Named Entity Recognition in Electronic Health Records Using Transfer Learning Bootstrapped Neural Networks

Neural networks (NNs) have become the state of the art in many machine learning applications, especially in image and sound processing [1]. The same, although to a lesser extent [2,3], could be said in natural language processing (NLP) tasks, such as named entity recognition. However, the success of NNs remains dependent on the availability of large labelled datasets, which is a significant hurdle in many important applications. One such case are electronic health records (EHRs), which are arguably the largest source of medical data, most of which lies hidden in natural text [4,5]. Data access is difficult due to data privacy concerns, and therefore annotated datasets are scarce. With scarce data, NNs will likely not be able to extract this hidden information with practical accuracy. In our study, we develop an approach that solves these problems for named entity recognition, obtaining 94.6 F1 score in I2B2 2009 Medical Extraction Challenge [6], 4.3 above the architecture that won the competition. Beyond the official I2B2 challenge, we further achieve 82.4 F1 on extracting relationships between medical terms. To reach this state-of-the-art accuracy, our approach applies transfer learning to leverage on datasets annotated for other I2B2 tasks, and designs and trains embeddings that specially benefit from such transfer.Comment: 11 pages, 4 figures, 8 table

Headache and type 2 diabetes association: a US national ambulatory case-control study

Objective We investigate the joint observation between type 2 diabetes and headache using a case-control study of a US ambulatory dataset. Background Recent whole-population cohort studies propose that type 2 diabetes may have a protective effect against headache prevalence. With headaches ranked as a leading cause of disability, headache-associated comorbidities could help identify shared molecular mechanisms. Methods We performed a case-control study using the US National Ambulatory Medical Care Survey, 2009, on the joint observation between headache and specific comorbidities, namely type 2 diabetes, hypertension and anxiety, for all patients between 18 and 65 years of age. The odds ratio of having a headache and a comorbidity were calculated using conditional logistic regression, controlling for gender and age over a study population of 3,327,947 electronic health records in the absence of prescription medication data. Results We observed estimated odds ratio of 0.89 (95% CI: 0.83-0.95) of having a headache and a record of type 2 diabetes over the population, and 0.83 (95% CI: 2.02-2.57) and 0.89 (95% CI: 3.00-3.49) for male and female, respectively. Conclusions We find that patients with type 2 diabetes are less likely to present a recorded headache indication. Patients with hypertension are almost twice as likely of having a headache indication and patients with an anxiety disorder are almost three times as likely. Given the possibility of confounding indications and prescribed medications, additional studies are recommended

Clinical prompt learning with frozen language models

When the first transformer-based language models were published in the late 2010s, pretraining with general text and then fine-tuning the model on a task-specific dataset often achieved the state-of-the-art performance. However, more recent work suggests that for some tasks, directly prompting the pretrained model matches or surpasses fine-tuning in performance with few or no model parameter updates required. The use of prompts with language models for natural language processing (NLP) tasks is known as prompt learning. We investigated the viability of prompt learning on clinically meaningful decision tasks and directly compared this with more traditional fine-tuning methods. Results show that prompt learning methods were able to match or surpass the performance of traditional fine-tuning with up to 1000 times fewer trainable parameters, less training time, less training data, and lower computation resource requirements. We argue that these characteristics make prompt learning a very desirable alternative to traditional fine-tuning for clinical tasks, where the computational resources of public health providers are limited, and where data can often not be made available or not be used for fine-tuning due to patient privacy concerns. The complementary code to reproduce the experiments presented in this work can be found at https://github.com/NtaylorOX/Public_Clinical_Prompt

Learning to Detect Bipolar Disorder and Borderline Personality Disorder with Language and Speech in Non-Clinical Interviews

Bipolar disorder (BD) and borderline personality disorder (BPD) are both chronic psychiatric disorders. However, their overlapping symptoms and common comorbidity make it challenging for the clinicians to distinguish the two conditions on the basis of a clinical interview. In this work, we first present a new multi-modal dataset containing interviews involving individuals with BD or BPD being interviewed about a non-clinical topic . We investigate the automatic detection of the two conditions, and demonstrate a good linear classifier that can be learnt using a down-selected set of features from the different aspects of the interviews and a novel approach of summarising these features. Finally, we find that different sets of features characterise BD and BPD, thus providing insights into the difference between the automatic screening of the two conditions

Identifying predictors of suicide in severe mental illness : a feasibility study of a clinical prediction rule (Oxford Mental Illness and Suicide tool or OxMIS)

Background: Oxford Mental Illness and Suicide tool (OxMIS) is a brief, scalable, freely available, structured risk assessment tool to assess suicide risk in patients with severe mental illness (schizophrenia-spectrum disorders or bipolar disorder). OxMIS requires further external validation, but a lack of large-scale cohorts with relevant variables makes this challenging. Electronic health records provide possible data sources for external validation of risk prediction tools. However, they contain large amounts of information within free-text that is not readily extractable. In this study, we examined the feasibility of identifying suicide predictors needed to validate OxMIS in routinely collected electronic health records. Methods: In study 1, we manually reviewed electronic health records of 57 patients with severe mental illness to calculate OxMIS risk scores. In study 2, we examined the feasibility of using natural language processing to scale up this process. We used anonymized free-text documents from the Clinical Record Interactive Search database to train a named entity recognition model, a machine learning technique which recognizes concepts in free-text. The model identified eight concepts relevant for suicide risk assessment: medication (antidepressant/antipsychotic treatment), violence, education, self-harm, benefits receipt, drug/alcohol use disorder, suicide, and psychiatric admission. We assessed model performance in terms of precision (similar to positive predictive value), recall (similar to sensitivity) and F1 statistic (an overall performance measure). Results: In study 1, we estimated suicide risk for all patients using the OxMIS calculator, giving a range of 12 month risk estimates from 0.1-3.4%. For 13 out of 17 predictors, there was no missing information in electronic health records. For the remaining 4 predictors missingness ranged from 7-26%; to account for these missing variables, it was possible for OxMIS to estimate suicide risk using a range of scores. In study 2, the named entity recognition model had an overall precision of 0.77, recall of 0.90 and F1 score of 0.83. The concept with the best precision and recall was medication (precision 0.84, recall 0.96) and the weakest were suicide (precision 0.37), and drug/alcohol use disorder (recall 0.61). Conclusions: It is feasible to estimate suicide risk with the OxMIS tool using predictors identified in routine clinical records. Predictors could be extracted using natural language processing. However, electronic health records differ from other data sources, particularly for family history variables, which creates methodological challenges

Personalised treatment for cognitive impairment in dementia : development and validation of an artificial intelligence model

Background Donepezil, galantamine, rivastigmine and memantine are potentially effective interventions for cognitive impairment in dementia, but the use of these drugs has not been personalised to individual patients yet. We examined whether artificial intelligence-based recommendations can identify the best treatment using routinely collected patient-level information. Methods Six thousand eight hundred four patients aged 59–102 years with a diagnosis of dementia from two National Health Service (NHS) Foundation Trusts in the UK were used for model training/internal validation and external validation, respectively. A personalised prescription model based on the Recurrent Neural Network machine learning architecture was developed to predict the Mini-Mental State Examination (MMSE) and Montreal Cognitive Assessment (MoCA) scores post-drug initiation. The drug that resulted in the smallest decline in cognitive scores between prescription and the next visit was selected as the treatment of choice. Change of cognitive scores up to 2 years after treatment initiation was compared for model evaluation. Results Overall, 1343 patients with MMSE scores were identified for internal validation and 285 [21.22%] took the drug recommended. After 2 years, the reduction of mean [standard deviation] MMSE score in this group was significantly smaller than the remaining 1058 [78.78%] patients (0.60 [0.26] vs 2.80 [0.28]; P = 0.02). In the external validation cohort (N = 1772), 222 [12.53%] patients took the drug recommended and reported a smaller MMSE reduction compared to the 1550 [87.47%] patients who did not (1.01 [0.49] vs 4.23 [0.60]; P = 0.01). A similar performance gap was seen when testing the model on patients prescribed with AChEIs only. Conclusions It was possible to identify the most effective drug for the real-world treatment of cognitive impairment in dementia at an individual patient level. Routine care patients whose prescribed medications were the best fit according to the model had better cognitive performance after 2 years