Publications

These are the recent publications. For the full list, please click here.

Journal Articles

  1.  R. Tatton, E. Ayday, Y. Yoo, and A. Halimi, “ShareTrace: Contact Tracing with Asynchronous, Parallel Message Passing on a Temporal Graph,” arXiv [cs.DC], Mar. 23, 2022. [Online]. Available: http://arxiv.org/abs/2203.12445. Description: Provides a design and implementation of an efficient form of the ShareTrace algorithm for infection risk propagation by using asynchronous message passing on a temporal graph. Research was partly supported by the Cisco Research University Funding grant number 2800379.

  2.  T. Ji, E. Ayday, E. Yilmaz, and P. Li, “Towards Robust Fingerprinting of Relational Databases by Mitigating Correlation Attacks”, IEEE Transactions on Dependable and Secure Computing 2022.
  3.  X. Zhu, E. Ayday, and R. Vitenberg, “A Privacy-Preserving Framework for Conducting Genome-Wide Association Studies over Outsourced Patient Data”, IEEE Transactions on Dependable and Secure Computing 2022.
  4.  X. Zhu, E. Ayday, R. Vitenberg, and N.R. Veeraragavan. “Privacy-Preserving Search for a Similar Genomic Makeup in the Cloud”, IEEE Transactions on Dependable and Secure Computing 2021
  5.  A. C. Oksuz, E. Ayday, and U. Gudukbay “Privacy-Preserving and Robust Watermarking on Sequential Genome Data using Belief Propagation and Local Differential Privacy”, Bioinformatics, 2021.
  6.  M. B. Sariyildiz, R. G. Cinbis, and E. Ayday. “Key Protected Classification for GAN Attack Resilient Collaborative Learning,” Pattern Recognition, 2020.
  7.  N. Almadhoun, E. Ayday, and O. Ulusoy “Differential privacy under dependent tuples—the case of genomic privacy”, Bioinformatics, 2020.
  8.  H.I. Ozercan, A.M. Ileri, E. Ayday, C. Alkan, “Realizing the potential of blockchain technologies in genomics”, Genome Research, 28 (9), 2019.
  9.  N. Thenen, E. Ayday, and E. Cicek. “Re-Identification of Individuals in Genomic Data-Sharing Beacons via allele inference”, Bioinformatics, 2018.
  10.  X. Zhu, E. Ayday, and R. Vitenberg. “A privacy-preserving framework for outsourcing location-based services to the cloud”, IEEE Transactions on Dependable and Secure Computing, 2019.
  11.  G. Kale, E. Ayday, and O. Tastan. “A Utility Maximizing and Privacy Preserving Approach for Protecting Kinship in Genomic Databases”, Bioinformatics, 2017.
  12.  G. Tuna, D. G. Kogiasb, V. C. Gungor, C. Gezer. E. Taşkın, and E. Ayday. “A Survey on Information Security Threats and Solutions for Machine to Machine (M2M) Communications”, Journal of Parallel and Distributed Computing, Volume 109, Nov. 2017.
  13.  E. Ayday, Q. Tang, and A. Yilmaz. “Cryptographic Solutions for Credibility and Liability Issues of Genomic Data”, IEEE Transactions on Dependable and Secure Computing, Apr. 2017.
  14.  E. Ayday and M. Humbert, “Inference Attacks Against Kin Genomic Privacy”, IEEE Security and Privacy Magazine, Volume 15, No. 5, Sep. 2017.
  15.  M. Mobayen, I. Daznabi N. Jafari, O. Tastan, and E. Ayday. “An Inference Attack on Genomic Data Using Kinship, Complex Correlations, and Phenotype Information”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2017.
  16.  E. Yilmaz, E. Ayday, and H. Ferhatosmanoglu. “Privacy-Preserving Aggregate Queries for Optimal Location Selection”, IEEE Transactions on Dependable and Secure Computing, 2017.
  17.  M. Humbert, E. Ayday, A. Telenti, and J. P. Hubaux, “Quantifying Interdependent Risks in Genomic Privacy”, ACM Transaction on Privacy and Security (formerly known as TISSEC), Volume 20, No. 1, Feb. 2017.
  18.  Z. Huang, E. Ayday, H. Lin, et al. “A Privacy-Preserving Solution for Compressed Storage and Selective Retrieval of Genomic Data”, Genome Research, 26: 1687-1696, 2016.
  19.  P.-J. McLaren, J.-L. Raisaro, M. Aouri, M. Rotger, E. Ayday et al. “Privacy-preserving genomic testing in the clinic: a model using HIV treatment”, Journal of Genetics in Medicine, January 2016.
  20.  E. Ayday, E. De Cristofaro, G. Tsudik, and J. P. Hubaux. “Whole Genome Sequencing: Revolutionary Medicine or Privacy Nightmare?”, IEEE Computer Magazine, February 2015.
  21.  A. Telenti, E. Ayday, and J.-P. Hubaux. “On genomics, kin, and privacy”, F1000Research 3:80 (doi: 10.12688/f1000research.4089), 2014.
  22.  J.L. Reisaro, E. Ayday, and J.-P. Hubaux, “Patient Privacy in the Genomic Era”, PRAIX, 7 May 2014.
  23.  E. Ayday and F. Fekri. “An Iterative Algorithm for Trust Management and Adversary Detection for Delay Tolerant Networks”, IEEE Transactions on Mobile Computing, Volume 11, No.9, September 2012. 
  24.  E. Ayday and F. Fekri. “A Secure Broadcasting Scheme to Provide Availability, Reliability and Authentication for Wireless Sensor Networks”, Elsevier Ad Hoc Networks, Volume 10, No.7, September 2012,  Pages 1278-1290.
  25.  E. Ayday and F. Fekri. “Iterative Trust and Reputation Management Using Belief Propagation”, IEEE Transactions on Dependable and Secure Computing, Volume 9, No.3 May/June 2012. 
  26.  E. Ayday, F. Delgosha, and F. Fekri. “Data Authenticity and Availability in Multi-hop Wireless Sensor Networks”, ACM Transactions on Sensor Networks, Volume 8, Issue 2, March 2012.
  27.  E. Ayday and F. Fekri. “A Protocol for Data Availability in Mobile Ad-Hoc Networks in the Presence of Insider Attacks”, Elsevier Ad Hoc Networks, Volume 8, Issue 2, March 2010, Pages 181-192.

 

Poster

  1. chil22-poster: Poster for the CHIL 2022 Conference. Github. Accessed: May 03, 2022. [Online]. Available: https://github.com/share-trace/chil22-poster. Description: Presented at the 2022 Conference on Health, Inference, and Learning (CHIL). Research was partly supported by the Cisco Research University Funding grant number 2800379.
  2. J. Fellay, J. L. Raisaro, Z. Huang, M. Humbert, E. Ayday, P. J. McLaren, J.-P. Hubaux, and A. Telenti, “Practical Solutions for Protecting Individual Genomic Privacy”, American Society of Human Genetics (ASHG), San Diego, CA, USA, October 2014.
  3. E. Ayday, E. De Cristofaro, G. Tsudik, and J. P. Hubaux, “Whole Genome Sequencing: Innovation Dream or Privacy Nightmare? (poster),” In 22nd USENIX Security Symposium, Washington, DC, USA, Aug. 2013.
  4. E. Ayday, J. L. Raisaro, M. Humbert, and J. P. Hubaux, “Towards Quantifying and Preventing the Leakage of Genomic Data Using Privacy-Enhancing Technologies (poster),”  In 22nd USENIX Security Symposium, Washington, DC, USA, Aug. 2013.
  5. E. Ayday, J. L. Raisaro, U. Hengartner, A. Molyneaux, and J. P. Hubaux, “Towards Privacy Compliance in the Management of Raw Genomic Data (poster),” In USENIX Security Workshop on Health Information Technologies (HealthTech), Washington, DC, USA, Aug. 2013.
  6. E. Ayday, F. Delgosha, and F. Fekri, “Efficient Broadcast Authentication for Wireless Sensor Networks,” In Proceedings of  IEEE Communications Society Conference on Sensor, Mesh and Ad Hoc Communications and Networks - SECON, San Diego, CA, USA, Jun. 2007 (Best Poster Award).

Referred Conference Papers

  1.  X. Wang, L. Dervishi, W. Li, X. Jiang, E. Ayday, and J. Vaidya, “Efficient Federated Kinship Relationship Identification”, Proceedings of the American Medical Informatics Association (AMIA) Annual Symposium, 2023.
  2.  N.A. Alser, G. Kale, O. Mutlu, O. Tastan, and E. Ayday, “Near-Optimal Privacy-Utility Tradeoff in Genomic Studies Using Selective SNP Hiding”, Proceedings of Asia Pacific Bioinformatics Conference, 2023.
  3.  T. Ji, E. Ayday, E. Yilmaz, and P. Li, “Differentially-Private Fingerprinting of Relational Databases”, Proceedings of The Annual Network & Distributed System Security Symposium – NDSS, 2023.
  4.  Y. Jiang, E. Yilmaz, and E. Ayday, “Differentially Private Fingerprinting for Location Trajectories”, Proceedings of Privacy Enhancing Technologies Symposium (PETS), 2023.
  5.  R. Tatton, E. Ayday, Y. Yoo, and A. Halimi, “ShareTrace: Contact Tracing with the Actor Model”, In Proceedings of IEEE Healthcom 2022.
  6.  D. Demirag, J. Clark, and E. Ayday, “Privacy-Preserving Collaborative Link Prediction”, In Proceedings of Data Privacy Management (DPM) International Workshop (in conjunction with ESORICS), 2022.
  7.  A. Abourayya, M. Kamp, E. Ayday, J. Kleesiek, K. Rao, G. I. Webb, and B. Rao, “AIMHI: Protecting Sensitive Data through Federated Co-Training”, In Proceedings of Workshop on Federated Learning: Recent Advances and New Challenges (in Conjunction with NeurIPS), 2022.
  8.  L. Dervishi, X. Wang, W. Li, A. Halimi, J. Vaidya, X. Jiang, and E. Ayday, “Facilitating Federated Genomic Data Analysis by Identifying Record Correlations while Ensuring Privacy”, Proceedings of the American Medical Informatics Association (AMIA) Annual Symposium, 2022.
  9.  T. Ji, E. Ayday, E. Yilmaz, and P. Li, “Robust Fingerprinting of Genomic Databases”, Proceedings of Intelligent Systems for Molecular Biology (ISMB) 2022, also in Bioinformatics, 2022 (acceptance rate ~ 19%).
  10.  A .Halimi, L. Dervishi, E. Ayday, A. Pyrgelis, J.R. Troncoso-Pastoriza, J-P. Hubaux, X. Jiang, and J Vaidya, “Privacy-Preserving and Efficient Verification of the Outcome in Genome-Wide Association Studies”, Proceedings of Privacy Enhancing Technologies Symposium (PETS), 2022 (acceptance rate ~ 19%). 
  11.  E. Yilmax, T. Ji, E. Ayday, and P. Li, “Genomic Data Sharing under Dependent Local Differential Privacy”, Proceedings of ACM Conference on Data and Application Security and Privacy (CODASPY), 2022 (acceptance  rate ~ 20%).
  12.  A. Halimi and E. Ayday. ”Real-Time Privacy Risk Quantification in Online Social Networks”, Proceedings of the IEEE/ACM International Conference on Advances in Social Networks Analysis and Mining (ASONAM), 2021 (acceptance rate ~ 20%).
  13.  T. Ji, E. Yilmaz, E. Ayday, and P.Li, “The Curse of Correlations for Robust Fingerprinting of Relational Databases", Proceedings of International Symposium on Research in Attacks, Intrusions and Defenses (RAID), 2021 (acceptance rate ~ 20%).
  14.  E. Ayday, Y. Yoo, and A. Halimi, “ShareTrace: An Iterative Message Passing Algorithm for Efficient and Effective Disease Risk Assessment on an Interaction Graph”, ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM BCB), 2021 (acceptance rate ~ 25%).
  15.  K. Ayoz, E. Ayday, and A. E. Cicek, “Genome Reconstruction Attacks Against Genomic Data-Sharing Beacons", Proceedings of Privacy Enhancing Technologies Symposium (PETS), 2021 (acceptance rate ~ 19%).
  16.  T. Ji, P. Li, E. Yilmaz, E. Ayday, Y. Ye, J. Sun, “Differentially Private Binary- and Matrix-Valued Data Query: An XOR Mechanism", 47th International Conference on Very Large Data Bases (VLDB’21), Copenhagen, Denmark, August 16-20, 2021 (acceptance rate ~ 20%).
  17.  P. Fang, P. Gao, C. Liu, E. Ayday, K. Jee, T. Wang, Y. Ye, Z. Liu, and X. Xiao, “Back-Propagating System Dependency Impact for Attack Investigation”,  Proceedings of Usenix Security Symposium, 2022 (acceptance rate ~ 16%).
  18.  B. Durmaz and E. Ayday, “Entering Watch Dogs: Evaluating Privacy Risks Against Large-Scale Facial Search and Data”, Proceedings of BigSecurity: International Workshop on Security and Privacy in Big Data (IEEE INFOCOM workshop), 2021.
  19.  E. Yilmaz, E. Ayday, * T. Ji, and P. Li, “Preserving Genomic Privacy via Selective Sharing”, Proceedings of ACM Workshop on Privacy in the Electronic Society (WPES), 2020 (acceptance rate ~ 44%).
  20.  D. Demirag and E. Ayday, “Tracking the Invisible: Privacy-Preserving Contact Tracing to Control the Spread of a Virus”, In Proceedings of Data Privacy Management (DPM) International Workshop (in conjunction with ESORICS), 2020.
  21.  A. Halimi and E. Ayday. ”Efficient Quantification of Profile Matching Risk in Social Networks”, Proceedings of the 25th European Symposium on Research in Computer Security (ESORICS), UK, 2020 (acceptance rate ~ 19%).
  22.  A. Halimi and E. Ayday. ”Profile Matching Across Online  Social  Networks”, Proceedings of International Conference on Information and Communications Security (ICICS), Denmark, 2020 (acceptance rate ~ 23%).
  23.  K. Ayoz, M. Aysen, E. Ayday, and A. E. Cicek, “The Effect of Kinship in Re-identification Attacks Against Genomic Data Sharing Beacons", Proceedings of European Conference of Computational Biology (ECCB), 2020 (acceptance rate ~ 19%).
  24.  N. Almadhoun, E. Ayday, and O. Ulusoy “Inference attacks against differentially private query results from genomic datasets including dependent tuples”, Proceedings of Intelligent Systems for Molecular Biology (ISMB), 2020, also in Bioinformatics, 2020 (acceptance rate ~ 19%).
  25.  E. Ayday, E. Yilmaz, and A. Yilmaz, “Robust optimization-based watermarking scheme for sequential data”, Proceedings of International Symposium on Research in Attacks, Intrusions and Defenses (RAID), 2019 (acceptance rate ~ 20%).
  26.  M. Namazi, C. Eryonucu, E. Ayday, F. Pérez-González, “Dynamic attribute-based privacy-preserving genomic susceptibility testing”, Proceedings of the 34th ACM/SIGAPP Symposium on Applied Computing, 2019 (acceptance rate ~ 25%).
  27.  C. Eryonucu, E. Ayday, E. Zeydan, “A Demonstration of Privacy-Preserving Aggregate Queries for Optimal Location Selection”, IEEE 19th International Symposium on "A World of Wireless, Mobile and  Multimedia Networks", 2018.
  28.  J. Choi, V. Zhao, D. Demirag, J. Clark, M. Mannan, E. Ayday, and K. Butler. “One Time Programming Made Practical", Proceedings of Financial Cryptography, 2019.
  29.  N. Abubaker, L. Dervishi, and E. Ayday. “Privacy-Preserving Fog Computing Paradigm”, In Proceedings of IEEE CNS, 2017 (acceptance rate ~ 30%).
  30.  N. V. Thenen, A. E. Cicek, and E. Ayday. “Inference Attacks Against Genomic Data-Sharing Beacons”, in 4th International Workshop on Genome Privacy and Security, 2017.

Book Chapter

  1. E. Ayday, “Genome Privacy”, Encyclopedia of Cryptography, Security and Privacy, 2021. 
  2. E. Ayday, “Responsible Genomic Data Sharing”, Elsevier 2019. 
  3. E. Ayday and J.-P. Hubaux. “Threats and Solutions for Genomic Data Privacy” in Medical Data Privacy Handbook, Editors: Gkoulalas-Divanis, Aris, Loukides, Grigorios, Springer, 2015

Technical Reports

  1. N.A. Alser, G. Kale, O. Mutlu, O. Tastan, and E. Ayday, “Near-Optimal Privacy-Utility Tradeoff in Genomic Studies Using Selective SNP Hiding”, arXiv preprint arXiv:2106.05211, 2021.
  2. E. Yilmaz, T.Ji, E. Ayday, and P.Li, “Genomic Data Sharing under Dependent Local Differential Privacy”, arXiv preprint arXiv:2102.07357, 2021.
  3. A. Halimi, L. Dervishi, E. Ayday, A. Pyrgelis, J.R. Troncoso-Pastoriza, J-P. Hubaux, X. Jiang, and J Vaidya, “Privacy-Preserving and Efficient Verification of the Outcome in Genome-Wide Association Studies”, arXiv preprint arXiv:2101.08879, 2021.
  4. M. Humbert, E. Ayday, A. Telenti, and J. P. Hubaux, “Reconciling Utility with Privacy in Genomics”, EPFL-REPORT- 201547, Sep. 2014.
  5. E. Ayday, J.L. Raisaro, U. Hengartner, A. Molyneaux, and J.P. Hubaux, “Privacy-Preserving Processing of Raw Genomic Data”, EPFL-REPORT- 187573, Jul. 2013.