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

Mining Primary Care Electronic Health Records for Automatic Disease Phenotyping: A Transparent Machine Learning Framework

(1) Background: We aimed to develop a transparent machine-learning (ML) framework to automatically identify patients with a condition from electronic health records (EHRs) via a parsimonious set of features. (2) Methods: We linked multiple sources of EHRs, including 917,496,869 primary care records and 40,656,805 secondary care records and 694,954 records from specialist surgeries between 2002 and 2012, to generate a unique dataset. Then, we treated patient identification as a problem of text classification and proposed a transparent disease-phenotyping framework. This framework comprises a generation of patient representation, feature selection, and optimal phenotyping algorithm development to tackle the imbalanced nature of the data. This framework was extensively evaluated by identifying rheumatoid arthritis (RA) and ankylosing spondylitis (AS). (3) Results: Being applied to the linked dataset of 9657 patients with 1484 cases of rheumatoid arthritis (RA) and 204 cases of ankylosing spondylitis (AS), this framework achieved accuracy and positive predictive values of 86.19% and 88.46%, respectively, for RA and 99.23% and 97.75% for AS, comparable with expert knowledge-driven methods. (4) Conclusions: This framework could potentially be used as an efficient tool for identifying patients with a condition of interest from EHRs, helping clinicians in clinical decision-support process

EDMON - Electronic Disease Surveillance and Monitoring Network: A Personalized Health Model-based Digital Infectious Disease Detection Mechanism using Self-Recorded Data from People with Type 1 Diabetes

Through time, we as a society have been tested with infectious disease outbreaks of different magnitude, which often pose major public health challenges. To mitigate the challenges, research endeavors have been focused on early detection mechanisms through identifying potential data sources, mode of data collection and transmission, case and outbreak detection methods. Driven by the ubiquitous nature of smartphones and wearables, the current endeavor is targeted towards individualizing the surveillance effort through a personalized health model, where the case detection is realized by exploiting self-collected physiological data from wearables and smartphones. This dissertation aims to demonstrate the concept of a personalized health model as a case detector for outbreak detection by utilizing self-recorded data from people with type 1 diabetes. The results have shown that infection onset triggers substantial deviations, i.e. prolonged hyperglycemia regardless of higher insulin injections and fewer carbohydrate consumptions. Per the findings, key parameters such as blood glucose level, insulin, carbohydrate, and insulin-to-carbohydrate ratio are found to carry high discriminative power. A personalized health model devised based on a one-class classifier and unsupervised method using selected parameters achieved promising detection performance. Experimental results show the superior performance of the one-class classifier and, models such as one-class support vector machine, k-nearest neighbor and, k-means achieved better performance. Further, the result also revealed the effect of input parameters, data granularity, and sample sizes on model performances. The presented results have practical significance for understanding the effect of infection episodes amongst people with type 1 diabetes, and the potential of a personalized health model in outbreak detection settings. The added benefit of the personalized health model concept introduced in this dissertation lies in its usefulness beyond the surveillance purpose, i.e. to devise decision support tools and learning platforms for the patient to manage infection-induced crises

A Performance-Explainability-Fairness Framework For Benchmarking ML Models

Machine learning (ML) models have achieved remarkable success in various applications; however, ensuring their robustness and fairness remains a critical challenge. In this research, we present a comprehensive framework designed to evaluate and benchmark ML models through the lenses of performance, explainability, and fairness. This framework addresses the increasing need for a holistic assessment of ML models, considering not only their predictive power but also their interpretability and equitable deployment. The proposed framework leverages a multi-faceted evaluation approach, integrating performance metrics with explainability and fairness assessments. Performance evaluation incorporates standard measures such as accuracy, precision, and recall, but extends to overall balanced error rate, overall area under the receiver operating characteristic (ROC) curve (AUC), to capture model behavior across different performance aspects. Explainability assessment employs state-of-the-art techniques to quantify the interpretability of model decisions, ensuring that model behavior can be understood and trusted by stakeholders. The fairness evaluation examines model predictions in terms of demographic parity, equalized odds, thereby addressing concerns of bias and discrimination in the deployment of ML systems. To demonstrate the practical utility of the framework, we apply it to a diverse set of ML algorithms across various functional domains, including finance, criminology, education, and healthcare prediction. The results showcase the importance of a balanced evaluation approach, revealing trade-offs between performance, explainability, and fairness that can inform model selection and deployment decisions. Furthermore, we provide insights into the analysis of tradeoffs in selecting the appropriate model for use cases where performance, interpretability and fairness are important. In summary, the Performance-Explainability-Fairness Framework offers a unified methodology for evaluating and benchmarking ML models, enabling practitioners and researchers to make informed decisions about model suitability and ensuring responsible and equitable AI deployment. We believe that this framework represents a crucial step towards building trustworthy and accountable ML systems in an era where AI plays an increasingly prominent role in decision-making processes

Inferring Complex Activities for Context-aware Systems within Smart Environments

The rising ageing population worldwide and the prevalence of age-related conditions such as physical fragility, mental impairments and chronic diseases have significantly impacted the quality of life and caused a shortage of health and care services. Over-stretched healthcare providers are leading to a paradigm shift in public healthcare provisioning. Thus, Ambient Assisted Living (AAL) using Smart Homes (SH) technologies has been rigorously investigated to help address the aforementioned problems. Human Activity Recognition (HAR) is a critical component in AAL systems which enables applications such as just-in-time assistance, behaviour analysis, anomalies detection and emergency notifications. This thesis is aimed at investigating challenges faced in accurately recognising Activities of Daily Living (ADLs) performed by single or multiple inhabitants within smart environments. Specifically, this thesis explores five complementary research challenges in HAR. The first study contributes to knowledge by developing a semantic-enabled data segmentation approach with user-preferences. The second study takes the segmented set of sensor data to investigate and recognise human ADLs at multi-granular action level; coarse- and fine-grained action level. At the coarse-grained actions level, semantic relationships between the sensor, object and ADLs are deduced, whereas, at fine-grained action level, object usage at the satisfactory threshold with the evidence fused from multimodal sensor data is leveraged to verify the intended actions. Moreover, due to imprecise/vague interpretations of multimodal sensors and data fusion challenges, fuzzy set theory and fuzzy web ontology language (fuzzy-OWL) are leveraged. The third study focuses on incorporating uncertainties caused in HAR due to factors such as technological failure, object malfunction, and human errors. Hence, existing studies uncertainty theories and approaches are analysed and based on the findings, probabilistic ontology (PR-OWL) based HAR approach is proposed. The fourth study extends the first three studies to distinguish activities conducted by more than one inhabitant in a shared smart environment with the use of discriminative sensor-based techniques and time-series pattern analysis. The final study investigates in a suitable system architecture with a real-time smart environment tailored to AAL system and proposes microservices architecture with sensor-based off-the-shelf and bespoke sensing methods. The initial semantic-enabled data segmentation study was evaluated with 100% and 97.8% accuracy to segment sensor events under single and mixed activities scenarios. However, the average classification time taken to segment each sensor events have suffered from 3971ms and 62183ms for single and mixed activities scenarios, respectively. The second study to detect fine-grained-level user actions was evaluated with 30 and 153 fuzzy rules to detect two fine-grained movements with a pre-collected dataset from the real-time smart environment. The result of the second study indicate good average accuracy of 83.33% and 100% but with the high average duration of 24648ms and 105318ms, and posing further challenges for the scalability of fusion rule creations. The third study was evaluated by incorporating PR-OWL ontology with ADL ontologies and Semantic-Sensor-Network (SSN) ontology to define four types of uncertainties presented in the kitchen-based activity. The fourth study illustrated a case study to extended single-user AR to multi-user AR by combining RFID tags and fingerprint sensors discriminative sensors to identify and associate user actions with the aid of time-series analysis. The last study responds to the computations and performance requirements for the four studies by analysing and proposing microservices-based system architecture for AAL system. A future research investigation towards adopting fog/edge computing paradigms from cloud computing is discussed for higher availability, reduced network traffic/energy, cost, and creating a decentralised system. As a result of the five studies, this thesis develops a knowledge-driven framework to estimate and recognise multi-user activities at fine-grained level user actions. This framework integrates three complementary ontologies to conceptualise factual, fuzzy and uncertainties in the environment/ADLs, time-series analysis and discriminative sensing environment. Moreover, a distributed software architecture, multimodal sensor-based hardware prototypes, and other supportive utility tools such as simulator and synthetic ADL data generator for the experimentation were developed to support the evaluation of the proposed approaches. The distributed system is platform-independent and currently supported by an Android mobile application and web-browser based client interfaces for retrieving information such as live sensor events and HAR results

A Framework for Analyzing and Optimizing Regional Bio-Emergency Response Plans

The presence of naturally occurring and man-made public health threats necessitate the design and implementation of mitigation strategies, such that adequate response is provided in a timely manner. Since multiple variables, such as geographic properties, resource constraints, and government mandated time-frames must be accounted for, computational methods provide the necessary tools to develop contingency response plans while respecting underlying data and assumptions. A typical response scenario involves the placement of points of dispensing (PODs) in the affected geographic region to supply vaccines or medications to the general public. Computational tools aid in the analysis of such response plans, as well as in the strategic placement of PODs, such that feasible response scenarios can be developed. Due to the sensitivity of bio-emergency response plans, geographic information, such as POD locations, must be kept confidential. The generation of synthetic geographic regions allows for the development of emergency response plans on non-sensitive data, as well as for the study of the effects of single geographic parameters. Further, synthetic representations of geographic regions allow for results to be published and evaluated by the scientific community. This dissertation presents methodology for the analysis of bio-emergency response plans, methods for plan optimization, as well as methodology for the generation of synthetic geographic regions

Hierarchical Modelling and Recognition of Activities of Daily Living

Activity recognition is becoming an increasingly important task in artificial intelligence. Successful activity recognition systems must be able to model and recognise activities ranging from simple short activities spanning a few seconds to complex longer activities spanning minutes or hours. We define activities as a set of qualitatively interesting interactions between people, objects and the environment. Accurate activity recognition is a desirable task in many scenarios such as surveillance, smart environments, robotic vision etc. In the domain of robotic vision specifically, there is now an increasing interest in autonomous robots that are able to operate without human intervention for long periods of time. The goal of this research is to build activity recognition approaches for such systems that are able to model and recognise simple short activities as well as complex longer activities arising from long-term autonomous operation of intelligent systems. The research makes the following key contributions: 1. We present a qualitative and quantitative representation to model simple activities as observed by autonomous systems. 2. We present a hierarchical framework to efficiently model complex activities that comprise of many sub-activities at varying levels of granularity. Simple activities are modelled using a discriminative model where a combined feature space, consisting of qualitative and quantitative spatio-temporal features, is generated in order to encode various aspects of the activity. Qualitative features are computed using qualitative spatio-temporal relations between human subjects and objects in order to abstractly represent the simple activity. Unlike current state-of-the-art approaches, our approach uses significantly fewer assumptions and does not require any knowledge about object types, their affordances, or the constituent activities of an activity. The optimal and most discriminating features are then extracted, using an entropy-based feature selection process, to best represent the training data. A novel approach for building models of complex long-term activities is presented as well. The proposed approach builds a hierarchical activity model from mark-up of activities acquired from multiple annotators in a video corpus. Multiple human annotators identify activities at different levels of conceptual granularity. Our method automatically infers a ‘part-of’ hierarchical activity model from this data using semantic similarity of textual annotations and temporal consistency. We then consolidate hierarchical structures learned from different training videos into a generalised hierarchical model represented as an extended grammar describing the over all activity. We then describe an inference mechanism to interpret new instances of activities. Simple short activity classes are first recognised using our previously learned generalised model. Given a test video, simple activities are detected as a stream of temporally complex low-level actions. We then use the learned extended grammar to infer the higher-level activities as a hierarchy over the low-level action input stream. We make use of three publicly available datasets to validate our two approaches of modelling simple to complex activities. These datasets have been annotated by multiple annotators through crowd-sourcing and in-house annotations. They consist of daily activity videos such as ‘cleaning microwave’, ‘having lunch in a restaurant’, ‘working in an office’ etc. The activities in these datasets have all been marked up at multiple levels of abstraction by multiple annotators, however no information on the ‘part-of’ relationship between activities is provided. The complexity of the videos and their annotations allows us to demonstrate the effectiveness of the proposed methods

Visualisation of Integrated Patient-Centric Data as Pathways: Enhancing Electronic Medical Records in Clinical Practice

Routinely collected data in hospital Electronic Medical Records (EMR) is rich and abundant but often not linked or analysed for purposes other than direct patient care. We have created a methodology to integrate patient-centric data from different EMR systems into clinical pathways that represent the history of all patient interactions with the hospital during the course of a disease and beyond. In this paper, the literature in the area of data visualisation in healthcare is reviewed and a method for visualising the journeys that patients take through care is discussed. Examples of the hidden knowledge that could be discovered using this approach are explored and the main application areas of visualisation tools are identified. This paper also highlights the challenges of collecting and analysing such data and making the visualisations extensively used in the medical domain. This paper starts by presenting the state-of-the-art in visualisation of clinical and other health related data. Then, it describes an example clinical problem and discusses the visualisation tools and techniques created for the utilisation of these data by clinicians and researchers. Finally, we look at the open problems in this area of research and discuss future challenges

Human activity recognition using wearable sensors: a deep learning approach

In the past decades, Human Activity Recognition (HAR) grabbed considerable research attentions from a wide range of pattern recognition and human–computer interaction researchers due to its prominent applications such as smart home health care. The wealth of information requires efficient classification and analysis methods. Deep learning represents a promising technique for large-scale data analytics. There are various ways of using different sensors for human activity recognition in a smartly controlled environment. Among them, physical human activity recognition through wearable sensors provides valuable information about an individual’s degree of functional ability and lifestyle. There is abundant research that works upon real time processing and causes more power consumption of mobile devices. Mobile phones are resource-limited devices. It is a thought-provoking task to implement and evaluate different recognition systems on mobile devices. This work proposes a Deep Belief Network (DBN) model for successful human activity recognition. Various experiments are performed on a real-world wearable sensor dataset to verify the effectiveness of the deep learning algorithm. The results show that the proposed DBN performs competitively in comparison with other algorithms and achieves satisfactory activity recognition performance. Some open problems and ideas are also presented and should be investigated as future research