Vibhor Gupta

Jingqing Zhang, Luis Bolanos, Tong Li et al.

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.

Jingqing Zhang, Luis Bolanos, Ashwani Tanwar et al.

Objective: Clinical notes contain information not present elsewhere, including drug response and symptoms, all of which are highly important when predicting key outcomes in acute care patients. We propose the automatic annotation of phenotypes from clinical notes as a method to capture essential information, which is complementary to typically used vital signs and laboratory test results, to predict outcomes in the Intensive Care Unit (ICU). Methods: We develop a novel phenotype annotation model to annotate phenotypic features of patients which are then used as input features of predictive models to predict ICU patient outcomes. We demonstrate and validate our approach conducting experiments on three ICU prediction tasks including in-hospital mortality, physiological decompensation and length of stay for over 24,000 patients by using MIMIC-III dataset. Results: The predictive models incorporating phenotypic information achieve 0.845 (AUC-ROC) to predict in-hospital mortality, 0.839 (AUC-ROC) for physiological decompensation and 0.430 (Kappa) for length of stay, all of which consistently outperform the baseline models leveraging only vital signs and laboratory test results. Moreover, we conduct a thorough interpretability study, showing that phenotypes provide valuable insights at the patient and cohort levels. Conclusion: The proposed approach demonstrates phenotypic information complements traditionally used vital signs and laboratory test results, improving significantly forecast of outcomes in the ICU.

Vibhor Gupta, Jyoti Narwariya, Pankaj Malhotra et al.

Several applications of Internet of Things (IoT) technology involve capturing data from multiple sensors resulting in multi-sensor time series. Existing neural networks based approaches for such multi-sensor or multivariate time series modeling assume fixed input dimension or number of sensors. Such approaches can struggle in the practical setting where different instances of the same device or equipment such as mobiles, wearables, engines, etc. come with different combinations of installed sensors. We consider training neural network models from such multi-sensor time series, where the time series have varying input dimensionality owing to availability or installation of a different subset of sensors at each source of time series. We propose a novel neural network architecture suitable for zero-shot transfer learning allowing robust inference for multivariate time series with previously unseen combination of available dimensions or sensors at test time. Such a combinatorial generalization is achieved by conditioning the layers of a core neural network-based time series model with a "conditioning vector" that carries information of the available combination of sensors for each time series. This conditioning vector is obtained by summarizing the set of learned "sensor embedding vectors" corresponding to the available sensors in a time series via a graph neural network. We evaluate the proposed approach on publicly available activity recognition and equipment prognostics datasets, and show that the proposed approach allows for better generalization in comparison to a deep gated recurrent neural network baseline.