Question: How do the traditional natural language processing tools work?
Evidence: The vast amounts of data collected by healthcare providers in conjunction with modern data analytics techniques present a unique opportunity to improve health service provision and the quality and safety of medical care for patient benefit BIBREF0 . Much of the recent research in this area has been on personalised medicine and its aim to deliver better diagnostics aided by the integration of diverse datasets providing complementary information. Another large source of healthcare data is organisational. In the United Kingdom, the National Health Service (NHS) has a long history of documenting extensively the different aspects of healthcare provision. The NHS is currently in the process of increasing the availability of several databases, properly anonymised, with the aim of leveraging advanced analytics to identify areas of improvement in NHS services.
One such database is the National Reporting and Learning System (NRLS), a central repository of patient safety incident reports from the NHS in England and Wales. Set up in 2003, the NRLS now contains more than 13 million detailed records. The incidents are reported using a set of standardised categories and contain a wealth of organisational and spatio-temporal information (structured data), as well as, crucially, a substantial component of free text (unstructured data) where incidents are described in the `voice' of the person reporting. The incidents are wide ranging: from patient accidents to lost forms or referrals; from delays in admission and discharge to serious untoward incidents, such as retained foreign objects after operations. The review and analysis of such data provides critical insight into the complex functioning of different processes and procedures in healthcare towards service improvement for safer carer.
Although statistical analyses are routinely performed on the structured component of the data (dates, locations, assigned categories, etc), the free text remains largely unused in systematic processes. Free text is usually read manually but this is time-consuming, meaning that it is often ignored in practice, unless a detailed review of a case is undertaken because of the severity of harm that resulted. There is a lack of methodologies that can summarise content and provide content-based groupings across the large volume of reports submitted nationally for organisational learning. Methods that could provide automatic categorisation of incidents from the free text would sidestep problems such as difficulties in assigning an incident category by virtue of a priori pre-defined lists in the reporting system or human error, as well as offering a unique insight into the root cause analysis of incidents that could improve the safety and quality of care and efficiency of healthcare services.
Our goal in this work is to showcase an algorithmic methodology that detects content-based groups of records in a given dataset in an unsupervised manner, based only on the free and unstructured textual description of the incidents. To do so, we combine recently developed deep neural-network high-dimensional text-embedding algorithms with network-theoretical methods. In particular, we apply multiscale Markov Stability (MS) community detection to a sparsified geometric similarity graph of documents obtained from text vector similarities. Our method departs from traditional natural language processing tools, which have generally used bag-of-words (BoW) representation of documents and statistical methods based on Latent Dirichlet Allocation (LDA) to cluster documents BIBREF1 . More recent approaches have used deep neural network based language models clustered with k-means, without a full multiscale graph analysis BIBREF2 . There have been some previous applications of network theory to text analysis. For example, Lanchichinetti and co-workers BIBREF3 used a probabilistic graph construction analysed with the InfoMap algorithm BIBREF4 ; however, their community detection was carried out at a single-scale and the representation of text as BoW arrays lacks the power of neural network text embeddings. The application of multiscale community detection allows us to find groups of records with consistent content at different levels of resolution; hence the content categories emerge from the textual data, rather than fitting with pre-designed classifications. The obtained results could thus help mitigate possible human error or effort in finding the right category in complex category classification trees.
We showcase the methodology through the analysis of a dataset of patient incidents reported to the NRLS. First, we use the 13 million records collected by the NRLS since 2004 to train our text embedding (although a much smaller corpus can be used). We then analyse a subset of 3229 records reported from St Mary's Hospital, London (Imperial College Healthcare NHS Trust) over three months in 2014 to extract clusters of incidents at different levels of resolution in terms of content. Our method reveals multiple levels of intrinsic structure in the topics of the dataset, as shown by the extraction of relevant word descriptors from the grouped records and a high level of topic coherence. Originally, the records had been manually coded by the operator upon reporting with up to 170 features per case, including a two-level manual classification of the incidents. Therefore, we also carried out an a posteriori comparison against the hand-coded categories assigned by the reporter (healthcare personnel) at the time of the report submission. Our results show good overall correspondence with the hand-coded categories across resolutions and, specifically, at the medium level of granularity. Several of our clusters of content correspond strongly to well-defined categories, yet our results also reveal complementary categories of incidents not defined in the external classification. In addition, the tuning of the granularity afforded by the method can be used to provide a distinct level of resolution in certain areas corresponding to specialise or particular sub-themes.
Our method departs from traditional natural language processing tools, which have generally used bag-of-words (BoW) representation of documents and statistical methods based on Latent Dirichlet Allocation (LDA) to cluster documents [2].
Answer: They have generally used bag-of-words (BoW) representation of documents and statistical methods based on Latent Dirichlet Allocation (LDA) to cluster documents.