arXiv subjects

Honghan Wu

Publications and source records attributed to Honghan Wu.

46 records · Page 3Linked to original sources

arXiv2022

Quantifying Health Inequalities Induced by Data and AI Models

AI technologies are being increasingly tested and applied in critical environments including healthcare. Without an effective way to detect and mitigate AI induced inequalities, AI might do more harm than good, potentially leading to the widening of underlying inequalities. This paper proposes a generic allocation-deterioration framework for detecting and quantifying AI induced inequality. Specifically, AI induced inequalities are quantified as the area between two allocation-deterioration curves. To assess the framework's performance, experiments were conducted on ten synthetic datasets (N>33,000) generated from HiRID - a real-world Intensive Care Unit (ICU) dataset, showing its ability to accurately detect and quantify inequality proportionally to controlled inequalities. Extensive analyses were carried out to quantify health inequalities (a) embedded in two real-world ICU datasets; (b) induced by AI models trained for two resource allocation scenarios. Results showed that compared to men, women had up to 33% poorer deterioration in markers of prognosis when admitted to HiRID ICUs. All four AI models assessed were shown to induce significant inequalities (2.45% to 43.2%) for non-White compared to White patients. The models exacerbated data embedded inequalities significantly in 3 out of 8 assessments, one of which was >9 times worse. The codebase is at https://github.com/knowlab/DAindex-Framework.

cs.CY↗

arXiv2021

Rare Disease Identification from Clinical Notes with Ontologies and Weak Supervision

The identification of rare diseases from clinical notes with Natural Language Processing (NLP) is challenging due to the few cases available for machine learning and the need of data annotation from clinical experts. We propose a method using ontologies and weak supervision. The approach includes two steps: (i) Text-to-UMLS, linking text mentions to concepts in Unified Medical Language System (UMLS), with a named entity linking tool (e.g. SemEHR) and weak supervision based on customised rules and Bidirectional Encoder Representations from Transformers (BERT) based contextual representations, and (ii) UMLS-to-ORDO, matching UMLS concepts to rare diseases in Orphanet Rare Disease Ontology (ORDO). Using MIMIC-III US intensive care discharge summaries as a case study, we show that the Text-to-UMLS process can be greatly improved with weak supervision, without any annotated data from domain experts. Our analysis shows that the overall pipeline processing discharge summaries can surface rare disease cases, which are mostly uncaptured in manual ICD codes of the hospital admissions.

cs.CL↗

arXiv2021

Explainable Automated Coding of Clinical Notes using Hierarchical Label-wise Attention Networks and Label Embedding Initialisation

Diagnostic or procedural coding of clinical notes aims to derive a coded summary of disease-related information about patients. Such coding is usually done manually in hospitals but could potentially be automated to improve the efficiency and accuracy of medical coding. Recent studies on deep learning for automated medical coding achieved promising performances. However, the explainability of these models is usually poor, preventing them to be used confidently in supporting clinical practice. Another limitation is that these models mostly assume independence among labels, ignoring the complex correlation among medical codes which can potentially be exploited to improve the performance. We propose a Hierarchical Label-wise Attention Network (HLAN), which aimed to interpret the model by quantifying importance (as attention weights) of words and sentences related to each of the labels. Secondly, we propose to enhance the major deep learning models with a label embedding (LE) initialisation approach, which learns a dense, continuous vector representation and then injects the representation into the final layers and the label-wise attention layers in the models. We evaluated the methods using three settings on the MIMIC-III discharge summaries: full codes, top-50 codes, and the UK NHS COVID-19 shielding codes. Experiments were conducted to compare HLAN and LE initialisation to the state-of-the-art neural network based methods. HLAN achieved the best Micro-level AUC and $F_1$ on the top-50 code prediction and comparable results on the NHS COVID-19 shielding code prediction to other models. By highlighting the most salient words and sentences for each label, HLAN showed more meaningful and comprehensive model interpretation compared to its downgraded baselines and the CNN-based models. LE initialisation consistently boosted most deep learning models for automated medical coding.

cs.CL↗

arXiv2021

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.

cs.LG↗

arXiv2021

A Systematic Review of Natural Language Processing Applied to Radiology Reports

NLP has a significant role in advancing healthcare and has been found to be key in extracting structured information from radiology reports. Understanding recent developments in NLP application to radiology is of significance but recent reviews on this are limited. This study systematically assesses recent literature in NLP applied to radiology reports. Our automated literature search yields 4,799 results using automated filtering, metadata enriching steps and citation search combined with manual review. Our analysis is based on 21 variables including radiology characteristics, NLP methodology, performance, study, and clinical application characteristics. We present a comprehensive analysis of the 164 publications retrieved with each categorised into one of 6 clinical application categories. Deep learning use increases but conventional machine learning approaches are still prevalent. Deep learning remains challenged when data is scarce and there is little evidence of adoption into clinical practice. Despite 17% of studies reporting greater than 0.85 F1 scores, it is hard to comparatively evaluate these approaches given that most of them use different datasets. Only 14 studies made their data and 15 their code available with 10 externally validating results. Automated understanding of clinical narratives of the radiology reports has the potential to enhance the healthcare process but reproducibility and explainability of models are important if the domain is to move applications into clinical use. More could be done to share code enabling validation of methods on different institutional data and to reduce heterogeneity in reporting of study properties allowing inter-study comparisons. Our results have significance for researchers providing a systematic synthesis of existing work to build on, identify gaps, opportunities for collaboration and avoid duplication.

cs.CL↗

arXiv2020

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.

cs.AI↗

arXiv2020

Identifying physical health comorbidities in a cohort of individuals with severe mental illness: An application of SemEHR

Multimorbidity research in mental health services requires data from physical health conditions which is traditionally limited in mental health care electronic health records. In this study, we aimed to extract data from physical health conditions from clinical notes using SemEHR. Data was extracted from Clinical Record Interactive Search (CRIS) system at South London and Maudsley Biomedical Research Centre (SLaM BRC) and the cohort consisted of all individuals who had received a primary or secondary diagnosis of severe mental illness between 2007 and 2018. Three pairs of annotators annotated 2403 documents with an average Cohen's Kappa of 0.757. Results show that the NLP performance varies across different diseases areas (F1 0.601 - 0.954) suggesting that the language patterns or terminologies of different condition groups entail different technical challenges to the same NLP task.

cs.CL↗

arXiv2019

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.

q-bio.QM↗

arXiv2019

Efficiently Reusing Natural Language Processing Models for Phenotype-Mention Identification in Free-text Electronic Medical Records: Methodology Study

Background: Many efforts have been put into the use of automated approaches, such as natural language processing (NLP), to mine or extract data from free-text medical records to construct comprehensive patient profiles for delivering better health-care. Reusing NLP models in new settings, however, remains cumbersome - requiring validation and/or retraining on new data iteratively to achieve convergent results. Objective: The aim of this work is to minimize the effort involved in reusing NLP models on free-text medical records. Methods: We formally define and analyse the model adaptation problem in phenotype-mention identification tasks. We identify "duplicate waste" and "imbalance waste", which collectively impede efficient model reuse. We propose a phenotype embedding based approach to minimize these sources of waste without the need for labelled data from new settings. Results: We conduct experiments on data from a large mental health registry to reuse NLP models in four phenotype-mention identification tasks. The proposed approach can choose the best model for a new task, identifying up to 76% (duplicate waste), i.e. phenotype mentions without the need for validation and model retraining, and with very good performance (93-97% accuracy). It can also provide guidance for validating and retraining the selected model for novel language patterns in new tasks, saving around 80% (imbalance waste), i.e. the effort required in "blind" model-adaptation approaches. Conclusions: Adapting pre-trained NLP models for new tasks can be more efficient and effective if the language pattern landscapes of old settings and new settings can be made explicit and comparable. Our experiments show that the phenotype-mention embedding approach is an effective way to model language patterns for phenotype-mention identification tasks and that its use can guide efficient NLP model reuse.

cs.CL↗

arXiv2019

Named Entity Recognition for Electronic Health Records: A Comparison of Rule-based and Machine Learning Approaches

This work investigates multiple approaches to Named Entity Recognition (NER) for text in Electronic Health Record (EHR) data. In particular, we look into the application of (i) rule-based, (ii) deep learning and (iii) transfer learning systems for the task of NER on brain imaging reports with a focus on records from patients with stroke. We explore the strengths and weaknesses of each approach, develop rules and train on a common dataset, and evaluate each system's performance on common test sets of Scottish radiology reports from two sources (brain imaging reports in ESS -- Edinburgh Stroke Study data collected by NHS Lothian as well as radiology reports created in NHS Tayside). Our comparison shows that a hand-crafted system is the most accurate way to automatically label EHR, but machine learning approaches can provide a feasible alternative where resources for a manual system are not readily available.

cs.CL↗