Nour Almadhoun Alserr

Mohammed Alser, Jeremie S. Kim, Nour Almadhoun Alserr et al.

Early detection and isolation of COVID-19 patients are essential for successful implementation of mitigation strategies and eventually curbing the disease spread. With a limited number of daily COVID-19 tests performed in every country, simulating the COVID-19 spread along with the potential effect of each mitigation strategy currently remains one of the most effective ways in managing the healthcare system and guiding policy-makers. We introduce COVIDHunter, a flexible and accurate COVID-19 outbreak simulation model that evaluates the current mitigation measures that are applied to a region, predicts COVID-19 statistics (the daily number of cases, hospitalizations, and deaths), and provides suggestions on what strength the upcoming mitigation measure should be. The key idea of COVIDHunter is to quantify the spread of COVID-19 in a geographical region by simulating the average number of new infections caused by an infected person considering the effect of external factors, such as environmental conditions (e.g., climate, temperature, humidity), different variants of concern, vaccination rate, and mitigation measures. Using Switzerland as a case study, COVIDHunter estimates that we are experiencing a deadly new wave that will peak on 26 January 2022, which is very similar in numbers to the wave we had in February 2020. The policy-makers have only one choice that is to increase the strength of the currently applied mitigation measures for 30 days. Unlike existing models, the COVIDHunter model accurately monitors and predicts the daily number of cases, hospitalizations, and deaths due to COVID-19. Our model is flexible to configure and simple to modify for modeling different scenarios under different environmental conditions and mitigation measures. We release the source code of the COVIDHunter implementation at https://github.com/CMU-SAFARI/COVIDHunter.

Nour Almadhoun Alserr, Ozgur Ulusoy, Erman Ayday et al.

Motivation: Cutting the cost of DNA sequencing technology led to a quantum leap in the availability of genomic data. While sharing genomic data across researchers is an essential driver of advances in health and biomedical research, the sharing process is often infeasible due to data privacy concerns. Differential privacy is one of the rigorous mechanisms utilized to facilitate the sharing of aggregate statistics from genomic datasets without disclosing any private individual-level data. However, differential privacy can still divulge sensitive information about the dataset participants due to the correlation between dataset tuples. Results: Here, we propose GenShare model built upon Laplace-perturbation-mechanism-based DP to introduce a privacy-preserving query-answering sharing model for statistical genomic datasets that include dependency due to the inherent correlations between genomes of individuals (i.e., family ties). We demonstrate our privacy improvement over the state-of-the-art approaches for a range of practical queries including cohort discovery, minor allele frequency, and chi^2 association tests. With a fine-grained analysis of sensitivity in the Laplace perturbation mechanism and considering joint distributions, GenShare results near-achieve the formal privacy guarantees permitted by the theory of differential privacy as the queries that computed over independent tuples (only up to 6% differences). GenShare ensures that query results are as accurate as theoretically guaranteed by differential privacy. For empowering the advances in different scientific and medical research areas, GenShare presents a path toward an interactive genomic data sharing system when the datasets include participants with familial relationships.

Nour Almadhoun Alserr, Gulce Kale, Onur Mutlu et al.

Motivation: Researchers need a rich trove of genomic datasets that they can leverage to gain a better understanding of the genetic basis of the human genome and identify associations between phenotypes and specific parts of DNA. However, sharing genomic datasets that include sensitive genetic or medical information of individuals can lead to serious privacy-related consequences if data lands in the wrong hands. Restricting access to genomic datasets is one solution, but this greatly reduces their usefulness for research purposes. To allow sharing of genomic datasets while addressing these privacy concerns, several studies propose privacy-preserving mechanisms for data sharing. Differential privacy (DP) is one of such mechanisms that formalize rigorous mathematical foundations to provide privacy guarantees while sharing aggregated statistical information about a dataset. However, it has been shown that the original privacy guarantees of DP-based solutions degrade when there are dependent tuples in the dataset, which is a common scenario for genomic datasets (due to the existence of family members). Results: In this work, we introduce a near-optimal mechanism to mitigate the vulnerabilities of the inference attacks on differentially private query results from genomic datasets including dependent tuples. We propose a utility-maximizing and privacy-preserving approach for sharing statistics by hiding selective SNPs of the family members as they participate in a genomic dataset. By evaluating our mechanism on a real-world genomic dataset, we empirically demonstrate that our proposed mechanism can achieve up to 40% better privacy than state-of-the-art DP-based solutions, while near-optimally minimizing the utility loss.

Mohammed Alser, Jeremie S. Kim, Nour Almadhoun Alserr et al.

Background: Early detection and isolation of COVID-19 patients are essential for successful implementation of mitigation strategies and eventually curbing the disease spread. With a limited number of daily COVID-19 tests performed in every country, simulating the COVID-19 spread along with the potential effect of each mitigation strategy currently remains one of the most effective ways in managing the healthcare system and guiding policy-makers. Methods: We introduce COVIDHunter, a flexible and accurate COVID-19 outbreak simulation model that evaluates the current mitigation measures that are applied to a region and provides suggestions on what strength the upcoming mitigation measure should be. The key idea of COVIDHunter is to quantify the spread of COVID-19 in a geographical region by simulating the average number of new infections caused by an infected person considering the effect of external factors, such as environmental conditions (e.g., climate, temperature, humidity) and mitigation measures. Results: Using Switzerland as a case study, COVIDHunter estimates that if the policy-makers relax the mitigation measures by 50% for 30 days then both the daily capacity need for hospital beds and daily number of deaths increase exponentially by an average of 5.1x, who may occupy ICU beds and ventilators for a period of time. Unlike existing models, the COVIDHunter model accurately monitors and predicts the daily number of cases, hospitalizations, and deaths due to COVID-19. Our model is flexible to configure and simple to modify for modeling different scenarios under different environmental conditions and mitigation measures. Availability: We release the source code of the COVIDHunter implementation at https://github.com/CMU- SAFARI/COVIDHunter and show how to flexibly configure our model for any scenario and easily extend it for different measures and conditions than we account for.