Question: How is the clinical text structuring task defined?
Evidence: Clinical text structuring (CTS) is a critical task for fetching medical research data from electronic health records (EHRs), where structural patient medical data, such as whether the patient has specific symptoms, diseases, or what the tumor size is, how far from the tumor is cut at during the surgery, or what the specific laboratory test result is, are obtained. It is important to extract structured data from clinical text because bio-medical systems or bio-medical researches greatly rely on structured data but they cannot obtain them directly. In addition, clinical text often contains abundant healthcare information. CTS is able to provide large-scale extracted structured data for enormous down-stream clinical researches.
However, end-to-end CTS is a very challenging task. Different CTS tasks often have non-uniform output formats, such as specific-class classifications (e.g. tumor stage), strings in the original text (e.g. result for a laboratory test) and inferred values from part of the original text (e.g. calculated tumor size). Researchers have to construct different models for it, which is already costly, and hence it calls for a lot of labeled data for each model. Moreover, labeling necessary amount of data for training neural network requires expensive labor cost. To handle it, researchers turn to some rule-based structuring methods which often have lower labor cost.
To reduce the pipeline depth and break the barrier of non-uniform output formats, we present a question answering based clinical text structuring (QA-CTS) task (see Fig. FIGREF1). Unlike the traditional CTS task, our QA-CTS task aims to discover the most related text from original paragraph text. For some cases, it is already the final answer in deed (e.g., extracting sub-string). While for other cases, it needs several steps to obtain the final answer, such as entity names conversion and negative words recognition. Our presented QA-CTS task unifies the output format of the traditional CTS task and make the training data shareable, thus enriching the training data. The main contributions of this work can be summarized as follows.
Clinical text structuring (CTS) is a critical task for fetching medical research data from electronic health records (EHRs), where structural patient medical data, such as whether the patient has specific symptoms, diseases, or what the tumor size is, how far from the tumor is cut at during the surgery, or what the specific laboratory test result is, are obtained. It is important to extract structured data from clinical text because bio-medical systems or bio-medical researches greatly rely on structured data but they cannot obtain them directly.
However, end-to-end CTS is a very challenging task. Different CTS tasks often have non-uniform output formats, such as specific-class classifications (e.g. tumor stage), strings in the original text (e.g. result for a laboratory test) and inferred values from part of the original text (e.g. calculated tumor size).
To reduce the pipeline depth and break the barrier of non-uniform output formats, we present a question answering based clinical text structuring (QA-CTS) task (see Fig. FIGREF1). Unlike the traditional CTS task, our QA-CTS task aims to discover the most related text from original paragraph text.
Answer: CTS is extracting structural data from medical research data (unstructured). Authors define QA-CTS task that aims to discover most related text from original text.