PASCAL: a pseudo cascade learning framework for breast cancer treatment entity normalization in Chinese clinical text

Abstract

Backgrounds: Knowledge discovery from breast cancer treatment records has promoted downstream clinical studies such as careflow mining and therapy analysis. However, the clinical treatment text from electronic health data might be recorded by different doctors under their hospital guidelines, making the final data rich in author- and domain-specific idiosyncrasies. Therefore, breast cancer treatment entity normalization becomes an essential task for the above downstream clinical studies. The latest studies have demonstrated the superiority of deep learning methods in named entity normalization tasks. Fundamentally, most existing approaches adopt pipeline implementations that treat it as an independent process after named entity recognition, which can propagate errors to later tasks. In addition, despite its importance in clinical and translational research, few studies directly deal with the normalization task in Chinese clinical text due to the complexity of composition forms.

Methods: To address these issues, we propose PASCAL, an end-to-end and accurate framework for breast cancer treatment entity normalization (TEN). PASCAL leverages a gated convolutional neural network to obtain a representation vector that can capture contextual features and long-term dependencies. Additionally, it treats treatment entity recognition (TER) as an auxiliary task that can provide meaningful information to the primary TEN task and as a particular regularization to further optimize the shared parameters. Finally, by concatenating the context-aware vector and probabilistic distribution vector from TEN, we utilize the conditional random field layer (CRF) to model the normalization sequence and predict the TEN sequential results.

Results: To evaluate the effectiveness of the proposed framework, we employ the three latest sequential models as baselines and build the model in single- and multitask on a real-world database. Experimental results show that our method achieves better accuracy and efficiency than state-of-the-art approaches.

Conclusions: The effectiveness and efficiency of the presented pseudo cascade learning framework were validated for breast cancer treatment normalization in clinical text. We believe the predominant performance lies in its ability to extract valuable information from unstructured text data, which will significantly contribute to downstream tasks, such as treatment recommendations, breast cancer staging and careflow mining.

Keywords: Breast cancer; Cascade learning; Chinese clinical text mining; Treatment entity normalization.

Fig. 1

Illustration of clinical text, normalization examples and possible applications. a EHR data; b Clinical text from EHRs : an example of real clinical text and translated version; c Real-world data and standard entity; d Applied scenarios

Fig. 2

Main architecture of PASCAL model. PASCAL consists of four modules: character embedding module, encoder module (containing a gated convolutional neural network to learn the shared representation with temporal relationship), pseudo cascade structure module (including the enhanced primary task TEN and an auxiliary task TER)

Fig. 3

Detailed structure of encoder module: gated convolutional neural network (GCNN). GCNN consists of three key parts: convolutional block, gating block and residual connection

Fig. 4

Accuracy comparison between PASCAL and Feedback [17]

Fig. 5

Computational efficiency comparison of PASCAL with different encoders