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

A Hybrid Siamese Neural Network for Natural Language Inference in Cyber-Physical Systems

Cyber-Physical Systems (CPS), as a multi-dimensional complex system that connects the physical world and the cyber world, has a strong demand for processing large amounts of heterogeneous data. These tasks also include Natural Language Inference (NLI) tasks based on text from different sources. However, the current research on natural language processing in CPS does not involve exploration in this field. Therefore, this study proposes a Siamese Network structure that combines Stacked Residual Long Short-Term Memory (bidirectional) with the Attention mechanism and Capsule Network for the NLI module in CPS, which is used to infer the relationship between text/language data from different sources. This model is mainly used to implement NLI tasks and conduct a detailed evaluation in three main NLI benchmarks as the basic semantic understanding module in CPS. Comparative experiments prove that the proposed method achieves competitive performance, has a certain generalization ability, and can balance the performance and the number of trained parameters