skip to main content


Title: Secure Comparisons of Single Nucleotide Polymorphisms Using Secure Multiparty Computation: Method Development
Background While genomic variations can provide valuable information for health care and ancestry, the privacy of individual genomic data must be protected. Thus, a secure environment is desirable for a human DNA database such that the total data are queryable but not directly accessible to involved parties (eg, data hosts and hospitals) and that the query results are learned only by the user or authorized party. Objective In this study, we provide efficient and secure computations on panels of single nucleotide polymorphisms (SNPs) from genomic sequences as computed under the following set operations: union, intersection, set difference, and symmetric difference. Methods Using these operations, we can compute similarity metrics, such as the Jaccard similarity, which could allow querying a DNA database to find the same person and genetic relatives securely. We analyzed various security paradigms and show metrics for the protocols under several security assumptions, such as semihonest, malicious with honest majority, and malicious with a malicious majority. Results We show that our methods can be used practically on realistically sized data. Specifically, we can compute the Jaccard similarity of two genomes when considering sets of SNPs, each with 400,000 SNPs, in 2.16 seconds with the assumption of a malicious adversary in an honest majority and 0.36 seconds under a semihonest model. Conclusions Our methods may help adopt trusted environments for hosting individual genomic data with end-to-end data security.  more » « less
Award ID(s):
1946619
NSF-PAR ID:
10435769
Author(s) / Creator(s):
; ; ;
Date Published:
Journal Name:
JMIR Bioinformatics and Biotechnology
Volume:
4
ISSN:
2563-3570
Page Range / eLocation ID:
e44700
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. Federated learning (FL) is an increasingly popular approach for machine learning (ML) when the training dataset is highly distributed. Clients perform local training on their datasets and the updates are then aggregated into the global model. Existing protocols for aggregation are either inefficient or don’t consider the case of malicious actors in the system. This is a major barrier to making FL an ideal solution for privacy-sensitive ML applications. In this talk, I will present ELSA, a secure aggregation protocol for FL that breaks this barrier - it is efficient and addresses the existence of malicious actors (clients + servers) at the core of its design. Similar to prior work Prio and Prio+, ELSA provides a novel secure aggregation protocol built out of distributed trust across two servers that keeps individual client updates private as long as one server is honest, defends against malicious clients, and is efficient end-to-end. Compared to prior works, the distinguishing theme in ELSA is that instead of the servers generating cryptographic correlations interactively, the clients act as untrusted dealers of these correlations without compromising the protocol’s security. This leads to a much faster protocol while also achieving stronger security at that efficiency compared to prior work. We introduce new techniques that retain privacy even when a server is malicious at a small added cost of 7-25% in runtime with a negligible increase in communication over the case of a semi-honest server. ELSA improves end-to-end runtime over prior work with similar security guarantees by big margins - single-aggregator RoFL by up to 305x (for the models we consider), and distributed-trust Prio by up to 8x (with up to 16x faster server-side protocol). Additionally, ELSA can be run in a bandwidth-saver mode for clients who are geographically bandwidth-constrained - an important property that is missing from prior works. 
    more » « less
  2. Federated learning (FL) is an increasingly popular approach for machine learning (ML) in cases where the training dataset is highly distributed. Clients perform local training on their datasets and the updates are then aggregated into the global model. Existing protocols for aggregation are either inefficient, or don’t consider the case of malicious actors in the system. This is a major barrier in making FL an ideal solution for privacy-sensitive ML applications. We present ELSA, a secure aggregation protocol for FL, which breaks this barrier - it is efficient and addresses the existence of malicious actors at the core of its design. Similar to prior work on Prio and Prio+, ELSA provides a novel secure aggregation protocol built out of distributed trust across two servers that keeps individual client updates private as long as one server is honest, defends against malicious clients, and is efficient end-to-end. Compared to prior works, the distinguishing theme in ELSA is that instead of the servers generating cryptographic correlations interactively, the clients act as untrusted dealers of these correlations without compromising the protocol’s security. This leads to a much faster protocol while also achieving stronger security at that efficiency compared to prior work. We introduce new techniques that retain privacy even when a server is malicious at a small added cost of 7-25% in runtime with negligible increase in communication over the case of semi-honest server. Our work improves end-to-end runtime over prior work with similar security guarantees by big margins - single-aggregator RoFL by up to 305x (for the models we consider), and distributed trust Prio by up to 8x. 
    more » « less
  3. null (Ed.)
    Oblivious Random Access Machine (ORAM) allows a client to hide the access pattern and thus, offers a strong level of privacy for data outsourcing. An ideal ORAM scheme is expected to offer desirable properties such as low client bandwidth, low server computation overhead, and the ability to compute over encrypted data. S3ORAM (CCS’17) is an efficient active ORAM scheme, which takes advantage of secret sharing to provide ideal properties for data outsourcing such as low client bandwidth, low server computation and low delay. Despite its merits, S3ORAM only offers security in the semi-honest setting. In practice, an ORAM protocol is likely to operate in the presence of malicious adversaries who might deviate from the protocol to compromise the client privacy. In this paper, we propose MACAO, a new multi-server ORAM framework, which offers integrity, access pattern obliviousness against active adversaries, and the ability to perform secure computation over the accessed data. MACAO harnesses authenticated secret sharing techniques and tree-ORAM paradigm to achieve low client communication, efficient server computation, and low storage overhead at the same time. We fully implemented MACAO and conducted extensive experiments in real cloud platforms (Amazon EC2) to validate the performance of MACAO compared with the state-of-the-art. Our results indicate that MACAO can achieve comparable performance to S3ORAM while offering security against malicious adversaries. MACAO is a suitable candidate for integration into distributed file systems with encrypted computation capabilities towards enabling an oblivious functional data outsourcing infrastructure. 
    more » « less
  4. We present TVA, a multi-party computation (MPC) system for secure analytics on secret-shared time series data. TVA achieves strong security guarantees in the semi-honest and malicious settings, and high expressivity by enabling complex analytics on inputs with unordered and irregular timestamps. TVA is the first system to support arbitrary composition of oblivious window operators, keyed aggregations, and multiple filter predicates, while keeping all data attributes private, including record timestamps and user-defined values in query predicates. At the core of the TVA system lie novel protocols for secure window assignment: (i) a tumbling window protocol that groups records into fixed-length time buckets and (ii) two session window protocols that identify periods of activity followed by periods of inactivity. We also contribute a new protocol for secure division with a public divisor, which may be of independent interest. We evaluate TVA on real LAN and WAN environments and show that it can efficiently compute complex window-based analytics on inputs of 2^22 records with modest use of resources. When compared to the state-of-the-art, TVA achieves up to 5.8× lower latency in queries with multiple filters and two orders of magnitude better performance in window aggregation. 
    more » « less
  5. Abstract Background

    In order to accurately accumulate delivered dose for head and neck cancer patients treated with the Adapt to Position workflow on the 1.5T magnetic resonance imaging (MRI)‐linear accelerator (MR‐linac), the low‐resolution T2‐weighted MRIs used for daily setup must be segmented to enable reconstruction of the delivered dose at each fraction.

    Purpose

    In this pilot study, we evaluate various autosegmentation methods for head and neck organs at risk (OARs) on on‐board setup MRIs from the MR‐linac for off‐line reconstruction of delivered dose.

    Methods

    Seven OARs (parotid glands, submandibular glands, mandible, spinal cord, and brainstem) were contoured on 43 images by seven observers each. Ground truth contours were generated using a simultaneous truth and performance level estimation (STAPLE) algorithm. Twenty total autosegmentation methods were evaluated in ADMIRE: 1–9) atlas‐based autosegmentation using a population atlas library (PAL) of 5/10/15 patients with STAPLE, patch fusion (PF), random forest (RF) for label fusion; 10–19) autosegmentation using images from a patient's 1–4 prior fractions (individualized patient prior [IPP]) using STAPLE/PF/RF; 20) deep learning (DL) (3D ResUNet trained on 43 ground truth structure sets plus 45 contoured by one observer). Execution time was measured for each method. Autosegmented structures were compared to ground truth structures using the Dice similarity coefficient, mean surface distance (MSD), Hausdorff distance (HD), and Jaccard index (JI). For each metric and OAR, performance was compared to the inter‐observer variability using Dunn's test with control. Methods were compared pairwise using the Steel‐Dwass test for each metric pooled across all OARs. Further dosimetric analysis was performed on three high‐performing autosegmentation methods (DL, IPP with RF and 4 fractions [IPP_RF_4], IPP with 1 fraction [IPP_1]), and one low‐performing (PAL with STAPLE and 5 atlases [PAL_ST_5]). For five patients, delivered doses from clinical plans were recalculated on setup images with ground truth and autosegmented structure sets. Differences in maximum and mean dose to each structure between the ground truth and autosegmented structures were calculated and correlated with geometric metrics.

    Results

    DL and IPP methods performed best overall, all significantly outperforming inter‐observer variability and with no significant difference between methods in pairwise comparison. PAL methods performed worst overall; most were not significantly different from the inter‐observer variability or from each other. DL was the fastest method (33 s per case) and PAL methods the slowest (3.7–13.8 min per case). Execution time increased with a number of prior fractions/atlases for IPP and PAL. For DL, IPP_1, and IPP_RF_4, the majority (95%) of dose differences were within ± 250 cGy from ground truth, but outlier differences up to 785 cGy occurred. Dose differences were much higher for PAL_ST_5, with outlier differences up to 1920 cGy. Dose differences showed weak but significant correlations with all geometric metrics (R2 between 0.030 and 0.314).

    Conclusions

    The autosegmentation methods offering the best combination of performance and execution time are DL and IPP_1. Dose reconstruction on on‐board T2‐weighted MRIs is feasible with autosegmented structures with minimal dosimetric variation from ground truth, but contours should be visually inspected prior to dose reconstruction in an end‐to‐end dose accumulation workflow.

     
    more » « less