A Privacy-Preserving Federated Learning Framework with Fully Homomorphic Encryption for Reproductive Health Analytics
Published: 2026/06/28
Abstract
With the increasing use of cloud analytics technology, machine learning is now being used to help with fertility tracking and predict risks of pregnancy. However, reproductive health data is considered highly sensitive data, and with traditional analytics training, data must be sent to an external server, which is raising giant red flags regarding data privacy and security. This paper will address these issues by proposing a privacy-preserving analytics platform for fertility and pregnancy data by combining Federated Learning (FL) with Fully Homomorphic Encryption (FHE) technology. FL will be utilized so that multiple hospitals can collaborate and come up with a shared model for pregnancy risks. However, with FL, inference leaks occur when data is sent to the server, which compromises sensitive data. To address inference leaks, we will be using the Cheon-Kim-Kim-Song (CKKS) method to encrypt data before it is sent to the server, which will then be aggregated with other data without any sensitive reproductive health data being compromised or exposed during training. We will be using TenSEAL and Scikit-learn to implement our proposed framework and will be testing it with the Maternal Health Risk Dataset. Our results will show that our proposed FL+FHE model is able to achieve reliable prediction accuracy with reasonable encryption overhead.
Keywords
A Privacy-Preserving Federated Learning Framework with Fully Homomorphic Encryption for Reproductive Health Analytics is licensed under CC BY 4.0
References
- Chaudhry, B., Wang, J., Wu, S., Maglione, M., Mojica, W., Roth, E., Morton, S. C., & Shekelle, P. G. (2006). Systematic review: Impact of health information technology on quality, efficiency, and costs of medical care. Annals of Internal Medicine, 144(10), 742–752.
- Wu, F., Gao, Y., Xu, L. D., & Zhao, W. (2018). Security and privacy in cloud-based wearable health monitoring systems: A survey. IEEE Transactions on Industrial Informatics, 14(5), 1864–1876.
- Arora, S., Yttri, J., Nilse, W., & Press, A. (2017). Challenges in using electronic health record data for CER: Experience of four learning organizations and solutions applied. Medical Care, 55(8), S65–S72.
- Huang, L., Yin, Y., Fu, Z., Zhang, S., Deng, H., & Liu, D. (2018). LoAdaBoost: Loss-based AdaBoost federated machine learning on medical data. arXiv preprint arXiv:1811.12629.
- Al Badawi, A., & Faizal Bin Yusof, M. (2024). Private pathological assessment via machine learning and homomorphic encryption. BioData Mining, 17(1), 33.
- Yurdem, B., Kuzlu, M., Gullu, M. K., Catak, F. O., & Tabassum, M. (2024). Federated learning: Overview, strategies, applications, tools and future directions. Heliyon, 10, e38137.
- Rauniyar, A., Hagos, D. H., Jha, D., Håkegård, J. E., Bagci, U., Rawat, D. B., & Vlassov, V. (2024). Federated learning for medical applications: A taxonomy, current trends, challenges, and future research directions. IEEE Internet of Things Journal, 11, 7374–7398.
- Zhao, D. (2025). Advances and applications in fully homomorphic encryption research. Applied and Computational Engineering, 135, 39–48. https://doi.org/10.54254/2755-2721/2025.20959
- Pan, Y., Chao, Z., He, W., et al. (2024). FedSHE: Privacy preserving and efficient federated learning with adaptive segmented CKKS homomorphic encryption. Cybersecurity, 7, 40.
- Sachdeva, S., Bhatia, S., Al Harrasi, A., Shah, Y. A., Anwer, K., Philip, A. K., Shah, S. F. A., Khan, A., & Halim, S. A. (2024). Unraveling the role of cloud computing in health care system and biomedical sciences. Heliyon, 10(7), e29044.
- Tajabadi, M., Martin, R., & Heider, D. (2024). Privacy-preserving decentralized learning methods for biomedical applications. Computational and Structural Biotechnology Journal, 23, 3281–3287.
- Rehman, M. H., Lopez Pinaya, W. H., Nachev, P., Teo, J. T., Ourselin, S., & Cardoso, M. J. (2023). Federated learning for medical imaging radiology. British Journal of Radiology. https://doi.org/10.1259/bjr.20220890
- Rajeswari, B. L., & Chakravarthy, A. S. N. (2026). Enhancing privacy and security in federated learning: Protecting electronic health records data from adversarial attacks. Informatics for Health and Social Care, 1–18.
- Sathishkumar, P., Pugalarasan, K., Ponnparamaguru, C., & Vasanthkumar, M. (2024). Improving healthcare data security using Cheon–Kim–Kim–Song (CKKS) homomorphic encryption. In Proceedings of the International Conference on Knowledge Engineering and Communication Systems (pp. 1–6). https://doi.org/10.1109/ICKECS61492.2024.10616691
- Qiu, F., Yang, H., Zhou, L., Ma, C., & Fang, L. (2022). Privacy-preserving federated learning using CKKS homomorphic encryption. In Advances in Cryptology (pp. 409–437). Springer. https://doi.org/10.1007/978-3-031-19208-1_35
- Aouedi, O., Sacco, A., Piamrat, K., & Marchetto, G. (2023). Handling privacy-sensitive medical data with federated learning: Challenges and future directions. IEEE Journal of Biomedical and Health Informatics, 27, 790–803.
- Mhamdi, E. M. E., Guerraoui, R., & Rouault, S. L. A. (2018). The hidden vulnerability of distributed learning in Byzantium. In Proceedings of the 35th International Conference on Machine Learning (pp. 3521–3530).
- Carlini, N., Liu, C., Erlingsson, Ú., Kos, J., & Song, D. (2019). The secret sharer: Evaluating and testing unintended memorization in neural networks. In Proceedings of the 28th USENIX Security Symposium (pp. 267–284).
- Munjal, K., & Bhatia, R. (2022). A systematic review of homomorphic encryption and its contributions in healthcare industry. Complex Intelligent Systems, 9, 3759–3786.
- Liu, Y., Yang, C., Liu, Q., Xu, M., Zhang, C., Cheng, L., & Wang, W. (2024). PDPHE: Personal data protection for trans-border transmission based on homomorphic encryption. Electronics, 13, 1959.
- Fan, J., & Vercauteren, F. (2012). Somewhat practical fully homomorphic encryption. Cryptology ePrint Archive.
- Cheon, J. H., Kim, A., Kim, M., & Song, Y. (2017). Homomorphic encryption for arithmetic of approximate numbers. In Advances in Cryptology – ASIACRYPT 2017 (pp. 409–437). Springer.
- Aledhari, M., Razzak, R., Parizi, R. M., & Saeed, F. (2020). Federated learning: A survey on enabling technologies, protocols, and applications. IEEE Access, 8, 140699–140725.
- McMahan, H. B., Moore, E., Ramage, D., Hampson, S., & Arcas, B. A. Y. (2017). Communication-efficient learning of deep networks from decentralized data. In Proceedings of the 20th International Conference on Artificial Intelligence and Statistics (pp. 1273–1282).
- Correia, P., Silva, I., Amorim, I., Maia, E., & Praça, I. (2025). Federated learning: An approach with hybrid homomorphic encryption. arXiv. https://doi.org/10.48550/arXiv.2509.03427
- Haq, F., Chen, C., & Chen, Z. (2025). Privacy-preserving classification of medical tabular data with homomorphic encryption. Algorithms, 18(12), 731.
- Abdinasibfar, H., Nuoskala, C., & Michalas, A. (2025). The HHE land: Exploring the landscape of hybrid homomorphic encryption. Cryptology ePrint Archive, Paper 2025/071.
- Jin, W., Yao, Y., Han, S., Joe-Wong, C., Ravi, S., Avestimehr, S., & He, C. (2023). FedML-HE: An efficient homomorphic-encryption-based privacy-preserving federated learning system. arXiv preprint.
