Abstract

BackgroundsKnowledge 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.MethodsTo 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.ResultsTo 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.ConclusionsThe 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.

Highlights

  • Breast cancer is one of the leading cancers with a high mortality rate

  • 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

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Summary

Introduction

Breast cancer is one of the leading cancers with a high mortality rate. WHO reported that it is the second most common cause of cancer death in women [1]. Developing countries are suffering from an increasing breast cancer epidemic with a growing number of younger women who are susceptible to cancer. The mortality rate caused by breast cancer has significantly decreased in recent years due to the increased emphasis on early detection and the development of more effective treatment [2]. The widespread application of modern medical devices has accumulated large-scale electronic health record (EHR) data, especially historical breast cancer treatment records, which create a foundation for drug therapy analysis, regimen adjustment, and careflow mining [3]. Breast cancer patients can receive better healthcare and more accurate treatment

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