Contextualised word embeddings is a powerful tool to detect contextual synonyms. However, most of the current state-of-the-art (SOTA) deep learning concept extraction methods remain supervised and underexploit the potential of the context. In this paper, we propose a self-supervised pre-training approach which is able to detect contextual synonyms of concepts being training on the data created by shallow matching. We apply our methodology in the sparse multi-class setting (over 15,000 concepts) to extract phenotype information from electronic health records. We further investigate data augmentation techniques to address the problem of the class sparsity. Our approach achieves a new SOTA for the unsupervised phenotype concept annotation on clinical text on F1 and Recall outperforming the previous SOTA with a gain of up to 4.5 and 4.0 absolute points, respectively. After fine-tuning with as little as 20% of the labelled data, we also outperform BioBERT and ClinicalBERT. The extrinsic evaluation on three ICU benchmarks also shows the benefit of using the phenotypes annotated by our model as features.

Background and Objective: Various risk factors have been evaluated to predict the mortality associated with COVID-19. We aim to explore and compare the clinical and laboratory risk factors with various outcomes of the disease between survivors and non-survivors amongst patients with moderate to severe COVID-19 disease. Methods: All COVID-19 adult (≥ 18 years old) ICU in-patients with a definite outcome i.e. either death or discharge were included. The demographic, clinical, laboratory, treatment, and outcome data were retrieved. To explore the association between factors, univariate and multivariate logistic regression were done. Results: A total of 163 patients were included out of which eight patients were shifted to other hospitals. Finally, a total of 145 patients were included in the study. Out of 145, 47 patients didn’t survive and 98 survived. A significant proportion (85%) of non-survivors were current smokers and were observed to have COPD, HT, and CAD as comorbidities when compared to the survivors. The qSOFA score, CRP, and TLC counts were included in the multivariable logistic regression with the former being the independent risk factor. Interpretation and Conclusion: Our study highlighted that older age, higher SOFA score, increased levels of total leucocyte count, and C-Reactive protein were independent risk factors affecting the clinical outcome in moderate to severe COVID-19 patients; however, qSOFA was found to be an independent risk factor predictor.

We consider a sequence of related multivariate time series learning tasks, such as predicting failures for different instances of a machine from time series of multi-sensor data, or activity recognition tasks over different individuals from multiple wearable sensors. We focus on two under-explored practical challenges arising in such settings: (i) Each task may have a different subset of sensors, i.e., providing different partial observations of the underlying 'system'. This restriction can be due to different manufacturers in the former case, and people wearing more or less measurement devices in the latter (ii) We are not allowed to store or re-access data from a task once it has been observed at the task level. This may be due to privacy considerations in the case of people, or legal restrictions placed by machine owners. Nevertheless, we would like to (a) improve performance on subsequent tasks using experience from completed tasks as well as (b) continue to perform better on past tasks, e.g., update the model and improve predictions on even the first machine after learning from subsequently observed ones. We note that existing continual learning methods do not take into account variability in input dimensions arising due to different subsets of sensors being available across tasks, and struggle to adapt to such variable input dimensions (VID) tasks. In this work, we address this shortcoming of existing methods. To this end, we learn task-specific generative models and classifiers, and use these to augment data for target tasks. Since the input dimensions across tasks vary, we propose a novel conditioning module based on graph neural networks to aid a standard recurrent neural network. We evaluate the efficacy of the proposed approach on three publicly available datasets corresponding to two activity recognition tasks (classification) and one prognostics task (regression). We demonstrate that it is possible to significantly enhance the performance on future and previous tasks while learning continuously from VID tasks without storing data.

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Phenotypic information of patients, as expressed in clinical text, is important in many clinical applications such as identifying patients at risk of hard-to-diagnose conditions. Extracting and inferring some phenotypes from clinical text requires numerical reasoning, for example, a temperature of 102°F suggests the phenotype Fever. However, while current state-of-the-art phenotyping models using natural language processing (NLP) are in general very efficient in extracting phenotypes, they struggle to extract phenotypes that require numerical reasoning. In this article, we propose a novel unsupervised method that leverages external clinical knowledge and contextualized word embeddings by ClinicalBERT for numerical reasoning in different phenotypic contexts. Experiments show that the proposed method achieves significant improvement against unsupervised baseline methods with absolute increase in generalized Recall and F1 scores of up to 79% and 71%, respectively. Also, the proposed method outperforms supervised baseline methods with absolute increase in generalized Recall and F1 scores of up to 70% and 44%, respectively. In addition, we validate the methodology on clinical use cases where the detected phenotypes significantly contribute to patient stratification systems for a set of diseases, namely, HIV and myocardial infarction (heart attack). Moreover, we find that these phenotypes from clinical text can be used to impute the missing values in structured data, which enrich and improve data quality.

ObjectiveClinical notes contain information that has not been documented elsewhere, including responses to treatment and clinical findings, which are crucial for predicting key outcomes in patients in acute care. In this study, we propose the automatic annotation of phenotypes from clinical notes as a method to capture essential information to predict outcomes in the intensive care unit (ICU). This information is complementary to typically used vital signs and laboratory test results.MethodsIn this study, we developed a novel phenotype annotation model to extract the phenotypical features of patients, which were then used as input features of predictive models to predict ICU patient outcomes. We demonstrated and validated this approach by conducting experiments on three ICU prediction tasks, including in-hospital mortality, physiological decompensation and length of stay (LOS) for over 24 000 patients using the Medical Information Mart for Intensive Care (MIMIC-III) dataset.ResultsThe predictive models incorporating phenotypical information achieved 0.845 (area under the curve–receiver operating characteristic (AUC-ROC)) for in-hospital mortality, 0.839 (AUC-ROC) for physiological decompensation and 0.430 (kappa) for LOS, all of which consistently outperformed the baseline models using only vital signs and laboratory test results. Moreover, we conducted a thorough interpretability study showing that phenotypes provide valuable insights at both the patient and cohort levels.ConclusionThe proposed approach demonstrates that phenotypical information complements traditionally used vital signs and laboratory test results and significantly improves the accuracy of outcome prediction in the ICU.

Contextualised word embeddings is a powerful tool to detect contextual synonyms. However, most of the current state-of-the-art (SOTA) deep learning concept extraction methods remain supervised and underexploit the potential of the context. In this paper, we propose a self-supervised pre-training approach which is able to detect contextual synonyms of concepts being training on the data created by shallow matching. We apply our methodology in the sparse multi-class setting (over 15,000 concepts) to extract phenotype information from electronic health records. We further investigate data augmentation techniques to address the problem of the class sparsity. Our approach achieves a new SOTA for the unsupervised phenotype concept annotation on clinical text on F1 and Recall outperforming the previous SOTA with a gain of up to 4.5 and 4.0 absolute points, respectively. After fine-tuning with as little as 20% of the labelled data, we also outperform BioBERT and ClinicalBERT. The extrinsic evaluation on three ICU benchmarks also shows the benefit of using the phenotypes annotated by our model as features.

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