Question Answering based Clinical Text Structuring Using Pre-trained Language Model

Abstract: Clinical text structuring is a critical and fundamental task for clinical research. Traditional methods such as taskspecific end-to-end models and pipeline models usually suffer from the lack of dataset and error propagation. In this paper, we present a question answering based clinical text structuring (QA-CTS) task to unify different specific tasks and make dataset shareable. A novel model that aims to introduce domain-specific features (e.g., clinical named entity information) into pre-trained language model is also proposed for QA-CTS task. Experimental results on Chinese pathology reports collected from Ruijing Hospital demonstrate our presented QA-CTS task is very effective to improve the performance on specific tasks. Our proposed model also competes favorably with strong baseline models in specific tasks.

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.
Traditionally, CTS tasks can be addressed by rule and dictionary based methods BIBREF0, BIBREF1, BIBREF2, task-specific end-to-end methods BIBREF3, BIBREF4, BIBREF5, BIBREF6 and pipeline methods BIBREF7, BIBREF8, BIBREF9. Rule and dictionary based methods suffer from costly human-designed extraction rules, while task-specific end-to-end methods have non-uniform output formats and require task-specific training dataset. Pipeline methods break down the entire process into several pieces which improves the performance and generality. However, when the pipeline depth grows, error propagation will have a greater impact on the performance.
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.
We first present a question answering based clinical text structuring (QA-CTS) task, which unifies different specific tasks and make dataset shareable. We also propose an effective model to integrate clinical named entity information into pre-trained language model.
Experimental results show that QA-CTS task leads to significant improvement due to shared dataset. Our proposed model also achieves significantly better performance than the strong baseline methods. In addition, we also show that two-stage training mechanism has a great improvement on QA-CTS task.
The rest of the paper is organized as follows. We briefly review the related work on clinical text structuring in Section SECREF2. Then, we present question answer based clinical text structuring task in Section SECREF3. In Section SECREF4, we present an effective model for this task. Section SECREF5 is devoted to computational studies and several investigations on the key issues of our proposed model. Finally, conclusions are given in Section SECREF6.
Clinical text structuring is a final problem which is highly related to practical applications. Most of existing studies are case-by-case. Few of them are developed for the general purpose structuring task. These studies can be roughly divided into three categories: rule and dictionary based methods, task-specific end-to-end methods and pipeline methods.
Rule and dictionary based methods BIBREF0, BIBREF1, BIBREF2 rely extremely on heuristics and handcrafted extraction rules which is more of an art than a science and incurring extensive trial-and-error experiments. Fukuda et al. BIBREF0 identified protein names from biological papers by dictionaries and several features of protein names. Wang et al. BIBREF1 developed some linguistic rules (i.e. normalised/expanded term matching and substring term matching) to map specific terminology to SNOMED CT. Song et al. BIBREF2 proposed a hybrid dictionary-based bio-entity extraction technique and expands the bio-entity dictionary by combining different data sources and improves the recall rate through the shortest path edit distance algorithm. This kind of approach features its interpretability and easy modifiability. However, with the increase of the rule amount, supplementing new rules to existing system will turn to be a rule disaster.
Task-specific end-to-end methods BIBREF3, BIBREF4 use large amount of data to automatically model the specific task. Topaz et al. BIBREF3 constructed an automated wound information identification model with five output. Tan et al. BIBREF4 identified patients undergoing radical cystectomy for bladder cancer. Although they achieved good performance, none of their models could be used to another task due to output format difference. This makes building a new model for a new task a costly job.
Pipeline methods BIBREF7, BIBREF8, BIBREF9 break down the entire task into several basic natural language processing tasks. Bill et al. BIBREF7 focused on attributes extraction which mainly relied on dependency parsing and named entity recognition BIBREF10, BIBREF11, BIBREF12. Meanwhile, Fonferko et al. BIBREF9 used more components like noun phrase chunking BIBREF13, BIBREF14, BIBREF15, part-of-speech tagging BIBREF16, BIBREF17, BIBREF18, sentence splitter, named entity linking BIBREF19, BIBREF20, BIBREF21, relation extraction BIBREF22, BIBREF23. This kind of method focus on language itself, so it can handle tasks more general. However, as the depth of pipeline grows, it is obvious that error propagation will be more and more serious. In contrary, using less components to decrease the pipeline depth will lead to a poor performance. So the upper limit of this method depends mainly on the worst component.
Recently, some works focused on pre-trained language representation models to capture language information from text and then utilizing the information to improve the performance of specific natural language processing tasks BIBREF24, BIBREF25, BIBREF26, BIBREF27 which makes language model a shared model to all natural language processing tasks. Radford et al. BIBREF24 proposed a framework for fine-tuning pre-trained language model. Peters et al. BIBREF25 proposed ELMo which concatenates forward and backward language models in a shallow manner. Devlin et al. BIBREF26 used bidirectional Transformers to model deep interactions between the two directions. Yang et al. BIBREF27 replaced the fixed forward or backward factorization order with all possible permutations of the factorization order and avoided using the [MASK] tag which causes pretrain-finetune discrepancy that BERT is subject to.
The main motivation of introducing pre-trained language model is to solve the shortage of labeled data and polysemy problem. Although polysemy problem is not a common phenomenon in biomedical domain, shortage of labeled data is always a non-trivial problem. Lee et al. BIBREF28 applied BERT on large-scale biomedical unannotated data and achieved improvement on biomedical named entity recognition, relation extraction and question answering. Kim et al. BIBREF29 adapted BioBERT into multi-type named entity recognition and discovered new entities. Both of them demonstrates the usefulness of introducing pre-trained language model into biomedical domain.
Given a sequence of paragraph text $X=<x_1, x_2, ..., x_n>$, clinical text structuring (CTS) can be regarded to extract or generate a key-value pair where key $Q$ is typically a query term such as proximal resection margin and value $V$ is a result of query term $Q$ according to the paragraph text $X$.
Generally, researchers solve CTS problem in two steps. Firstly, the answer-related text is pick out. And then several steps such as entity names conversion and negative words recognition are deployed to generate the final answer. While final answer varies from task to task, which truly causes non-uniform output formats, finding the answer-related text is a common action among all tasks. Traditional methods regard both the steps as a whole. In this paper, we focus on finding the answer-related substring $Xs = <X_i, X_i+1, X_i+2, ... X_j> (1 <= i < j <= n)$ from paragraph text $X$. For example, given sentence UTF8gkai“远端胃切除标本：小弯长11.5cm，大弯长17.0cm。距上切端6.0cm、下切端8.0cm" (Distal gastrectomy specimen: measuring 11.5cm in length along the lesser curvature, 17.0cm in length along the greater curvature; 6.0cm from the proximal resection margin, and 8.0cm from the distal resection margin) and query UTF8gkai“上切缘距离"(proximal resection margin), the answer should be 6.0cm which is located in original text from index 32 to 37. With such definition, it unifies the output format of CTS tasks and therefore make the training data shareable, in order to reduce the training data quantity requirement.
Since BERT BIBREF26 has already demonstrated the usefulness of shared model, we suppose extracting commonality of this problem and unifying the output format will make the model more powerful than dedicated model and meanwhile, for a specific clinical task, use the data for other tasks to supplement the training data.
In this section, we present an effective model for the question answering based clinical text structuring (QA-CTS). As shown in Fig. FIGREF8, paragraph text $X$ is first passed to a clinical named entity recognition (CNER) model BIBREF12 to capture named entity information and obtain one-hot CNER output tagging sequence for query text $I_{nq}$ and paragraph text $I_{nt}$ with BIEOS (Begin, Inside, End, Outside, Single) tag scheme. $I_{nq}$ and $I_{nt}$ are then integrated together into $I_n$. Meanwhile, the paragraph text $X$ and query text $Q$ are organized and passed to contextualized representation model which is pre-trained language model BERT BIBREF26 here to obtain the contextualized representation vector $V_s$ of both text and query. Afterwards, $V_s$ and $I_n$ are integrated together and fed into a feed forward network to calculate the start and end index of answer-related text. Here we define this calculation problem as a classification for each word to be the start or end word.
For any clinical free-text paragraph $X$ and query $Q$, contextualized representation is to generate the encoded vector of both of them. Here we use pre-trained language model BERT-base BIBREF26 model to capture contextual information.
The text input is constructed as `[CLS] $Q$ [SEP] $X$ [SEP]'. For Chinese sentence, each word in this input will be mapped to a pre-trained embedding $e_i$. To tell the model $Q$ and $X$ is two different sentence, a sentence type input is generated which is a binary label sequence to denote what sentence each character in the input belongs to. Positional encoding and mask matrix is also constructed automatically to bring in absolute position information and eliminate the impact of zero padding respectively. Then a hidden vector $V_s$ which contains both query and text information is generated through BERT-base model.
Since BERT is trained on general corpus, its performance on biomedical domain can be improved by introducing biomedical domain-specific features. In this paper, we introduce clinical named entity information into the model.
The CNER task aims to identify and classify important clinical terms such as diseases, symptoms, treatments, exams, and body parts from Chinese EHRs. It can be regarded as a sequence labeling task. A CNER model typically outputs a sequence of tags. Each character of the original sentence will be tagged a label following a tag scheme. In this paper we recognize the entities by the model of our previous work BIBREF12 but trained on another corpus which has 44 entity types including operations, numbers, unit words, examinations, symptoms, negative words, etc. An illustrative example of named entity information sequence is demonstrated in Table TABREF2. In Table TABREF2, UTF8gkai“远端胃切除" is tagged as an operation, `11.5' is a number word and `cm' is an unit word. The named entity tag sequence is organized in one-hot type. We denote the sequence for clinical sentence and query term as $I_{nt}$ and $I_{nq}$, respectively.
There are two ways to integrate two named entity information vectors $I_{nt}$ and $I_{nq}$ or hidden contextualized representation $V_s$ and named entity information $I_n$, where $I_n = [I_{nt}; I_{nq}]$. The first one is to concatenate them together because they have sequence output with a common dimension. The second one is to transform them into a new hidden representation. For the concatenation method, the integrated representation is described as follows.
While for the transformation method, we use multi-head attention BIBREF30 to encode the two vectors. It can be defined as follows where $h$ is the number of heads and $W_o$ is used to projects back the dimension of concatenated matrix.
$Attention$ denotes the traditional attention and it can be defined as follows.
where $d_k$ is the length of hidden vector.
The final step is to use integrated representation $H_i$ to predict the start and end index of answer-related text. Here we define this calculation problem as a classification for each word to be the start or end word. We use a feed forward network (FFN) to compress and calculate the score of each word $H_f$ which makes the dimension to $\left\langle l_s, 2\right\rangle $ where $l_s$ denotes the length of sequence.
Then we permute the two dimensions for softmax calculation. The calculation process of loss function can be defined as followed.
where $O_s = softmax(permute(H_f)_0)$ denotes the probability score of each word to be the start word and similarly $O_e = softmax(permute(H_f)_1)$ denotes the end. $y_s$ and $y_e$ denotes the true answer of the output for start word and end word respectively.
Two-stage training mechanism is previously applied on bilinear model in fine-grained visual recognition BIBREF31, BIBREF32, BIBREF33. Two CNNs are deployed in the model. One is trained at first for coarse-graind features while freezing the parameter of the other. Then unfreeze the other one and train the entire model in a low learning rate for fetching fine-grained features.
Inspired by this and due to the large amount of parameters in BERT model, to speed up the training process, we fine tune the BERT model with new prediction layer first to achieve a better contextualized representation performance. Then we deploy the proposed model and load the fine tuned BERT weights, attach named entity information layers and retrain the model.
In this section, we devote to experimentally evaluating our proposed task and approach. The best results in tables are in bold.
Our dataset is annotated based on Chinese pathology reports provided by the Department of Gastrointestinal Surgery, Ruijin Hospital. It contains 17,833 sentences, 826,987 characters and 2,714 question-answer pairs. All question-answer pairs are annotated and reviewed by four clinicians with three types of questions, namely tumor size, proximal resection margin and distal resection margin. These annotated instances have been partitioned into 1,899 training instances (12,412 sentences) and 815 test instances (5,421 sentences). Each instance has one or several sentences. Detailed statistics of different types of entities are listed in Table TABREF20.
In the following experiments, two widely-used performance measures (i.e., EM-score BIBREF34 and (macro-averaged) F$_1$-score BIBREF35) are used to evaluate the methods. The Exact Match (EM-score) metric measures the percentage of predictions that match any one of the ground truth answers exactly. The F$_1$-score metric is a looser metric measures the average overlap between the prediction and ground truth answer.
To implement deep neural network models, we utilize the Keras library BIBREF36 with TensorFlow BIBREF37 backend. Each model is run on a single NVIDIA GeForce GTX 1080 Ti GPU. The models are trained by Adam optimization algorithm BIBREF38 whose parameters are the same as the default settings except for learning rate set to $5\times 10^{-5}$. Batch size is set to 3 or 4 due to the lack of graphical memory. We select BERT-base as the pre-trained language model in this paper. Due to the high cost of pre-training BERT language model, we directly adopt parameters pre-trained by Google in Chinese general corpus. The named entity recognition is applied on both pathology report texts and query texts.
Since BERT has already achieved the state-of-the-art performance of question-answering, in this section we compare our proposed model with state-of-the-art question answering models (i.e. QANet BIBREF39) and BERT-Base BIBREF26. As BERT has two versions: BERT-Base and BERT-Large, due to the lack of computational resource, we can only compare with BERT-Base model instead of BERT-Large. Prediction layer is attached at the end of the original BERT-Base model and we fine tune it on our dataset. In this section, the named entity integration method is chosen to pure concatenation (Concatenate the named entity information on pathology report text and query text first and then concatenate contextualized representation and concatenated named entity information). Comparative results are summarized in Table TABREF23.
Table TABREF23 indicates that our proposed model achieved the best performance both in EM-score and F$_1$-score with EM-score of 91.84% and F$_1$-score of 93.75%. QANet outperformed BERT-Base with 3.56% score in F$_1$-score but underperformed it with 0.75% score in EM-score. Compared with BERT-Base, our model led to a 5.64% performance improvement in EM-score and 3.69% in F$_1$-score. Although our model didn't outperform much with QANet in F$_1$-score (only 0.13%), our model significantly outperformed it with 6.39% score in EM-score.
To further investigate the effects of named entity information and two-stage training mechanism for our model, we apply ablation analysis to see the improvement brought by each of them, where $\times $ refers to removing that part from our model.
As demonstrated in Table TABREF25, with named entity information enabled, two-stage training mechanism improved the result by 4.36% in EM-score and 3.8% in F$_1$-score. Without two-stage training mechanism, named entity information led to an improvement by 1.28% in EM-score but it also led to a weak deterioration by 0.12% in F$_1$-score. With both of them enabled, our proposed model achieved a 5.64% score improvement in EM-score and a 3.69% score improvement in F$_1$-score. The experimental results show that both named entity information and two-stage training mechanism are helpful to our model.
There are two methods to integrate named entity information into existing model, we experimentally compare these two integration methods. As named entity recognition has been applied on both pathology report text and query text, there will be two integration here. One is for two named entity information and the other is for contextualized representation and integrated named entity information. For multi-head attention BIBREF30, we set heads number $h = 16$ with 256-dimension hidden vector size for each head.
From Table TABREF27, we can observe that applying concatenation on both periods achieved the best performance on both EM-score and F$_1$-score. Unfortunately, applying multi-head attention on both period one and period two can not reach convergence in our experiments. This probably because it makes the model too complex to train. The difference on other two methods are the order of concatenation and multi-head attention. Applying multi-head attention on two named entity information $I_{nt}$ and $I_{nq}$ first achieved a better performance with 89.87% in EM-score and 92.88% in F$_1$-score. Applying Concatenation first can only achieve 80.74% in EM-score and 84.42% in F$_1$-score. This is probably due to the processing depth of hidden vectors and dataset size. BERT's output has been modified after many layers but named entity information representation is very close to input. With big amount of parameters in multi-head attention, it requires massive training to find out the optimal parameters. However, our dataset is significantly smaller than what pre-trained BERT uses. This probably can also explain why applying multi-head attention method on both periods can not converge.
Although Table TABREF27 shows the best integration method is concatenation, multi-head attention still has great potential. Due to the lack of computational resources, our experiment fixed the head number and hidden vector size. However, tuning these hyper parameters may have impact on the result. Tuning integration method and try to utilize larger datasets may give help to improving the performance.
To investigate how shared task and shared model can benefit, we split our dataset by query types, train our proposed model with different datasets and demonstrate their performance on different datasets. Firstly, we investigate the performance on model without two-stage training and named entity information.
As indicated in Table TABREF30, The model trained by mixed data outperforms 2 of the 3 original tasks in EM-score with 81.55% for proximal resection margin and 86.85% for distal resection margin. The performance on tumor size declined by 1.57% score in EM-score and 3.14% score in F$_1$-score but they were still above 90%. 0.69% and 0.37% score improvement in EM-score was brought by shared model for proximal and distal resection margin prediction. Meanwhile F$_1$-score for those two tasks declined 3.11% and 0.77% score.
Then we investigate the performance on model with two-stage training and named entity information. In this experiment, pre-training process only use the specific dataset not the mixed data. From Table TABREF31 we can observe that the performance on proximal and distal resection margin achieved the best performance on both EM-score and F$_1$-score. Compared with Table TABREF30, the best performance on proximal resection margin improved by 6.9% in EM-score and 7.94% in F$_1$-score. Meanwhile, the best performance on distal resection margin improved by 5.56% in EM-score and 6.32% in F$_1$-score. Other performances also usually improved a lot. This proves the usefulness of two-stage training and named entity information as well.
Lastly, we fine tune the model for each task with a pre-trained parameter. Table TABREF32 summarizes the result. (Add some explanations for the Table TABREF32). Comparing Table TABREF32 with Table TABREF31, using mixed-data pre-trained parameters can significantly improve the model performance than task-specific data trained model. Except tumor size, the result was improved by 0.52% score in EM-score, 1.39% score in F$_1$-score for proximal resection margin and 2.6% score in EM-score, 2.96% score in F$_1$-score for distal resection margin. This proves mixed-data pre-trained parameters can lead to a great benefit for specific task. Meanwhile, the model performance on other tasks which are not trained in the final stage was also improved from around 0 to 60 or 70 percent. This proves that there is commonality between different tasks and our proposed QA-CTS task make this learnable. In conclusion, to achieve the best performance for a specific dataset, pre-training the model in multiple datasets and then fine tuning the model on the specific dataset is the best way.
In this paper, we present a question answering based clinical text structuring (QA-CTS) task, which unifies different clinical text structuring tasks and utilize different datasets. A novel model is also proposed to integrate named entity information into a pre-trained language model and adapt it to QA-CTS task. Initially, sequential results of named entity recognition on both paragraph and query texts are integrated together. Contextualized representation on both paragraph and query texts are transformed by a pre-trained language model. Then, the integrated named entity information and contextualized representation are integrated together and fed into a feed forward network for final prediction. Experimental results on real-world dataset demonstrate that our proposed model competes favorably with strong baseline models in all three specific tasks. The shared task and shared model introduced by QA-CTS task has also been proved to be useful for improving the performance on most of the task-specific datasets. In conclusion, the best way to achieve the best performance for a specific dataset is to pre-train the model in multiple datasets and then fine tune it on the specific dataset.
We would like to thank Ting Li and Xizhou Hong (Ruijin Hospital) who have helped us very much in data fetching and data cleansing. This work is supported by the National Key R&D Program of China for “Precision Medical Research" (No. 2018YFC0910500).

Figure and table captions:
Fig. 1. An illustrative example of QA-CTS task.
TABLE I AN ILLUSTRATIVE EXAMPLE OF NAMED ENTITY FEATURE TAGS
Fig. 2. The architecture of our proposed model for QA-CTS task
TABLE II STATISTICS OF DIFFERENT TYPES OF QUESTION ANSWER INSTANCES
TABLE V COMPARATIVE RESULTS FOR DIFFERENT INTEGRATION METHOD OF OUR PROPOSED MODEL
TABLE III COMPARATIVE RESULTS BETWEEN BERT AND OUR PROPOSED MODEL
TABLE VI COMPARATIVE RESULTS FOR DATA INTEGRATION ANALYSIS (WITHOUT TWO-STAGE TRAINING AND NAMED ENTITY INFORMATION)
TABLE VII COMPARATIVE RESULTS FOR DATA INTEGRATION ANALYSIS (WITH TWO-STAGE TRAINING AND NAMED ENTITY INFORMATION)
TABLE VIII COMPARATIVE RESULTS FOR DATA INTEGRATION ANALYSIS (USING MIXED-DATA PRE-TRAINED PARAMETERS)

Questions about this paper:
How is the clinical text structuring task defined?
Is all text in this dataset a question, or are there unrelated sentences in between questions?
How many questions are in the dataset?

Answers:
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.
the dataset consists of pathology reports including sentences and questions and answers about tumor size and resection margins so it does include additional sentences 
2,714