A Translate-Edit Model for Natural Language Question to SQL Query Generation on Multi-relational Healthcare Data

Electronic health record (EHR) data contains most of the important patient health information and is typically stored in a relational database with multiple tables. One important way for doctors to make use of EHR data is to retrieve intuitive information by posing a sequence of questions against it. However, due to a large amount of information stored in it, effectively retrieving patient information from EHR data in a short time is still a challenging issue for medical experts since it requires a good understanding of a query language to get access to the database. We tackle this challenge by developing a deep learning based approach that can translate a natural language question on multi-relational EHR data into its corresponding SQL query, which is referred to as a Question-to-SQL generation task. Most of the existing methods cannot solve this problem since they primarily focus on tackling the questions related to a single table under the table-aware assumption. While in our problem, it is possible that questions asked by clinicians are related to multiple unspecified tables. In this paper, we first create a new question to query dataset designed for healthcare to perform the Question-to-SQL generation task, named MIMICSQL, based on a publicly available electronic medical database. To address the challenge of generating queries on multi-relational databases from natural language questions, we propose a TRanslate-Edit Model for Question-to-SQL query (TREQS), which adopts the sequence-to-sequence model to directly generate SQL query for a given question, and further edits it with an attentive-copying mechanism and task-specific look-up tables. Both quantitative and qualitative experimental results indicate the flexibility and efficiency of our proposed method in tackling challenges that are unique in MIMICSQL.