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題名 以進階生成對抗網路合成擬真資料
Realistic data synthesis using enhanced generative adversarial networks作者 包諾克
Baowaly, Mrinal Kanti貢獻者 陳昇瑋<br>劉昭麟
Chen, Sheng-Wei<br>Liu, Chao-Lin
包諾克
Mrinal Kanti Baowaly關鍵詞 電子健康記錄
合成資料生成
資料合成
生成對抗網路
梯度懲罰型沃瑟斯坦GAN
邊界尋求GAN
Electronic health records
Synthetic data generation
Data synthesis
Generative adversarial networks
Wasserstein GANs with Gradient Penalty
Boundary-seeking GANs日期 2019 上傳時間 3-六月-2019 13:08:37 (UTC+8) 摘要 真實資料在許多情況下無法取得，或者在時間和金錢方面都太昂貴。這是因為這些資料可能存在隱私和保密問題。在這些情況下，使用合成資料是一個可行的選擇。本研究的主要目的是生成近乎真實的合成電子健康記錄（EHR），以便人們可以自由地使用，進行醫療保健或相關領域的研究。我們提出了兩種合成資料的生成模型，分別稱為具有梯度懲罰的醫學沃瑟斯坦GAN（medWGAN），以及醫學邊界尋求GAN（medBGAN），並且將其表現與現有的醫學GAN（medGAN）進行比較。本研究所提出的模型是基於生成對抗網絡（GAN）的兩種增強方法，即具有梯度懲罰的沃瑟斯坦GAN（WGAN-GP），以及邊界尋求GAN（BGAN）。我們在醫學領域中具有離散特徵（例如，二元和計數）的三個匯總EHR資料集上進行資料合成，分別是MIMIC-III，擴展的MIMIC-III，以及台灣國家健康保險研究資料庫（NHIRD）。首先，我們訓練上述模型並生成合成EHR資料。接著，我們應用統計方法（維度平均值以及柯爾莫哥洛夫-斯米爾諾夫檢定）和兩個機器學習任務（關聯規則挖掘以及預測）來分析和比較模型的表現。綜合分析的結果顯示，與使用medGAN模型相比，本研究所提出的模型在生成近乎真實的合成EHR資料方面是更為有效的。 我們的模型可用於生成任何近乎真實的合成資料，而不限於醫學領域。為了證明模型的一般性，在醫學領域之外，我們還研究了洛杉磯市警察局的一個匯總的犯罪資料集，進一步證實了本研究所提出的模型在廣泛應用中的能力。我們證明本研究所提出的模型可用於生成具有離散特徵的高品質合成資料，這些資料在統計上是合理的，並且足以用於機器學習任務。 我們相信，以提供更好的服務來生成近乎真實的合成資料的角度來看，本研究所提出的模型將在工業和學術研究中起到作用。本研究將有助於消除機密資料的存取限制等障礙，從而加速醫學資訊學、醫療保健或相關領域的發展。
There are many situations when the real data are not available or are too expensive to afford in respect of both time and money. This is because those data may have privacy and confidentiality concerns. In these situations, it is a good alternative to use synthetic data. The primary objective of this study is to generate realistic synthetic electronic health records (EHRs) so that people can use it freely for progressing research in healthcare or related fields. We propose two synthetic data generation models – designated as medical Wasserstein GAN with gradient penalty (medWGAN) and medical boundary-seeking GAN (medBGAN) – and compare the performances with an existing method medical GAN (medGAN). The proposed models are based on the two enhanced methods of generative adversarial networks (GANs), namely, Wasserstein GAN with gradient penalty (WGAN-GP) and boundary-seeking GAN (BGAN). We perform data synthesis on three aggregated EHR datasets with discrete features (e.g., binary and count) in the medical domain. They are MIMIC-III, extended MIMIC-III and National Health Insurance Research Database (NHIRD), Taiwan. Firstly, we train the models and generate synthetic EHR data by using these trained models. We then analyze and compare the models’ performance by applying some statistical methods (dimension-wise average and Kolmogorov–Smirnov test) and two machine learning tasks (association rule mining and prediction). The comprehensive analysis of this study shows that the proposed models are more effective in generating realistic synthetic EHR data than those generated using medGAN.Our models can be applied to generate any realistic synthetic data, even beyond the medical domain. To prove the generality of our models, we also investigate an aggregated crime dataset in the City of Los Angeles Police Department apart from the medical domain which confirms our models’ capability to work in a wide range of applications. We prove that the proposed models are suitable for producing high-quality synthetic data with discrete features that are statistically sound and good enough for machine learning tasks. We believe the proposed models will be effective in industry and research from the viewpoint of providing better services in generating realistic synthetic data. This study will help to eliminate barriers including limited access to confidential data and thus accelerate the development of medical informatics, healthcare or related fields.參考文獻 [1] Mrinal Kanti Baowaly, Chia-Ching Lin, Chao-Lin Liu, and Kuan-Ta Chen. Synthesizing Electronic Health Records Using Improved Generative Adversarial Networks. Journal of the American Medical Informatics Association, 26(3):228–241, 12 2018.[2] Mrinal Kanti Baowaly, Chao-Lin Liu, and Kuan-Ta Chen. Realistic Data Synthesis Using Enhanced Generative Adversarial Networks. In 2019 IEEE International Confer- ence on Artificial Intelligence and Knowledge Engineering (IEEE AIKE 2019). IEEE, June 2019.[3] Donald B Rubin. Statistical disclosure limitation. Journal of official Statistics, 9(2):461– 468, 1993.[4] Office for Civil Rights. Guidance Regarding Methods for De-identification of Pro- tected Health Information in Accordance with the Health Insurance Portability and Accountability Act (HIPAA) Privacy Rule. U.S. Department of Health and Human Ser- vices, November 2013. [online] https://www.hhs.gov/hipaa/for-professionals/privacy/ special-topics/de-identification/index.html, Accessed 12 Mar 2017.[5] Khaled El Emam, Elizabeth Jonker, Luk Arbuckle, and Bradley Malin. A systematic review of re-identification attacks on health data. 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國立政治大學
社群網路與人智計算國際研究生博士學位學程(TIGP)
104761507資料來源 http://thesis.lib.nccu.edu.tw/record/#G0104761507 資料類型 thesis dc.contributor.advisor 陳昇瑋<br>劉昭麟 zh_TW dc.contributor.advisor Chen, Sheng-Wei<br>Liu, Chao-Lin en_US dc.contributor.author (作者) 包諾克 zh_TW dc.contributor.author (作者) Mrinal Kanti Baowaly en_US dc.creator (作者) 包諾克 zh_TW dc.creator (作者) Baowaly, Mrinal Kanti en_US dc.date (日期) 2019 en_US dc.date.accessioned 3-六月-2019 13:08:37 (UTC+8) - dc.date.available 3-六月-2019 13:08:37 (UTC+8) - dc.date.issued (上傳時間) 3-六月-2019 13:08:37 (UTC+8) - dc.identifier (其他 識別碼) G0104761507 en_US dc.identifier.uri (URI) http://nccur.lib.nccu.edu.tw/handle/140.119/123696 - dc.description (描述) 博士 zh_TW dc.description (描述) 國立政治大學 zh_TW dc.description (描述) 社群網路與人智計算國際研究生博士學位學程(TIGP) zh_TW dc.description (描述) 104761507 zh_TW dc.description.abstract (摘要) 真實資料在許多情況下無法取得，或者在時間和金錢方面都太昂貴。這是因為這些資料可能存在隱私和保密問題。在這些情況下，使用合成資料是一個可行的選擇。本研究的主要目的是生成近乎真實的合成電子健康記錄（EHR），以便人們可以自由地使用，進行醫療保健或相關領域的研究。我們提出了兩種合成資料的生成模型，分別稱為具有梯度懲罰的醫學沃瑟斯坦GAN（medWGAN），以及醫學邊界尋求GAN（medBGAN），並且將其表現與現有的醫學GAN（medGAN）進行比較。本研究所提出的模型是基於生成對抗網絡（GAN）的兩種增強方法，即具有梯度懲罰的沃瑟斯坦GAN（WGAN-GP），以及邊界尋求GAN（BGAN）。我們在醫學領域中具有離散特徵（例如，二元和計數）的三個匯總EHR資料集上進行資料合成，分別是MIMIC-III，擴展的MIMIC-III，以及台灣國家健康保險研究資料庫（NHIRD）。首先，我們訓練上述模型並生成合成EHR資料。接著，我們應用統計方法（維度平均值以及柯爾莫哥洛夫-斯米爾諾夫檢定）和兩個機器學習任務（關聯規則挖掘以及預測）來分析和比較模型的表現。綜合分析的結果顯示，與使用medGAN模型相比，本研究所提出的模型在生成近乎真實的合成EHR資料方面是更為有效的。 我們的模型可用於生成任何近乎真實的合成資料，而不限於醫學領域。為了證明模型的一般性，在醫學領域之外，我們還研究了洛杉磯市警察局的一個匯總的犯罪資料集，進一步證實了本研究所提出的模型在廣泛應用中的能力。我們證明本研究所提出的模型可用於生成具有離散特徵的高品質合成資料，這些資料在統計上是合理的，並且足以用於機器學習任務。 我們相信，以提供更好的服務來生成近乎真實的合成資料的角度來看，本研究所提出的模型將在工業和學術研究中起到作用。本研究將有助於消除機密資料的存取限制等障礙，從而加速醫學資訊學、醫療保健或相關領域的發展。 zh_TW dc.description.abstract (摘要) There are many situations when the real data are not available or are too expensive to afford in respect of both time and money. This is because those data may have privacy and confidentiality concerns. In these situations, it is a good alternative to use synthetic data. The primary objective of this study is to generate realistic synthetic electronic health records (EHRs) so that people can use it freely for progressing research in healthcare or related fields. We propose two synthetic data generation models – designated as medical Wasserstein GAN with gradient penalty (medWGAN) and medical boundary-seeking GAN (medBGAN) – and compare the performances with an existing method medical GAN (medGAN). The proposed models are based on the two enhanced methods of generative adversarial networks (GANs), namely, Wasserstein GAN with gradient penalty (WGAN-GP) and boundary-seeking GAN (BGAN). We perform data synthesis on three aggregated EHR datasets with discrete features (e.g., binary and count) in the medical domain. They are MIMIC-III, extended MIMIC-III and National Health Insurance Research Database (NHIRD), Taiwan. Firstly, we train the models and generate synthetic EHR data by using these trained models. We then analyze and compare the models’ performance by applying some statistical methods (dimension-wise average and Kolmogorov–Smirnov test) and two machine learning tasks (association rule mining and prediction). The comprehensive analysis of this study shows that the proposed models are more effective in generating realistic synthetic EHR data than those generated using medGAN.Our models can be applied to generate any realistic synthetic data, even beyond the medical domain. To prove the generality of our models, we also investigate an aggregated crime dataset in the City of Los Angeles Police Department apart from the medical domain which confirms our models’ capability to work in a wide range of applications. We prove that the proposed models are suitable for producing high-quality synthetic data with discrete features that are statistically sound and good enough for machine learning tasks. We believe the proposed models will be effective in industry and research from the viewpoint of providing better services in generating realistic synthetic data. This study will help to eliminate barriers including limited access to confidential data and thus accelerate the development of medical informatics, healthcare or related fields. en_US dc.description.tableofcontents Chapter One – Introduction 11.1 Background and Motivation 11.2 Related Works 21.2.1 History of synthetic data generation 31.2.2 Recent works in healthcare 41.3 Developing Idea of the Proposed Method 51.4 Objective and Contribution of this Research 61.5 Dissertation Organization 7Chapter Two - Materials and Methods 92.1 Overview 92.2 Synthetic Data and Its Applications 92.3 The Importance of Synthetic Data 112.4 AI-based Synthetic Data Generation 122.4.1 Generative adversarial networks (GANs) 122.4.2 Wasserstein GAN with gradient penalty (WGAN-GP) 142.4.3 Boundary-Seeking GAN (BGAN) 152.5 Medical GAN (medGAN) 172.6 The Proposed Models 19Chapter Three - Synthesizing Electronic Health Records 233.1 Data Collection, Processing and Analysis 233.1.1 Data collection 233.1.2 Convert to aggregated (count) data 243.1.3 Convert to binary data 253.1.4 Statistics of datasets 253.2 Experiments 273.2.1 Experimental setup 293.2.2 Training the models 303.2.3 Methods for evaluating synthetic data 313.3 Evaluation Results on Synthetic Data 343.3.1 Dimension-wise average for binary data 343.3.2 Dimension-wise average for count data 353.3.3 K–S test results 383.3.4 Association rule mining 393.3.5 Dimension-wise prediction performance 403.4 Discussion 493.4.1 Summary of the results 493.4.2 MIMIC-III versus extended MIMIC-III 493.4.3 medWGAN versus medBGAN 513.4.4 Privacy consideration 52Chapter Four - Synthesizing Crime Data 554.1 Data Collection, Processing and Analysis 554.1.1 Data collection 554.1.2 Data processing 564.1.3 Statistics of the Crime Dataset 564.2 Experiments on Crime Data 574.2.1 Experimental setup 594.2.2 Training the models 604.2.3 Methods for evaluating synthetic data 604.3 Evaluation Results on Synthetic Crime Data 614.3.1 Dimension-wise average for binary data 614.3.2 Dimension-wise average for count data 624.3.3 K–S test results 634.3.4 Association rule mining 644.3.5 Dimension-wise prediction performance 644.4 Discussion 684.4.1 Summary of the results 684.4.2 medWGAN versus medBGAN 68Chapter Five - Concluding Remarks 715.1 Limitations and Future Works 715.2 Conclusion 725.3 Funding 735.4 Competing Interests 735.5 Contributors 73References 75Appendix A How to install the models to generate synthetic data 81 zh_TW dc.format.extent 3857896 bytes - dc.format.mimetype application/pdf - dc.source.uri (資料來源) http://thesis.lib.nccu.edu.tw/record/#G0104761507 en_US dc.subject (關鍵詞) 電子健康記錄 zh_TW dc.subject (關鍵詞) 合成資料生成 zh_TW dc.subject (關鍵詞) 資料合成 zh_TW dc.subject (關鍵詞) 生成對抗網路 zh_TW dc.subject (關鍵詞) 梯度懲罰型沃瑟斯坦GAN zh_TW dc.subject (關鍵詞) 邊界尋求GAN zh_TW dc.subject (關鍵詞) Electronic health records en_US dc.subject (關鍵詞) Synthetic data generation en_US dc.subject (關鍵詞) Data synthesis en_US dc.subject (關鍵詞) Generative adversarial networks en_US dc.subject (關鍵詞) Wasserstein GANs with Gradient Penalty en_US dc.subject (關鍵詞) Boundary-seeking GANs en_US dc.title (題名) 以進階生成對抗網路合成擬真資料 zh_TW dc.title (題名) Realistic data synthesis using enhanced generative adversarial networks en_US dc.type (資料類型) thesis en_US dc.relation.reference (參考文獻) [1] Mrinal Kanti Baowaly, Chia-Ching Lin, Chao-Lin Liu, and Kuan-Ta Chen. 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