Privacy is of the utmost importance in genomic matching. Therefore a number of privacy-preserving protocols have been presented using secure computation. Nevertheless, none of these protocols prevents inferences from the result. Goodrich has shown that this resulting information is sufficient for an effective attack on genome databases. In this paper we present an approach that can detect and mitigate such an attack on encrypted messages while still preserving the privacy of both parties. Note that randomization, e.g. using differential privacy, will almost certainly destroy the utility of the matching result. We combine two known cryptographic primitives -- secure computation of the edit distance and fuzzy commitments -- in order to prevent submission of similar genome sequences. Particularly, we contribute an efficient zero-knowledge proof that the same input has been used in both primitives. We show that using our approach it is feasible to preserve privacy in genome matching and also detect and mitigate Goodrich's attack.
Although secure computation offers a formal security model -- semi-honest security @cite_2 , it does not prevent inferences from the result. Goodrich therefore presented an attack based on the information of the edit distance alone @cite_8 . With very few repeated queries it can infer real-world sized genomes. The contribution of this paper is to combine the approach of @cite_30 with mitigation of this and similar attacks.
@cite_30 @cite_8 @cite_2
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We provide formal definitions and efficient secure techniques for turning noisy information into keys usable for any cryptographic application, and, in particular, reliably and securely authenticating biometric data. Our techniques apply not just to biometric information, but to any keying material that, unlike traditional cryptographic keys, is (1) not reproducible precisely and (2) not distributed uniformly. We propose two primitives: a fuzzy extractor reliably extracts nearly uniform randomness @math from its input; the extraction is error-tolerant in the sense that @math will be the same even if the input changes, as long as it remains reasonably close to the original. Thus, @math can be used as a key in a cryptographic application. A secure sketch produces public information about its input @math that does not reveal @math and yet allows exact recovery of @math given another value that is close to @math . Thus, it can be used to reliably reproduce error-prone biometric inputs without incurring the security risk inherent in storing them. We define the primitives to be both formally secure and versatile, generalizing much prior work. In addition, we provide nearly optimal constructions of both primitives for various measures of “closeness” of input data, such as Hamming distance, edit distance, and set difference. While general secure function evaluation (SFE) with information-theoretical (IT) security is infeasible in presence of a corrupted majority in the standard model, there are SFE protocols ( [STOC'87]) that are computationally secure (without fairness) in presence of an actively corrupted majority of the participants. Now, computational assumptions can usually be well justified at the time of protocol execution. The concern is rather a potential violation of the privacy of sensitive data by an attacker whose power increases over time. Therefore, we ask which functions can be computed with long-term security, where we admit computational assumptions for the duration of a computation, but require IT security (privacy) once the computation is concluded. Towards a combinatorial characterization of this class of functions, we also characterize the classes of functions that can be computed IT securely in the authenticated channels model in presence of passive, semi-honest, active, and quantum adversaries. The continuous decrease in cost of molecular profiling tests is revolutionizing medical research and practice, but it also raises new privacy concerns. One of the first attacks against privacy of biological data, proposed by in 2008, showed that, by knowing parts of the genome of a given individual and summary statistics of a genome-based study, it is possible to detect if this individual participated in the study. Since then, a lot of work has been carried out to further study the theoretical limits and to counter the genome-based membership inference attack. However, genomic data are by no means the only or the most influential biological data threatening personal privacy. For instance, whereas the genome informs us about the risk of developing some diseases in the future, epigenetic biomarkers, such as microRNAs, are directly and deterministically affected by our health condition including most common severe diseases. In this paper, we show that the membership inference attack also threatens the privacy of individuals contributing their microRNA expressions to scientific studies. Our results on real and public microRNA expression data demonstrate that disease-specific datasets are especially prone to membership detection, offering a true-positive rate of up to 77 at a false-negative rate of less than 1 . We present two attacks: one relying on the L_1 distance and the other based on the likelihood-ratio test. We show that the likelihood-ratio test provides the highest adversarial success and we derive a theoretical limit on this success. In order to mitigate the membership inference, we propose and evaluate both a differentially private mechanism and a hiding mechanism. We also consider two types of adversarial prior knowledge for the differentially private mechanism and show that, for relatively large datasets, this mechanism can protect the privacy of participants in miRNA-based studies against strong adversaries without degrading the data utility too much. Based on our findings and given the current number of miRNAs, we recommend to only release summary statistics of datasets containing at least a couple of hundred individuals. Secure two-party computation enables two parties to evaluate a function cooperatively without revealing to either party anything beyond the function’s output. The garbled-circuit technique, a generic approach to secure two-party computation for semi-honest participants, was developed by Yao in the 1980s, but has been viewed as being of limited practical significance due to its inefficiency. We demonstrate several techniques for improving the running time and memory requirements of the garbled-circuit technique, resulting in an implementation of generic secure two-party computation that is significantly faster than any previously reported while also scaling to arbitrarily large circuits. We validate our approach by demonstrating secure computation of circuits with over 10 9 gates at a rate of roughly 10 ms per garbled gate, and showing order-of-magnitude improvements over the best previous privacy-preserving protocols for computing Hamming distance, Levenshtein distance, Smith-Waterman genome alignment, and AES.