Surprise: An Alternative Qualitative Uncertainty Model

This dissertation embodies a study of the concept of surprise as a base for constructing qualitative calculi for representing and reasoning about uncertain knowledge. Two functions are presented, kappa++} and z, which construct qualitative ranks for events by obtaining the order of magnitude abstraction of the degree of surprise associated with them. The functions use natural numbers to classify events based their associated surprise and aim at providing a ranking that improves those provided by existing ranking functions. This in turn enables the use of such functions in an a la carte probabilistic system where one can choose the level of detail required to represent uncertain knowledge depending on the requirements of the application. The proposed ranking functions are defined along with surprise-update models associated with them. The reasoning mechanisms associated with the functions are developed mathematically and graphically. The advantages and expected limitations of both functions are compared with respect to each other and with existing ranking functions in the context of a bioinformatics application known as \u27\u27reverse engineering of genetic regulatory networks\u27\u27 in which the relations among various genetic components are discovered through the examination of a large amount of collected data. The ranking functions are examined in this context via graphical models which are exclusively developed or this purpose and which utilize the developed functions to represent uncertain knowledge at various levels of details

Comparing Natural Language Processing Techniques for Alzheimer's Dementia Prediction in Spontaneous Speech

Alzheimer's Dementia (AD) is an incurable, debilitating, and progressive neurodegenerative condition that affects cognitive function. Early diagnosis is important as therapeutics can delay progression and give those diagnosed vital time. Developing models that analyse spontaneous speech could eventually provide an efficient diagnostic modality for earlier diagnosis of AD. The Alzheimer's Dementia Recognition through Spontaneous Speech task offers acoustically pre-processed and balanced datasets for the classification and prediction of AD and associated phenotypes through the modelling of spontaneous speech. We exclusively analyse the supplied textual transcripts of the spontaneous speech dataset, building and comparing performance across numerous models for the classification of AD vs controls and the prediction of Mental Mini State Exam scores. We rigorously train and evaluate Support Vector Machines (SVMs), Gradient Boosting Decision Trees (GBDT), and Conditional Random Fields (CRFs) alongside deep learning Transformer based models. We find our top performing models to be a simple Term Frequency-Inverse Document Frequency (TF-IDF) vectoriser as input into a SVM model and a pre-trained Transformer based model `DistilBERT' when used as an embedding layer into simple linear models. We demonstrate test set scores of 0.81-0.82 across classification metrics and a RMSE of 4.58.Comment: Submitted to INTERSPEECH 2020: Alzheimer's Dementia Recognition through Spontaneous Speech The ADReSS Challenge Worksho

Modeling Rare Interactions in Time Series Data Through Qualitative Change: Application to Outcome Prediction in Intensive Care Units

Many areas of research are characterised by the deluge of large-scale highly-dimensional time-series data. However, using the data available for prediction and decision making is hampered by the current lag in our ability to uncover and quantify true interactions that explain the outcomes.We are interested in areas such as intensive care medicine, which are characterised by i) continuous monitoring of multivariate variables and non-uniform sampling of data streams, ii) the outcomes are generally governed by interactions between a small set of rare events, iii) these interactions are not necessarily definable by specific values (or value ranges) of a given group of variables, but rather, by the deviations of these values from the normal state recorded over time, iv) the need to explain the predictions made by the model. Here, while numerous data mining models have been formulated for outcome prediction, they are unable to explain their predictions. We present a model for uncovering interactions with the highest likelihood of generating the outcomes seen from highly-dimensional time series data. Interactions among variables are represented by a relational graph structure, which relies on qualitative abstractions to overcome non-uniform sampling and to capture the semantics of the interactions corresponding to the changes and deviations from normality of variables of interest over time. Using the assumption that similar templates of small interactions are responsible for the outcomes (as prevalent in the medical domains), we reformulate the discovery task to retrieve the most-likely templates from the data.Comment: 8 pages, 3 figures. Accepted for publication in the European Conference of Artificial Intelligence (ECAI 2020

Experimental Evaluation and Development of a Silver-Standard for the MIMIC-III Clinical Coding Dataset

Clinical coding is currently a labour-intensive, error-prone, but critical administrative process whereby hospital patient episodes are manually assigned codes by qualified staff from large, standardised taxonomic hierarchies of codes. Automating clinical coding has a long history in NLP research and has recently seen novel developments setting new state of the art results. A popular dataset used in this task is MIMIC-III, a large intensive care database that includes clinical free text notes and associated codes. We argue for the reconsideration of the validity MIMIC-III's assigned codes that are often treated as gold-standard, especially when MIMIC-III has not undergone secondary validation. This work presents an open-source, reproducible experimental methodology for assessing the validity of codes derived from EHR discharge summaries. We exemplify the methodology with MIMIC-III discharge summaries and show the most frequently assigned codes in MIMIC-III are under-coded up to 35%

Discharge Summary Hospital Course Summarisation of In Patient Electronic Health Record Text with Clinical Concept Guided Deep Pre-Trained Transformer Models

Brief Hospital Course (BHC) summaries are succinct summaries of an entire hospital encounter, embedded within discharge summaries, written by senior clinicians responsible for the overall care of a patient. Methods to automatically produce summaries from inpatient documentation would be invaluable in reducing clinician manual burden of summarising documents under high time-pressure to admit and discharge patients. Automatically producing these summaries from the inpatient course, is a complex, multi-document summarisation task, as source notes are written from various perspectives (e.g. nursing, doctor, radiology), during the course of the hospitalisation. We demonstrate a range of methods for BHC summarisation demonstrating the performance of deep learning summarisation models across extractive and abstractive summarisation scenarios. We also test a novel ensemble extractive and abstractive summarisation model that incorporates a medical concept ontology (SNOMED) as a clinical guidance signal and shows superior performance in 2 real-world clinical data sets

On Classifying Sepsis Heterogeneity in the ICU: Insight Using Machine Learning

Current machine learning models aiming to predict sepsis from Electronic Health Records (EHR) do not account for the heterogeneity of the condition, despite its emerging importance in prognosis and treatment. This work demonstrates the added value of stratifying the types of organ dysfunction observed in patients who develop sepsis in the ICU in improving the ability to recognise patients at risk of sepsis from their EHR data. Using an ICU dataset of 13,728 records, we identify clinically significant sepsis subpopulations with distinct organ dysfunction patterns. Classification experiments using Random Forest, Gradient Boost Trees and Support Vector Machines, aiming to distinguish patients who develop sepsis in the ICU from those who do not, show that features selected using sepsis subpopulations as background knowledge yield a superior performance regardless of the classification model used. Our findings can steer machine learning efforts towards more personalised models for complex conditions including sepsis.Comment: 3 Figures and 2 tables. Accepted for publication at the Journal of American Medical Informatics Associatio

Knowledge graph prediction of unknown adverse drug reactions and validation in electronic health records

Abstract Unknown adverse reactions to drugs available on the market present a significant health risk and limit accurate judgement of the cost/benefit trade-off for medications. Machine learning has the potential to predict unknown adverse reactions from current knowledge. We constructed a knowledge graph containing four types of node: drugs, protein targets, indications and adverse reactions. Using this graph, we developed a machine learning algorithm based on a simple enrichment test and first demonstrated this method performs extremely well at classifying known causes of adverse reactions (AUC 0.92). A cross validation scheme in which 10% of drug-adverse reaction edges were systematically deleted per fold showed that the method correctly predicts 68% of the deleted edges on average. Next, a subset of adverse reactions that could be reliably detected in anonymised electronic health records from South London and Maudsley NHS Foundation Trust were used to validate predictions from the model that are not currently known in public databases. High-confidence predictions were validated in electronic records significantly more frequently than random models, and outperformed standard methods (logistic regression, decision trees and support vector machines). This approach has the potential to improve patient safety by predicting adverse reactions that were not observed during randomised trials

A Knowledge Distillation Ensemble Framework for Predicting Short and Long-term Hospitalisation Outcomes from Electronic Health Records Data

The ability to perform accurate prognosis of patients is crucial for proactive clinical decision making, informed resource management and personalised care. Existing outcome prediction models suffer from a low recall of infrequent positive outcomes. We present a highly-scalable and robust machine learning framework to automatically predict adversity represented by mortality and ICU admission from time-series vital signs and laboratory results obtained within the first 24 hours of hospital admission. The stacked platform comprises two components: a) an unsupervised LSTM Autoencoder that learns an optimal representation of the time-series, using it to differentiate the less frequent patterns which conclude with an adverse event from the majority patterns that do not, and b) a gradient boosting model, which relies on the constructed representation to refine prediction, incorporating static features of demographics, admission details and clinical summaries. The model is used to assess a patient's risk of adversity over time and provides visual justifications of its prediction based on the patient's static features and dynamic signals. Results of three case studies for predicting mortality and ICU admission show that the model outperforms all existing outcome prediction models, achieving PR-AUC of 0.891 (95$$ CI: 0.878 - 0.969) in predicting mortality in ICU and general ward settings and 0.908 (95$$ CI: 0.870-0.935) in predicting ICU admission.Comment: 14 page