Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review

Novel approaches that complement and go beyond evidence-based medicine are required in the domain of chronic diseases, given the growing incidence of such conditions on the worldwide population. A promising avenue is the secondary use of electronic health records (EHRs), where patient data are analyzed to conduct clinical and translational research. Methods based on machine learning to process EHRs are resulting in improved understanding of patient clinical trajectories and chronic disease risk prediction, creating a unique opportunity to derive previously unknown clinical insights. However, a wealth of clinical histories remains locked behind clinical narratives in free-form text. Consequently, unlocking the full potential of EHR data is contingent on the development of natural language processing (NLP) methods to automatically transform clinical text into structured clinical data that can guide clinical decisions and potentially delay or prevent disease onset

Natural Language Processing – Finding the Missing Link for Oncologic Data, 2022

Oncology like most medical specialties, is undergoing a data revolution at the center of which lie vast and growing amounts of clinical data in unstructured, semi-structured and structed formats. Artificial intelligence approaches are widely employed in research endeavors in an attempt to harness electronic medical records data to advance patient outcomes. The use of clinical oncologic data, although collected on large scale, particularly with the increased implementation of electronic medical records, remains limited due to missing, incorrect or manually entered data in registries and the lack of resource allocation to data curation in real world settings. Natural Language Processing (NLP) may provide an avenue to extract data from electronic medical records and as a result has grown considerably in medicine to be employed for documentation, outcome analysis, phenotyping and clinical trial eligibility. Barriers to NLP persist with inability to aggregate findings across studies due to use of different methods and significant heterogeneity at all levels with important parameters such as patient comorbidities and performance status lacking implementation in AI approaches. The goal of this review is to provide an updated overview of natural language processing (NLP) and the current state of its application in oncology for clinicians and researchers that wish to implement NLP to augment registries and/or advance research projects

Clinical text data in machine learning: Systematic review

Background: Clinical narratives represent the main form of communication within healthcare providing a personalized account of patient history and assessments, offering rich information for clinical decision making. Natural language processing (NLP) has repeatedly demonstrated its feasibility to unlock evidence buried in clinical narratives. Machine learning can facilitate rapid development of NLP tools by leveraging large amounts of text data. Objective: The main aim of this study is to provide systematic evidence on the properties of text data used to train machine learning approaches to clinical NLP. We also investigate the types of NLP tasks that have been supported by machine learning and how they can be applied in clinical practice. Methods: Our methodology was based on the guidelines for performing systematic reviews. In August 2018, we used PubMed, a multi-faceted interface, to perform a literature search against MEDLINE. We identified a total of 110 relevant studies and extracted information about the text data used to support machine learning, the NLP tasks supported and their clinical applications. The data properties considered included their size, provenance, collection methods, annotation and any relevant statistics. Results: The vast majority of datasets used to train machine learning models included only hundreds or thousands of documents. Only 10 studies used tens of thousands of documents with a handful of studies utilizing more. Relatively small datasets were utilized for training even when much larger datasets were available. The main reason for such poor data utilization is the annotation bottleneck faced by supervised machine learning algorithms. Active learning was explored to iteratively sample a subset of data for manual annotation as a strategy for minimizing the annotation effort while maximizing predictive performance of the model. Supervised learning was successfully used where clinical codes integrated with free text notes into electronic health records were utilized as class labels. Similarly, distant supervision was used to utilize an existing knowledge base to automatically annotate raw text. Where manual annotation was unavoidable, crowdsourcing was explored, but it remains unsuitable due to sensitive nature of data considered. Beside the small volume, training data were typically sourced from a small number of institutions, thus offering no hard evidence about the transferability of machine learning models. The vast majority of studies focused on the task of text classification. Most commonly, the classification results were used to support phenotyping, prognosis, care improvement, resource management and surveillance. Conclusions: We identified the data annotation bottleneck as one of the key obstacles to machine learning approaches in clinical NLP. Active learning and distant supervision were explored as a way of saving the annotation efforts. Future research in this field would benefit from alternatives such as data augmentation and transfer learning, or unsupervised learning, which does not require data annotation

Structured and unstructured data integration with electronic medical records

In recent years there has been a great population and technological evolution all over the world. At the same time, more areas beyond technology and information technology have also developed, namely medicine, which has led to an increase in average life expectancy which in turn, leads to a greater need for healthcare. In order to provide the best possible treatments and healthcare services, nowadays the hospitals store large amounts of data regarding patients and diseases (in the form of electronic medical records) or the logistics of some departments in their storage systems. Therefore, computer science techniques such as data mining and natural language processing have been used to extract knowledge and value from these information-rich sources in order not only to develop, for example, new models for disease prediction, as well as improving existing processes in healthcare centres and hospitals. This data storage can be done in one of three ways: structured, unstructured or semi-structured. In this paper, the author tested the integration of structured and unstructured data from two different departments of the same Portuguese hospital, in order to extract knowledge and improve hospital processes. Aiming to reduce the value loss of loading data that is not used in the healthcare providers systems.Nos últimos anos tem-se assistido a uma grande evolução populacional e tecnológica por todo o mundo. Paralelamente, mais áreas para além da tecnologia e informática têm-se também desenvolvido, nomeadamente a área da medicina, o que tem permitido um aumento na esperança média de vida que por sua vez leva a uma maior necessidade de cuidados de saúde. Com o intuito de fornecer os melhores serviços de saúde possíveis, nos dias que hoje os hospitais guardam nos seus sistemas informáticos grandes quantidades de dados relativamente aos pacientes e doenças (sobre a forma de registos médicos eletrónicos) ou relativos à logística de alguns departamentos dos hospitais, etc. Por conseguinte, a estes dados têm vindo a ser utilizadas técnicas da área das ciências da computação como o data mining e o processamento da língua natural para extrair conhecimento e valor dessas fontes ricas em informação com o intuito não só de desenvolver, por exemplo, novos modelos de predição de doenças, como também de melhorar processos já existentes em centros de saúde e hospitais. Este armazenamento de dados pode ser feito em uma de três formas: de forma estruturada, não estruturada ou semi-estruturada. Neste trabalho o autor testou a integração de dados estruturados e não estruturados de dois departamentos diferentes do mesmo hospital português, com o intuito de extrair conhecimento e melhorar os processos do hospital. Com o intuito de reduzir a perda do armazenamento de dados que não são utilizados

Assessing Information Congruence of Documented Cardiovascular Disease between Electronic Dental and Medical Records

Dentists are more often treating patients with Cardiovascular Diseases (CVD) in their clinics; therefore, dentists may need to alter treatment plans in the presence of CVD. However, it’s unclear to what extent patient-reported CVD information is accurately captured in Electronic Dental Records (EDRs). In this pilot study, we aimed to measure the reliability of patient-reported CVD conditions in EDRs. We assessed information congruence by comparing patients’ self-reported dental histories to their original diagnosis assigned by their medical providers in the Electronic Medical Record (EMR). To enable this comparison, we encoded patients CVD information from the free-text data of EDRs into a structured format using natural language processing (NLP). Overall, our NLP approach achieved promising performance extracting patients’ CVD-related information. We observed disagreement between self-reported EDR data and physician-diagnosed EMR data

Substituting clinical features using synthetic medical phrases: Medical text data augmentation techniques.

Biomedical natural language processing (NLP) has an important role in extracting consequential information in medical discharge notes. Detecting meaningful features from unstructured notes is a challenging task in medical document classification. The domain specific phrases and different synonyms within the medical documents make it hard to analyze them. Analyzing clinical notes becomes more challenging for short documents like abstract texts. All of these can result in poor classification performance, especially when there is a shortage of the clinical data in real life. Two new approaches (an ontology-guided approach and a combined ontology-based with dictionary-based approach) are suggested for augmenting medical data to enrich training data. Three different deep learning approaches are used to evaluate the classification performance of the proposed methods. The obtained results show that the proposed methods improved the classification accuracy in clinical notes classification

An Ontology-based Two-Stage Approach to Medical Text Classification with Feature Selection by Particle Swarm Optimisation

© 2019 IEEE. Document classification (DC) is the task of assigning pre-defined labels to unseen documents by utilizing a model trained on the available labeled documents. DC has attracted much attention in medical fields recently because many issues can be formulated as a classification problem. It can assist doctors in decision making and correct decisions can reduce the medical expenses. Medical documents have special attributes that distinguish them from other texts and make them difficult to analyze. For example, many acronyms and abbreviations, and short expressions make it more challenging to extract information. The classification accuracy of the current medical DC methods is not satisfactory. The goal of this work is to enhance the input feature sets of the DC method to improve the accuracy. To approach this goal, a novel two-stage approach is proposed. In the first stage, a domain-specific dictionary, namely the Unified Medical Language System (UMLS), is employed to extract the key features belonging to the most relevant concepts such as diseases or symptoms. In the second stage, PSO is applied to select more related features from the extracted features in the first stage. The performance of the proposed approach is evaluated on the 2010 Informatics for Integrating Biology and the Bedside (i2b2) data set which is a widely used medical text dataset. The experimental results show substantial improvement by the proposed method on the accuracy of classification