A New Data Representation Based on Training Data Characteristics to Extract Drug Name Entity in Medical Text

Hybrid Deep Learning for Medication-Related Information Extraction From Clinical Texts in French: MedExt Algorithm Development Study

BACKGROUND

Information related to patient medication is crucial for health care; however, up to 80% of the information resides solely in unstructured text. Manual extraction is difficult and time-consuming, and there is not a lot of research on natural language processing extracting medical information from unstructured text from French corpora.

OBJECTIVE

We aimed to develop a system to extract medication-related information from clinical text written in French.

METHODS

We developed a hybrid system combining an expert rule-based system, contextual word embedding (embedding for language model) trained on clinical notes, and a deep recurrent neural network (bidirectional long short term memory-conditional random field). The task consisted of extracting drug mentions and their related information (eg, dosage, frequency, duration, route, condition). We manually annotated 320 clinical notes from a French clinical data warehouse to train and evaluate the model. We compared the performance of our approach to those of standard approaches: rule-based or machine learning only and classic word embeddings. We evaluated the models using token-level recall, precision, and F-measure.

RESULTS

The overall F-measure was 89.9% (precision 90.8; recall: 89.2) when combining expert rules and contextualized embeddings, compared to 88.1% (precision 89.5; recall 87.2) without expert rules or contextualized embeddings. The F-measures for each category were 95.3% for medication name, 64.4% for drug class mentions, 95.3% for dosage, 92.2% for frequency, 78.8% for duration, and 62.2% for condition of the intake.

CONCLUSIONS

Associating expert rules, deep contextualized embedding, and deep neural networks improved medication information extraction. Our results revealed a synergy when associating expert knowledge and latent knowledge.

IARNN-Based Semantic-Containing Double-Level Embedding Bi-LSTM for Question-and-Answer Matching

We propose a novel end-to-end approach, namely, the semantic-containing double-level embedding Bi-LSTM model (SCDE-Bi-LSTM), to solve the three key problems of Q&A matching in the Chinese medical field. In the similarity calculation of the Q&A core module, we propose a text similarity calculation method that contains semantic information, to solve the problem that previous Q&A methods do not incorporate the deep information of a sentence into the similarity calculations. For the sentence vector representation module, we present a double-level embedding sentence representation method to reduce the error caused by Chinese medical word segmentation. In addition, due to the problem of the attention mechanism tending to cause backward deviation of the features, we propose an improved algorithm based on Bi-LSTM in the feature extraction stage. The Q&A framework proposed in this paper not only retains important timing features but also loses low-frequency features and noise. Additionally, it is applicable to different domains. To verify the framework, extensive Chinese medical Q&A corpora are created. We run several state-of-the-art Q&A methods as contrastive experiments on the medical corpora and the current popular insuranceQA dataset under different performance measures. The experimental results on the medical corpora show that our framework significantly outperforms several strong baselines and achieves an improvement of top-1 accuracy of up to 14%, reaching 79.15%.

Predicting life expectancy with a long short-term memory recurrent neural network using electronic medical records

BACKGROUND

Life expectancy is one of the most important factors in end-of-life decision making. Good prognostication for example helps to determine the course of treatment and helps to anticipate the procurement of health care services and facilities, or more broadly: facilitates Advance Care Planning. Advance Care Planning improves the quality of the final phase of life by stimulating doctors to explore the preferences for end-of-life care with their patients, and people close to the patients. Physicians, however, tend to overestimate life expectancy, and miss the window of opportunity to initiate Advance Care Planning. This research tests the potential of using machine learning and natural language processing techniques for predicting life expectancy from electronic medical records.

METHODS

We approached the task of predicting life expectancy as a supervised machine learning task. We trained and tested a long short-term memory recurrent neural network on the medical records of deceased patients. We developed the model with a ten-fold cross-validation procedure, and evaluated its performance on a held-out set of test data. We compared the performance of a model which does not use text features (baseline model) to the performance of a model which uses features extracted from the free texts of the medical records (keyword model), and to doctors' performance on a similar task as described in scientific literature.

RESULTS

Both doctors and the baseline model were correct in 20% of the cases, taking a margin of 33% around the actual life expectancy as the target. The keyword model, in comparison, attained an accuracy of 29% with its prognoses. While doctors overestimated life expectancy in 63% of the incorrect prognoses, which harms anticipation to appropriate end-of-life care, the keyword model overestimated life expectancy in only 31% of the incorrect prognoses.

CONCLUSIONS

Prognostication of life expectancy is difficult for humans. Our research shows that machine learning and natural language processing techniques offer a feasible and promising approach to predicting life expectancy. The research has potential for real-life applications, such as supporting timely recognition of the right moment to start Advance Care Planning.