Ranking Medical Terms to Support Expansion of Lay Language Resources for Patient Comprehension of Electronic Health Record Notes: Adapted Distant Supervision Approach

BACKGROUND: Medical terms are a major obstacle for patients to comprehend their electronic health record (EHR) notes. Clinical natural language processing (NLP) systems that link EHR terms to lay terms or definitions allow patients to easily access helpful information when reading through their EHR notes, and have shown to improve patient EHR comprehension. However, high-quality lay language resources for EHR terms are very limited in the public domain. Because expanding and curating such a resource is a costly process, it is beneficial and even necessary to identify terms important for patient EHR comprehension first. OBJECTIVE: We aimed to develop an NLP system, called adapted distant supervision (ADS), to rank candidate terms mined from EHR corpora. We will give EHR terms ranked as high by ADS a higher priority for lay language annotation-that is, creating lay definitions for these terms. METHODS: Adapted distant supervision uses distant supervision from consumer health vocabulary and transfer learning to adapt itself to solve the problem of ranking EHR terms in the target domain. We investigated 2 state-of-the-art transfer learning algorithms (ie, feature space augmentation and supervised distant supervision) and designed 5 types of learning features, including distributed word representations learned from large EHR data for ADS. For evaluating ADS, we asked domain experts to annotate 6038 candidate terms as important or nonimportant for EHR comprehension. We then randomly divided these data into the target-domain training data (1000 examples) and the evaluation data (5038 examples). We compared ADS with 2 strong baselines, including standard supervised learning, on the evaluation data. RESULTS: The ADS system using feature space augmentation achieved the best average precision, 0.850, on the evaluation set when using 1000 target-domain training examples. The ADS system using supervised distant supervision achieved the best average precision, 0.819, on the evaluation set when using only 100 target-domain training examples. The 2 ADS systems both performed significantly better than the baseline systems (P \u3c .001 for all measures and all conditions). Using a rich set of learning features contributed to ADS\u27s performance substantially. CONCLUSIONS: ADS can effectively rank terms mined from EHRs. Transfer learning improved ADS\u27s performance even with a small number of target-domain training examples. EHR terms prioritized by ADS were used to expand a lay language resource that supports patient EHR comprehension. The top 10,000 EHR terms ranked by ADS are available upon request

The Ensemble MESH-Term Query Expansion Models Using Multiple LDA Topic Models and ANN Classifiers in Health Information Retrieval

Information retrieval in the health field has several challenges. Health information terminology is difficult for consumers (laypeople) to understand. Formulating a query with professional terms is not easy for consumers because health-related terms are more familiar to health professionals. If health terms related to a query are automatically added, it would help consumers to find relevant information. The proposed query expansion (QE) models show how to expand a query using MeSH (Medical Subject Headings) terms. The documents were represented by MeSH terms (i.e. Bag-of-MeSH), which were included in the full-text articles. And then the MeSH terms were used to generate LDA (Latent Dirichlet Analysis) topic models. A query and the top k retrieved documents were used to find MeSH terms as topic words related to the query. LDA topic words were filtered by 1) threshold values of topic probability (TP) and word probability (WP) or 2) an ANN (Artificial Neural Network) classifier. Threshold values were effective in an LDA model with a specific number of topics to increase IR performance in terms of infAP (inferred Average Precision) and infNDCG (inferred Normalized Discounted Cumulative Gain), which are common IR metrics for large data collections with incomplete judgments. The top k words were chosen by the word score based on (TP *WP) and retrieved document ranking in an LDA model with specific thresholds. The QE model with specific thresholds for TP and WP showed improved mean infAP and infNDCG scores in an LDA model, comparing with the baseline result. However, the threshold values optimized for a particular LDA model did not perform well in other LDA models with different numbers of topics. An ANN classifier was employed to overcome the weakness of the QE model depending on LDA thresholds by automatically categorizing MeSH terms (positive/negative/neutral) for QE. ANN classifiers were trained on word features related to the LDA model and collection. Two types of QE models (WSW & PWS) using an LDA model and an ANN classifier were proposed: 1) Word Score Weighting (WSW) where the probability of being a positive/negative/neutral word was used to weight the original word score, and 2) Positive Word Selection (PWS) where positive words were identified by the ANN classifier. Forty WSW models showed better average mean infAP and infNDCG scores than the PWS models when the top 7 words were selected for QE. Both approaches based on a binary ANN classifier were effective in increasing infAP and infNDCG, statistically, significantly, compared with the scores of the baseline run. A 3-class classifier performed worse than the binary classifier. The proposed ensemble QE models integrated multiple ANN classifiers with multiple LDA models. Ensemble QE models combined multiple WSW/PWS models and one or multiple classifiers. Multiple classifiers were more effective in selecting relevant words for QE than one classifier. In ensemble QE (WSW/PWS) models, the top k words added to the original queries were effective to increase infAP and infNDCG scores. The ensemble QE model (WSW) using three classifiers showed statistically significant improvements for infAP and infNDCG in the mean scores for 30 queries when the top 3 words were added. The ensemble QE model (PWS) using four classifiers showed statistically significant improvements for 30 queries in the mean infAP and infNDCG scores

A Review on Explainable Artificial Intelligence for Healthcare: Why, How, and When?

Artificial intelligence (AI) models are increasingly finding applications in the field of medicine. Concerns have been raised about the explainability of the decisions that are made by these AI models. In this article, we give a systematic analysis of explainable artificial intelligence (XAI), with a primary focus on models that are currently being used in the field of healthcare. The literature search is conducted following the preferred reporting items for systematic reviews and meta-analyses (PRISMA) standards for relevant work published from 1 January 2012 to 02 February 2022. The review analyzes the prevailing trends in XAI and lays out the major directions in which research is headed. We investigate the why, how, and when of the uses of these XAI models and their implications. We present a comprehensive examination of XAI methodologies as well as an explanation of how a trustworthy AI can be derived from describing AI models for healthcare fields. The discussion of this work will contribute to the formalization of the XAI field.Comment: 15 pages, 3 figures, accepted for publication in the IEEE Transactions on Artificial Intelligenc

Active Learning for Text Classification

Text classification approaches are used extensively to solve real-world challenges. The success or failure of text classification systems hangs on the datasets used to train them, without a good dataset it is impossible to build a quality system. This thesis examines the applicability of active learning in text classification for the rapid and economical creation of labelled training data. Four main contributions are made in this thesis. First, we present two novel selection strategies to choose the most informative examples for manually labelling. One is an approach using an advanced aggregated confidence measurement instead of the direct output of classifiers to measure the confidence of the prediction and choose the examples with least confidence for querying. The other is a simple but effective exploration guided active learning selection strategy which uses only the notions of density and diversity, based on similarity, in its selection strategy. Second, we propose new methods of using deterministic clustering algorithms to help bootstrap the active learning process. We first illustrate the problems of using non-deterministic clustering for selecting initial training sets, showing how non-deterministic clustering methods can result in inconsistent behaviour in the active learning process. We then compare various deterministic clustering techniques and commonly used non-deterministic ones, and show that deterministic clustering algorithms are as good as non-deterministic clustering algorithms at selecting initial training examples for the active learning process. More importantly, we show that the use of deterministic approaches stabilises the active learning process. Our third direction is in the area of visualising the active learning process. We demonstrate the use of an existing visualisation technique in understanding active learning selection strategies to show that a better understanding of selection strategies can be achieved with the help of visualisation techniques. Finally, to evaluate the practicality and usefulness of active learning as a general dataset labelling methodology, it is desirable that actively labelled dataset can be reused more widely instead of being only limited to some particular classifier. We compare the reusability of popular active learning methods for text classification and identify the best classifiers to use in active learning for text classification. This thesis is concerned using active learning methods to label large unlabelled textual datasets. Our domain of interest is text classification, but most of the methods proposed are quite general and so are applicable to other domains having large collections of data with high dimensionality

A Survey on Biomedical Text Summarization with Pre-trained Language Model

The exponential growth of biomedical texts such as biomedical literature and electronic health records (EHRs), provides a big challenge for clinicians and researchers to access clinical information efficiently. To address the problem, biomedical text summarization has been proposed to support clinical information retrieval and management, aiming at generating concise summaries that distill key information from single or multiple biomedical documents. In recent years, pre-trained language models (PLMs) have been the de facto standard of various natural language processing tasks in the general domain. Most recently, PLMs have been further investigated in the biomedical field and brought new insights into the biomedical text summarization task. In this paper, we systematically summarize recent advances that explore PLMs for biomedical text summarization, to help understand recent progress, challenges, and future directions. We categorize PLMs-based approaches according to how they utilize PLMs and what PLMs they use. We then review available datasets, recent approaches and evaluation metrics of the task. We finally discuss existing challenges and promising future directions. To facilitate the research community, we line up open resources including available datasets, recent approaches, codes, evaluation metrics, and the leaderboard in a public project: https://github.com/KenZLuo/Biomedical-Text-Summarization-Survey/tree/master.Comment: 19 pages, 6 figures, TKDE under revie

Classification of socially generated medical data

The growth of online health communities, particularly those involving socially generated content, can provide considerable value for society. Participants can gain knowledge of medical information or interact with peers on medical forum platforms. However, the sheer volume of information so generated – and the consequent ‘noise’ associated with large data volumes – can create difficulties for information consumers. We propose a solution to this problem by applying high-level analytics to the data – primarily sentiment analysis, but also content and topic analysis - for accurate classification. We believe that such analysis can be of significant value to data users, such as identifying a particular aspect of an information space, determining themes that predominate among a large dataset, and allowing people to summarize topics within a big dataset. In this thesis, we apply machine learning strategies to identify sentiments expressed in online medical forums that discuss Lyme Disease. As part of this process, we distinguish a complete and relevant set of categories that can be used to characterize Lyme Disease discourse. We present a feature-based model that employs supervised learning algorithms and assess the feasibility and accuracy of this sentiment classification model. We further evaluate our model by assessing its ability to adapt to an online medical forum discussing a disease with similar characteristics, Lupus. The experimental results demonstrate the effectiveness of our approach. In many sentiment analysis applications, the labelled training datasets are expensive to obtain, whereas unlabelled datasets are readily available. Therefore, we present an adaptation of a well-known semi-supervised learning technique, in which co-training is implemented by combining labelled and unlabelled data. Our results would suggest the ability to learn even with limited labelled data. In addition, we investigate complementary analytic techniques – content and topic analysis – to leverage best used of the data for various consumer groups. Within the work described in this thesis, some particular research issues are addressed, specifically when applied to socially generated medical/health datasets: • When applying binary sentiment analysis to short-form text data (e.g. Twitter), could meta-level features improve performance of classification? • When applying more complex multi-class sentiment analysis to classification of long-form content-rich text data, would meta-level features be a useful addition to more conventional features? • Can this multi-class analysis approach be generalised to other medical/health domains? • How would alternative classification strategies benefit different groups of information consumers

Development of a simulation tool for measurements and analysis of simulated and real data to identify ADLs and behavioral trends through statistics techniques and ML algorithms

openCon una popolazione di anziani in crescita, il numero di soggetti a rischio di patologia è in rapido aumento. Molti gruppi di ricerca stanno studiando soluzioni pervasive per monitorare continuamente e discretamente i soggetti fragili nelle loro case, riducendo i costi sanitari e supportando la diagnosi medica. Comportamenti anomali durante l'esecuzione di attività di vita quotidiana (ADL) o variazioni sulle tendenze comportamentali sono di grande importanza.With a growing population of elderly people, the number of subjects at risk of pathology is rapidly increasing. Many research groups are studying pervasive solutions to continuously and unobtrusively monitor fragile subjects in their homes, reducing health-care costs and supporting the medical diagnosis. Anomalous behaviors while performing activities of daily living (ADLs) or variations on behavioral trends are of great importance. To measure ADLs a significant number of parameters need to be considering affecting the measurement such as sensors and environment characteristics or sensors disposition. To face the impossibility to study in the real context the best configuration of sensors able to minimize costs and maximize accuracy, simulation tools are being developed as powerful means. This thesis presents several contributions on this topic. In the following research work, a study of a measurement chain aimed to measure ADLs and represented by PIRs sensors and ML algorithm is conducted and a simulation tool in form of Web Application has been developed to generate datasets and to simulate how the measurement chain reacts varying the configuration of the sensors. Starting from eWare project results, the simulation tool has been thought to provide support for technicians, developers and installers being able to speed up analysis and monitoring times, to allow rapid identification of changes in behavioral trends, to guarantee system performance monitoring and to study the best configuration of the sensors network for a given environment. The UNIVPM Home Care Web App offers the chance to create ad hoc datasets related to ADLs and to conduct analysis thanks to statistical algorithms applied on data. To measure ADLs, machine learning algorithms have been implemented in the tool. Five different tasks have been identified. To test the validity of the developed instrument six case studies divided into two categories have been considered. To the first category belong those studies related to: 1) discover the best configuration of the sensors keeping environmental characteristics and user behavior as constants; 2) define the most performant ML algorithms. The second category aims to proof the stability of the algorithm implemented and its collapse condition by varying user habits. Noise perturbation on data has been applied to all case studies. Results show the validity of the generated datasets. By maximizing the sensors network is it possible to minimize the ML error to 0.8%. Due to cost is a key factor in this scenario, the fourth case studied considered has shown that minimizing the configuration of the sensors it is possible to reduce drastically the cost with a more than reasonable value for the ML error around 11.8%. Results in ADLs measurement can be considered more than satisfactory.INGEGNERIA INDUSTRIALEopenPirozzi, Michel

Extracting health information from social media

Social media platforms with large user bases such as Twitter, Reddit, and online health forums contain a rich amount of health-related information. Despite the advances achieved in natural language processing (NLP), extracting actionable health information from social media still remains challenging. This thesis proposes a set of methodologies that can be used to extract medical concepts and health information from social media that is related to drugs, symptoms, and side-effects. We first develop a rule-based relationship extraction system that utilises a set of dictionaries and linguistic rules in order to extract structured information from patients’ posts on online health forums. We then automate the concept extraction pro-cess via; i) a supervised algorithm that has been trained with a small labelled dataset, and ii) an iterative semi-supervised algorithm capable of learning new sentences and concepts. We test our machine-learning pipeline on a COVID-19 case study that involves patient authored social media posts. We develop a novel triage and diagnostic approach to extract symptoms, severity, and prevalence of the disease rather than to provide any actionable decisions at the individual level. Finally, we extend our approach by investigating the potential benefit of incorporating dictionary information into a neural network architecture for natural language processing