framework does not require any uninformed decision making about the underlying data such as the number of topics, instead, the framework extracts topics in multiple resolutions. To achieve this goal, we combine existing methods from natural language processing (NLP) for feature generation and graph theory, first for graph construction based on semantic document similarities, then for graph partitioning to extract corresponding topics in multiple resolutions. Finally, we use specific methods from statistical machine learning to obtain highly generalisable supervised models to deploy topic classifiers for the deployment of topic extraction in real-time. Our applications on both a noisy and specialised corpus of medical records (i.e., descriptions for patient incidents within the NHS) and public news articles in daily language show that our framework extracts coherent topics that have better quantitative benchmark scores than other methods in most cases. The resulting multi-scale topics in both applications enable us to capture specific details more easily and choose the relevant resolutions for the specific objective. This study contributes to topic clustering literature by introducing a novel graph theoretical perspective that provides a combination of new properties. These properties are multiple resolutions, independence from uninformed decisions about the corpus, and usage of recent NLP features, such as vector embeddings.Open Acces

Distributed Load Testing by Modeling and Simulating User Behavior

Modern human-machine systems such as microservices rely upon agile engineering practices which require changes to be tested and released more frequently than classically engineered systems. A critical step in the testing of such systems is the generation of realistic workloads or load testing. Generated workload emulates the expected behaviors of users and machines within a system under test in order to find potentially unknown failure states. Typical testing tools rely on static testing artifacts to generate realistic workload conditions. Such artifacts can be cumbersome and costly to maintain; however, even model-based alternatives can prevent adaptation to changes in a system or its usage. Lack of adaptation can prevent the integration of load testing into system quality assurance, leading to an incomplete evaluation of system quality. The goal of this research is to improve the state of software engineering by addressing open challenges in load testing of human-machine systems with a novel process that a) models and classifies user behavior from streaming and aggregated log data, b) adapts to changes in system and user behavior, and c) generates distributed workload by realistically simulating user behavior. This research contributes a Learning, Online, Distributed Engine for Simulation and Testing based on the Operational Norms of Entities within a system (LODESTONE): a novel process to distributed load testing by modeling and simulating user behavior. We specify LODESTONE within the context of a human-machine system to illustrate distributed adaptation and execution in load testing processes. LODESTONE uses log data to generate and update user behavior models, cluster them into similar behavior profiles, and instantiate distributed workload on software systems. We analyze user behavioral data having differing characteristics to replicate human-machine interactions in a modern microservice environment. We discuss tools, algorithms, software design, and implementation in two different computational environments: client-server and cloud-based microservices. We illustrate the advantages of LODESTONE through a qualitative comparison of key feature parameters and experimentation based on shared data and models. LODESTONE continuously adapts to changes in the system to be tested which allows for the integration of load testing into the quality assurance process for cloud-based microservices

On semantic differences: a multivariate corpus-based study of the semantic field of inchoativity in translated and non-translated Dutch

This dissertation places the study of semantic differences in translation compared to non-translation at the centre of its concerns. To date, much research in Corpus-based Translation Studies has focused on lexical and grammatical phenomena in an attempt to reveal presumed general tendencies of translation. On the semantic level, these general tendencies have rarely been investigated. Therefore, the goal of this study is to explore whether universal tendencies of translation also exist on the semantic level, thereby connecting the framework of translation universals to semantics

Biomedical Image Processing and Classification

Biomedical image processing is an interdisciplinary field involving a variety of disciplines, e.g., electronics, computer science, physics, mathematics, physiology, and medicine. Several imaging techniques have been developed, providing many approaches to the study of the human body. Biomedical image processing is finding an increasing number of important applications in, for example, the study of the internal structure or function of an organ and the diagnosis or treatment of a disease. If associated with classification methods, it can support the development of computer-aided diagnosis (CAD) systems, which could help medical doctors in refining their clinical picture

Extracting the Structure and Conformations of Biological Entities from Large Datasets

In biology, structure determines function, which often proceeds via changes in conformation. Efficient means for determining structure exist, but mapping conformations continue to present a serious challenge. Single-particles approaches, such as cryogenic electron microscopy (cryo-EM) and emerging diffract & destroy X-ray techniques are, in principle, ideally positioned to overcome these challenges. But the algorithmic ability to extract information from large heterogeneous datasets consisting of unsorted snapshots - each emanating from an unknown orientation of an object in an unknown conformation - remains elusive. It is the objective of this thesis to describe and validate a powerful suite of manifold-based algorithms able to extract structural and conformational information from large datasets. These computationally efficient algorithms offer a new approach to determining the structure and conformations of viruses and macromolecules. After an introduction, we demonstrate a distributed, exact k-Nearest Neighbor Graph (k-NNG) construction method, in order to establish a firm algorithmic basis for manifold-based analysis. The proposed algorithm uses Graphics Processing Units (GPUs) and exploits multiple levels of parallelism in distributed computational environment and it is scalable for different cluster sizes, with each compute node in the cluster containing multiple GPUs. Next, we present applications of manifold-based analysis in determining structure and conformational variability. Using the Diffusion Map algorithm, a new approach is presented, which is capable of determining structure of symmetric objects, such as viruses, to 1/100th of the object diameter, using low-signal diffraction snapshots. This is demonstrated by means of a successful 3D reconstruction of the Satellite Tobacco Necrosis Virus (STNV) to atomic resolution from simulated diffraction snapshots with and without noise. We next present a new approach for determining discrete conformational changes of the enzyme Adenylate kinase (ADK) from very large datasets of up to 20 million snapshots, each with ~104 pixels. This exceeds by an order of magnitude the largest dataset previously analyzed. Finally, we present a theoretical framework and an algorithmic pipeline for capturing continuous conformational changes of the ribosome from ultralow-signal (-12dB) experimental cryo-EM. Our analysis shows a smooth, concerted change in molecular structure in two-dimensional projection, which might be indicative of the way the ribosome functions as a molecular machine. The thesis ends with a summary and future prospects

Acquiring and Harnessing Verb Knowledge for Multilingual Natural Language Processing

Advances in representation learning have enabled natural language processing models to derive non-negligible linguistic information directly from text corpora in an unsupervised fashion. However, this signal is underused in downstream tasks, where they tend to fall back on superficial cues and heuristics to solve the problem at hand. Further progress relies on identifying and filling the gaps in linguistic knowledge captured in their parameters. The objective of this thesis is to address these challenges focusing on the issues of resource scarcity, interpretability, and lexical knowledge injection, with an emphasis on the category of verbs. To this end, I propose a novel paradigm for efficient acquisition of lexical knowledge leveraging native speakers’ intuitions about verb meaning to support development and downstream performance of NLP models across languages. First, I investigate the potential of acquiring semantic verb classes from non-experts through manual clustering. This subsequently informs the development of a two-phase semantic dataset creation methodology, which combines semantic clustering with fine-grained semantic similarity judgments collected through spatial arrangements of lexical stimuli. The method is tested on English and then applied to a typologically diverse sample of languages to produce the first large-scale multilingual verb dataset of this kind. I demonstrate its utility as a diagnostic tool by carrying out a comprehensive evaluation of state-of-the-art NLP models, probing representation quality across languages and domains of verb meaning, and shedding light on their deficiencies. Subsequently, I directly address these shortcomings by injecting lexical knowledge into large pretrained language models. I demonstrate that external manually curated information about verbs’ lexical properties can support data-driven models in tasks where accurate verb processing is key. Moreover, I examine the potential of extending these benefits from resource-rich to resource-poor languages through translation-based transfer. The results emphasise the usefulness of human-generated lexical knowledge in supporting NLP models and suggest that time-efficient construction of lexicons similar to those developed in this work, especially in under-resourced languages, can play an important role in boosting their linguistic capacity.ESRC Doctoral Fellowship [ES/J500033/1], ERC Consolidator Grant LEXICAL [648909