Privacy-preserving genomic prediction

Patent metadata

Field	Value
Publication number	US-10296709-B2
Application number	US-201615179777-A
Country	US
Kind code	B2
Filing date	Jun 10, 2016
Priority date	Jun 10, 2016
Publication date	May 21, 2019
Grant date	May 21, 2019

Abstract

The techniques and/or systems described herein are directed to improvements in genomic prediction using homomorphic encryption. For example, a genomic model can be generated by a prediction service provider to predict a risk of a disease or a presence of genetic traits. Genomic data corresponding to a genetic profile of an individual can be batch encoded into a plurality of polynomials, homomorphically encrypted, and provided to a service provider for evaluation. The genomic model can be batch encoded as well, and the genetic prediction may be determined by evaluating a dot product of the genomic model data the genomic data. A genomic prediction result value can be provided to a computing device associated with a user for subsequent decrypting and decoding. Homomorphic encoding and encryption can be used such that the genomic data may be applied to the prediction model and a result can be obtained without revealing any information about the model, the genomic data, or any genomic prediction.

First claim

What is claimed is:

1. A system comprising:
one or more processors; and
memory storing modules that, when executed by the one or more processors, cause the system to perform operations comprising:
receiving genomic data associated with an individual, the genomic data including a first representation of a plurality of genetic mutations batch encoded as a first plurality of polynomials and encrypted in accordance with a homomorphic encryption scheme;
receiving genomic model data, the genomic model data including a second representation of a plurality of coefficients determined using machine learning, the genomic model data batch encoded as a second plurality of polynomials;
computing, as a genomic result value, a dot product of the genomic data and the genomic model data, the dot product based at least in part on a sum of products of corresponding elements in the first representation and the second representation; and
transmitting the genomic result value to a computing device associated with the individual, the genomic result value including at least one genomic prediction associated with the genomic data.

2. The system of claim 1 , the operations further comprising:
representing the plurality of genetic mutations as a plurality of genomic data vectors of length m, wherein a polynomial of the first plurality of polynomials includes at most n number of terms; and
encoding the plurality of genomic data vectors as the first plurality of polynomials, the first plurality of polynomials consisting of m/n polynomials.

3. The system of claim 1 , wherein a polynomial of the second plurality of polynomials associated with the genomic model data is a plaintext polynomial.

4. The system of claim 1 , wherein the genomic result value is associated with a third plurality of polynomials, and wherein the computing the genomic result value includes homomorphically adding coefficients associated with the third plurality of polynomials.

5. The system of claim 4 , wherein the genomic result value is associated with a highest-degree term, and wherein a coefficient associated with the highest-degree term represents an evaluation of the dot product of the genomic data and the genomic model data.

6. A computer-implemented method comprising:
receiving, from a computing device as received genomic data, a first representation of genomic data batch encoded as a first plurality of polynomials and encrypted in accordance with a homomorphic encryption scheme;
receiving, from a prediction service provider as received genomic model data, a second representation of coefficients of a genomic model batch encoded as a second plurality of polynomials;
computing, as a genomic result value, a dot product of the received genomic data and the received genomic model data; and
transmitting the genomic result value to the computing device, the genomic result value including at least one genomic prediction associated with the genomic data.

7. The computer-implemented method of claim 6 , wherein polynomials of the first plurality of polynomials are represented in the received genomic data as homomorphically encrypted genomic data vectors.

8. The computer-implemented method of claim 6 , further comprising:
generating, at a service provider, encryption parameters associated with the homomorphic encryption scheme; and
transmitting the encryption parameters to at least the computing device associated with the genomic data,
wherein the received genomic data is batch encoded as the first plurality of polynomials based at least in part on the encryption parameters.

9. The computer-implemented method of claim 8 , wherein the encryption parameters include at least a plaintext modulus t and at least a size of a polynomial n, and wherein the generating the encoding parameters includes determining the plaintext modulus t such that the plaintext modulus t modulo a value twice the size of the polynomial n is equal to 1.

10. The computer-implemented method of claim 9 , wherein the encryption parameters further includes at least a coefficient modulus q, and wherein the generating the encryption parameters further includes determining the coefficient modulus q such that the coefficient modulus q modulo the plaintext modulus t is equal to 1.

11. The computer-implemented method of claim 6 , wherein the computing the dot product includes computing the dot product between a genomic data vector associated with the received genomic data and a genomic model vector associated with the received genomic model data.

12. The computer-implemented method of claim 11 , wherein the computing the dot product between the genomic data vector and the genomic model vector provides the genomic result value as an encrypted value.

13. The computer-implemented method of claim 6 , wherein the computing the dot product includes at least one homomorphic multiplication operation and at least one homomorphic addition operation.

14. The computer-implemented method of claim 6 , wherein the genomic result value is associated with a third plurality of polynomials, and wherein the computing the genomic result value includes homomorphically adding coefficients associated with the third plurality of polynomials.

15. The computer-implemented method of claim 14 , wherein the genomic result value is associated with a highest-degree term, and wherein a coefficient associated with the highest-degree term represents the dot product of the genomic data and the genomic model data.

16. A system comprising:
one or more processors; and
memory storing modules that, when executed by the one or more processors, cause the system to perform operations comprising:
receiving, as received genomic data, a first representation of genomic data batch encoded as a first plurality of polynomials and encrypted in accordance with a homomorphic encryption scheme;
receiving, as received genomic model data, a second representation of coefficients of a genomic model batch encoded as a second plurality of polynomials;
computing, as a genomic result value, a dot product of the received genomic data and the received genomic model data; and
transmitting the genomic result value to a computing device, the genomic result value including at least one genomic prediction associated with the genomic data.

17. The system as recited in claim 16 , the operations further comprising:
representing the genomic data as a plurality of genomic data vectors of length m, wherein a polynomial of the first plurality of polynomials includes at most n number of terms, and
encoding the plurality of genomic data vectors as the first plurality of polynomials, the first plurality of polynomials consisting of m/n polynomials.

18. The system as recited in claim 16 , the operations further comprising:
generating encryption parameters associated with the homomorphic encryption scheme; and
transmitting the encryption parameters to at least the computing device associated with the genomic data.

19. The system as recited in claim 18 , wherein the received genomic data is batch encoded as the first plurality of polynomials based at least in part on the encryption parameters.

20. The system as recited in claim 16 , wherein the computing the dot product includes at least one homomorphic multiplication operation and at least one homomorphic addition operation.

Assignees

• Microsoft Technology Licensing Llc

Inventors

• Laine Kim
• Fusi Nicolo
• Gilad-Bachrach Ran
• Lauter Kristin E

Classifications

• G06F19/24

  Physics · mapped topic

• G06F19/12 Primary

  Physics · mapped topic

• G06F21/6245

  Protecting personal data, e.g. for financial or medical purposes · CPC title

• G06F19/18

  Physics · mapped topic

• G06F21/6254

  by anonymising data, e.g. decorrelating personal data from the owner's identification · CPC title