CE Seminar by Ercüment Çiçek

Time: 16:00
Location: ENG 120







Speaker: Ercüment Çiçek

Title: Inference Attacks Against Genomic Data-Sharing Beacons

Date: 4 March 2019, Monday

Time: 16:00-17:00 

Place: ENG 120

Host: Alptekin Küpçü 



Genomic datasets are often associated with sensitive phenotypes.Therefore, the leak of membership information is a major privacy risk. Genomic beacons aim to provide a secure, and standardized interface for data sharing. Recent studies have demonstrated that it is possible to determine whether the victim is in the dataset, by repeatedly querying the beacon for his/her single nucleotide polymorphisms (SNPs). In this work, we propose a novel re-identification attack and show that the privacy risk is more serious than previously thought. Our method is based on the fact that alleles at different loci are not necessarily independent. We use the linkage disequilibrium and a high-order Markov chain-based algorithm for the inference. We show  that in a beacon with 65 individuals from the CEU population, we can  infer membership of individuals with 95% confidence with only 5 queries, even when SNPs with minor allele frequencies (MAF) less than  0.05 are hidden as a countermeasure (as proposed in previous work). This means, we need less than 0.5% of the number of queries that existing works require to determine beacon membership under the same conditions. We further show that, countermeasures such as hiding certain parts of the genome or setting a query budget for the user would fail to protect the privacy of the participants under our adversary model.


Ercument Cicek earned his BS (2007) and MS (2009) degrees in Computer Science and Engineering from Sabanci University. He received his Ph.D. degree in Computer Science from Case Western Reserve University in 2013. During his Ph.D., he visited Cold Spring Harbor Laboratory to work on gene discovery algorithms for Autism Spectrum Disorder in 2012. After graduation, he worked as a Lane Fellow in Computational Biology at Carnegie Mellon University till 2015. Since then, he is an Asst. Prof. in the Computer Engineering Department of Bilkent University and is an adjunct faculty member in Computational Biology Department of Carnegie Mellon University. His research is mainly focused on designing machine learning algorithms for analysis of large-scale biological data. He is the recipient of Simons Foundation Autism Research Initiative Explorer Award, TUBITAK Career Award, TUBA-GEBIP Award and Parlar Foundation Research Incentive Award.