Privacy preserving framework for federated learning in genomics

With the advent of machine learning, organizations today collect and process data at an unprecedented scale. This has led to rapid growth in innovation across industries, but also poses numerous challenges around maintaining user privacy. Specifically, in the field of healthcare and genomics where data is highly sensitive. Unlike credit cards or passwords, one's genomic information cannot be modified at will and has the ability to uniquely identify the individual. The objective of this thesis is to develop an easily configurable framework that would allow organizations to collaborate and advance genomic research without directly sharing user data with each other. This thesis includes the development of a privacy preserving framework for federated learning on genomic datasets that are distributed across organizational silos. PAGe (Privacy Aware Genomics) has been open-sourced and has a low barrier to entry. A packaged runtime environment is available that includes popular bioinformatics tools and machine learning libraries. Experimental setup is controlled through configuration files, allowing users to easily terminate, restart or reproduce results. Finally, there is an in depth evaluation of the framework using Type 2 Diabetes disease risk prediction as a case study with the 1000 genomes dataset as input.

Name thesis:degree_name

Master

Department dc:contributor.department

Massachusetts Institute of Technology. Engineering and Management Program

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2020

Author dc:creator

• Kokje, Yashashree.

Advisor dc:contributor.advisor

• Lalana Kagal.

• Engineering and Management Program.
• System Design and Management Program.

Statement dc:rights

• MIT theses may be protected by copyright. Please reuse MIT thesis content according to the MIT Libraries Permissions Policy, which is available through the URL provided.

Licence dc:rights.uri

• http://dspace.mit.edu/handle/1721.1/7582

Language dc:language.iso

eng

Handle dc:identifier.uri

https://hdl.handle.net/1721.1/132839

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/132839