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

Deep learning techniques for biomedical data processing

The interest in Deep Learning (DL) has seen an exponential growth in the last ten years, producing a significant increase in both theoretical and applicative studies. On the one hand, the versatility and the ability to tackle complex tasks have led to the rapid and widespread diffusion of DL technologies. On the other hand, the dizzying increase in the availability of biomedical data has made classical analyses, carried out by human experts, progressively more unlikely. Contextually, the need for efficient and reliable automatic tools to support clinicians, at least in the most demanding tasks, has become increasingly pressing. In this survey, we will introduce a broad overview of DL models and their applications to biomedical data processing, specifically to medical image analysis, sequence processing (RNA and proteins) and graph modeling of molecular data interactions. First, the fundamental key concepts of DL architectures will be introduced, with particular reference to neural networks for structured data, convolutional neural networks, generative adversarial models, and siamese architectures. Subsequently, their applicability for the analysis of different types of biomedical data will be shown, in areas ranging from diagnostics to the understanding of the characteristics underlying the process of transcription and translation of our genetic code, up to the discovery of new drugs. Finally, the prospects and future expectations of DL applications to biomedical data will be discussed

Deep Neural Architectures for End-to-End Relation Extraction

The rapid pace of scientific and technological advancements has led to a meteoric growth in knowledge, as evidenced by a sharp increase in the number of scholarly publications in recent years. PubMed, for example, archives more than 30 million biomedical articles across various domains and covers a wide range of topics including medicine, pharmacy, biology, and healthcare. Social media and digital journalism have similarly experienced their own accelerated growth in the age of big data. Hence, there is a compelling need for ways to organize and distill the vast, fragmented body of information (often unstructured in the form of natural human language) so that it can be assimilated, reasoned about, and ultimately harnessed. Relation extraction is an important natural language task toward that end. In relation extraction, semantic relationships are extracted from natural human language in the form of (subject, object, predicate) triples such that subject and object are mentions of discrete concepts and predicate indicates the type of relation between them. The difficulty of relation extraction becomes clear when we consider the myriad of ways the same relation can be expressed in natural language. Much of the current works in relation extraction assume that entities are known at extraction time, thus treating entity recognition as an entirely separate and independent task. However, recent studies have shown that entity recognition and relation extraction, when modeled together as interdependent tasks, can lead to overall improvements in extraction accuracy. When modeled in such a manner, the task is referred to as end-to-end relation extraction. In this work, we present four studies that introduce incrementally sophisticated architectures designed to tackle the task of end-to-end relation extraction. In the first study, we present a pipeline approach for extracting protein-protein interactions as affected by particular mutations. The pipeline system makes use of recurrent neural networks for protein detection, lexicons for gene normalization, and convolutional neural networks for relation extraction. In the second study, we show that a multi-task learning framework, with parameter sharing, can achieve state-of-the-art results for drug-drug interaction extraction. At its core, the model uses graph convolutions, with a novel attention-gating mechanism, over dependency parse trees. In the third study, we present a more efficient and general-purpose end-to-end neural architecture designed around the idea of the table-filling paradigm; for an input sentence of length n, all entities and relations are extracted in a single pass of the network in an indirect fashion by populating the cells of a corresponding n by n table using metric-based features. We show that this approach excels in both the general English and biomedical domains with extraction times that are up to an order of magnitude faster compared to the prior best. In the fourth and last study, we present an architecture for relation extraction that, in addition to being end-to-end, is able to handle cross-sentence and N-ary relations. Overall, our work contributes to the advancement of modern information extraction by exploring end-to-end solutions that are fast, accurate, and generalizable to many high-value domains

Mining Public Opinion on COVID-19 Vaccines using Unstructured Social Media Data

The emergence of the novel coronavirus (COVID-19), and the necessary separation of populations led to an unprecedented number of new social media users seeking information related to the pandemic. Nowadays, with an estimated 4.5 billion users worldwide, social media data offer an opportunity for near real-time analysis of large bodies of text related to disease outbreaks and vaccination. This study investigated and compared public discourse related to COVID-19 vaccines expressed on two popular social media platforms, Reddit and Twitter. Approximately 9.5 million Tweets and 70 thousand Reddit comments were analyzed from dates January 1, 2020, to March 1, 2022, and analyzed through topic modeling, sentiment analysis, and semantic network analysis. Sentiment analysis through the fine-tuned DistilRoBERTa model revealed that even though Twitter content was overall more negative than content expressed on Reddit, relatively similar changes in sentiment occurred among users of both online platforms. Reversals in sentiment trends typically occurred within relative proximity to events such as vaccine development news, vaccine release, frequent discussion of side-effects, the discovery of new variants, and pandemic fatigue. Topic modeling and semantic network analysis provided insight into how public discourse related to COVID-19 and vaccinations, misinformation, and vaccine hesitancy evolved over 26 months. Though misinformation and mention of conspiracy theories were detected with the analysis, the occurrence of both was less frequent than expected. This work provides a framework that could be scaled and utilized by public health officials to monitor disease outbreaks in near real-time in large communities as well as smaller local groups. Hopefully, the results from this study will help to guide and facilitate the implementation of targeted digital interventions among vaccine-hesitant populations and provide insights to public health officials to inform decision-making and effective policy development