arXiv subjects

Bradley A. Malin

Publications and source records attributed to Bradley A. Malin.

42 records · Page 3Linked to original sources

arXiv2021

Re-identification of Individuals in Genomic Datasets Using Public Face Images

DNA sequencing is becoming increasingly commonplace, both in medical and direct-to-consumer settings. To promote discovery, collected genomic data is often de-identified and shared, either in public repositories, such as OpenSNP, or with researchers through access-controlled repositories. However, recent studies have suggested that genomic data can be effectively matched to high-resolution three-dimensional face images, which raises a concern that the increasingly ubiquitous public face images can be linked to shared genomic data, thereby re-identifying individuals in the genomic data. While these investigations illustrate the possibility of such an attack, they assume that those performing the linkage have access to extremely well-curated data. Given that this is unlikely to be the case in practice, it calls into question the pragmatic nature of the attack. As such, we systematically study this re-identification risk from two perspectives: first, we investigate how successful such linkage attacks can be when real face images are used, and second, we consider how we can empower individuals to have better control over the associated re-identification risk. We observe that the true risk of re-identification is likely substantially smaller for most individuals than prior literature suggests. In addition, we demonstrate that the addition of a small amount of carefully crafted noise to images can enable a controlled trade-off between re-identification success and the quality of shared images, with risk typically significantly lowered even with noise that is imperceptible to humans.

cs.LG↗

arXiv2020

Generating Electronic Health Records with Multiple Data Types and Constraints

Sharing electronic health records (EHRs) on a large scale may lead to privacy intrusions. Recent research has shown that risks may be mitigated by simulating EHRs through generative adversarial network (GAN) frameworks. Yet the methods developed to date are limited because they 1) focus on generating data of a single type (e.g., diagnosis codes), neglecting other data types (e.g., demographics, procedures or vital signs) and 2) do not represent constraints between features. In this paper, we introduce a method to simulate EHRs composed of multiple data types by 1) refining the GAN model, 2) accounting for feature constraints, and 3) incorporating key utility measures for such generation tasks. Our analysis with over $770,000$ EHRs from Vanderbilt University Medical Center demonstrates that the new model achieves higher performance in terms of retaining basic statistics, cross-feature correlations, latent structural properties, feature constraints and associated patterns from real data, without sacrificing privacy.

cs.LG↗

arXiv2018

PIVETed-Granite: Computational Phenotypes through Constrained Tensor Factorization

It has been recently shown that sparse, nonnegative tensor factorization of multi-modal electronic health record data is a promising approach to high-throughput computational phenotyping. However, such approaches typically do not leverage available domain knowledge while extracting the phenotypes; hence, some of the suggested phenotypes may not map well to clinical concepts or may be very similar to other suggested phenotypes. To address these issues, we present a novel, automatic approach called PIVETed-Granite that mines existing biomedical literature (PubMed) to obtain cannot-link constraints that are then used as side-information during a tensor-factorization based computational phenotyping process. The resulting improvements are clearly observed in experiments using a large dataset from VUMC to identify phenotypes for hypertensive patients.

cs.LG↗

arXiv2017

A Data-Driven Analysis of the Influence of Care Coordination on Trauma Outcome

OBJECTIVE: To test the hypothesis that variation in care coordination is related to LOS. DESIGN We applied a spectral co-clustering methodology to simultaneously infer groups of patients and care coordination patterns, in the form of interaction networks of health care professionals, from electronic medical record (EMR) utilization data. The care coordination pattern for each patient group was represented by standard social network characteristics and its relationship with hospital LOS was assessed via a negative binomial regression with a 95% confidence interval. SETTING AND PATIENTS This study focuses on 5,588 adult patients hospitalized for trauma at the Vanderbilt University Medical Center. The EMRs were accessed by healthcare professionals from 179 operational areas during 158,467 operational actions. MAIN OUTCOME MEASURES: Hospital LOS for trauma inpatients, as an indicator of care coordination efficiency. RESULTS: Three general types of care coordination patterns were discovered, each of which was affiliated with a specific patient group. The first patient group exhibited the shortest hospital LOS and was managed by a care coordination pattern that involved the smallest number of operational areas (102 areas, as opposed to 125 and 138 for the other patient groups), but exhibited the largest number of collaborations between operational areas (e.g., an average of 27.1 connections per operational area compared to 22.5 and 23.3 for the other two groups). The hospital LOS for the second and third patient groups was 14 hours (P = 0.024) and 10 hours (P = 0.042) longer than the first patient group, respectively.

cs.CY↗

arXiv2017

Learning Bundled Care Opportunities from Electronic Medical Records

Objectives: The fee-for-service approach to healthcare leads to the management of a patient's conditions in an independent manner, inducing various negative consequences. It is recognized that a bundled care approach to healthcare-one that manages a collection of health conditions together-may enable greater efficacy and cost savings. However, it is not always evident which sets of conditions should be managed in a bundled program. Study Design: Retrospective inference of clusters of health conditions from an electronic medical record (EMR) system. A survey of healthcare experts to ascertain the plausibility of the clusters for bundled care programs. Methods: We designed a data-driven framework to infer clusters of health conditions via their shared clinical workflows according to EMR utilization by healthcare employees. We evaluated the framework with approximately 16,500 inpatient stays from a large medical center. The plausibility of the clusters for bundled care was assessed through a survey of a panel of healthcare experts using an analysis of variance (ANOVA) under a 95% confidence interval. Results: The framework inferred four condition clusters: 1) fetal abnormalities, 2) late pregnancies, 3) prostate problems, and 4) chronic diseases (with congestive heart failure featuring prominently). Each cluster was deemed plausible by the experts for bundled care. Conclusions: The findings suggest that data from EMRs may provide a basis for discovering new directions in bundled care. Still, translating such findings into actual care management will require further refinement, implementation, and evaluation.

cs.CY↗

arXiv2015

Privacy in the Genomic Era

Genome sequencing technology has advanced at a rapid pace and it is now possible to generate highly-detailed genotypes inexpensively. The collection and analysis of such data has the potential to support various applications, including personalized medical services. While the benefits of the genomics revolution are trumpeted by the biomedical community, the increased availability of such data has major implications for personal privacy; notably because the genome has certain essential features, which include (but are not limited to) (i) an association with traits and certain diseases, (ii) identification capability (e.g., forensics), and (iii) revelation of family relationships. Moreover, direct-to-consumer DNA testing increases the likelihood that genome data will be made available in less regulated environments, such as the Internet and for-profit companies. The problem of genome data privacy thus resides at the crossroads of computer science, medicine, and public policy. While the computer scientists have addressed data privacy for various data types, there has been less attention dedicated to genomic data. Thus, the goal of this paper is to provide a systematization of knowledge for the computer science community. In doing so, we address some of the (sometimes erroneous) beliefs of this field and we report on a survey we conducted about genome data privacy with biomedical specialists. Then, after characterizing the genome privacy problem, we review the state-of-the-art regarding privacy attacks on genomic data and strategies for mitigating such attacks, as well as contextualizing these attacks from the perspective of medicine and public policy. This paper concludes with an enumeration of the challenges for genome data privacy and presents a framework to systematize the analysis of threats and the design of countermeasures as the field moves forward.

cs.CR↗