ABSTRACT
BACKGROUND: Electronic health records (EHRs) are a valuable resource for data-driven medical research. However, the presence of protected health information (PHI) makes EHRs unsuitable to be shared for research purposes. De-identification, i.e. the process of removing PHI is a critical step in making EHR data accessible. Natural language processing has repeatedly demonstrated its feasibility in automating the de-identification process. OBJECTIVES: Our study aims to provide systematic evidence on how the de-identification of clinical free text written in English has evolved in the last thirteen years, and to report on the performances and limitations of the current state-of-the-art systems for the English language. In addition, we aim to identify challenges and potential research opportunities in this field. METHODS: A systematic search in PubMed, Web of Science, and the DBLP was conducted for studies published between January 2010 and February 2023. Titles and abstracts were examined to identify the relevant studies. Selected studies were then analysed in-depth, and information was collected on de-identification methodologies, data sources, and measured performance. RESULTS: A total of 2125 publications were identified for the title and abstract screening. 69 studies were found to be relevant. Machine learning (37 studies) and hybrid (26 studies) approaches are predominant, while six studies relied only on rules. The majority of the approaches were trained and evaluated on public corpora. The 2014 i2b2/UTHealth corpus is the most frequently used (36 studies), followed by the 2006 i2b2 (18 studies) and 2016 CEGS N-GRID (10 studies) corpora. CONCLUSION: Earlier de-identification approaches aimed at English were mainly rule and machine learning hybrids with extensive feature engineering and post-processing, while more recent performance improvements are due to feature-inferring recurrent neural networks. Current leading performance is achieved using attention-based neural models. Recent studies report state-of-the-art F1-scores (over 98 %) when evaluated in the manner usually adopted by the clinical natural language processing community. However, their performance needs to be more thoroughly assessed with different measures to judge their reliability to safely de-identify data in a real-world setting. Without additional manually labeled training data, state-of-the-art systems fail to generalise well across a wide range of clinical sub-domains.
Subject(s)
Electronic Health Records , Natural Language Processing , Humans , Machine LearningABSTRACT
BACKGROUND: Since the first COVID-19 vaccine appeared, there has been a growing tendency to automatically determine public attitudes toward it. In particular, it was important to find the reasons for vaccine hesitancy, since it was directly correlated with pandemic protraction. Natural language processing (NLP) and public health researchers have turned to social media (eg, Twitter, Reddit, and Facebook) for user-created content from which they can gauge public opinion on vaccination. To automatically process such content, they use a number of NLP techniques, most notably topic modeling. Topic modeling enables the automatic uncovering and grouping of hidden topics in the text. When applied to content that expresses a negative sentiment toward vaccination, it can give direct insight into the reasons for vaccine hesitancy. OBJECTIVE: This study applies NLP methods to classify vaccination-related tweets by sentiment polarity and uncover the reasons for vaccine hesitancy among the negative tweets in the Serbian language. METHODS: To study the attitudes and beliefs behind vaccine hesitancy, we collected 2 batches of tweets that mention some aspects of COVID-19 vaccination. The first batch of 8817 tweets was manually annotated as either relevant or irrelevant regarding the COVID-19 vaccination sentiment, and then the relevant tweets were annotated as positive, negative, or neutral. We used the annotated tweets to train a sequential bidirectional encoder representations from transformers (BERT)-based classifier for 2 tweet classification tasks to augment this initial data set. The first classifier distinguished between relevant and irrelevant tweets. The second classifier used the relevant tweets and classified them as negative, positive, or neutral. This sequential classifier was used to annotate the second batch of tweets. The combined data sets resulted in 3286 tweets with a negative sentiment: 1770 (53.9%) from the manually annotated data set and 1516 (46.1%) as a result of automatic classification. Topic modeling methods (latent Dirichlet allocation [LDA] and nonnegative matrix factorization [NMF]) were applied using the 3286 preprocessed tweets to detect the reasons for vaccine hesitancy. RESULTS: The relevance classifier achieved an F-score of 0.91 and 0.96 for relevant and irrelevant tweets, respectively. The sentiment polarity classifier achieved an F-score of 0.87, 0.85, and 0.85 for negative, neutral, and positive sentiments, respectively. By summarizing the topics obtained in both models, we extracted 5 main groups of reasons for vaccine hesitancy: concern over vaccine side effects, concern over vaccine effectiveness, concern over insufficiently tested vaccines, mistrust of authorities, and conspiracy theories. CONCLUSIONS: This paper presents a combination of NLP methods applied to find the reasons for vaccine hesitancy in Serbia. Given these reasons, it is now possible to better understand the concerns of people regarding the vaccination process.
