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Updating to Palisade 1.10, adding libplinkio

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Noah L. Schrick 2022-12-01 22:10:29 -06:00
parent c394312139
commit 1efbc18547
56 changed files with 2 additions and 58264 deletions
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Subproject commit 6bcc7faf2459c7c19dc1bb0866738817a4f2508c

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cmake_minimum_required (VERSION 3.5.1)
project(demo CXX)
set(CMAKE_CXX_STANDARD 11)
find_package(Palisade)
set( CMAKE_CXX_FLAGS ${PALISADE_CXX_FLAGS} )
set( CMAKE_EXE_LINKER_FLAGS ${PALISADE_EXE_LINKER_FLAGS} )
include_directories( ${OPENMP_INCLUDES} )
include_directories( ${PALISADE_INCLUDE} )
include_directories( ${PALISADE_INCLUDE}/core )
include_directories( ${PALISADE_INCLUDE}/pke )
link_directories( ${PALISADE_LIBDIR} )
link_directories( ${OPENMP_LIBRARIES} )
link_libraries( ${PALISADE_LIBRARIES} )
### ADD YOUR EXECUTABLE(s) HERE
### add_executable( EXECUTABLE-NAME SOURCES )
###
### EXAMPLE:
add_executable( demo-logistic demo-logistic.cpp )
add_executable( demo-chi2 demo-chi2.cpp )

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Code/Duality_Technologies/palisade-gwas-demos-master/LICENSE.md
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Copyright (c) 2020 Duality Technologies, Inc.
Licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License <https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode>
See the LICENSE file for the full text of the license.
If you share the Licensed Material (including in modified form) you must include the above attribution in the copy you share.
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Code/Duality_Technologies/palisade-gwas-demos-master/PreLoad.cmake
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set (CMAKE_GENERATOR "Unix Makefiles" CACHE INTERNAL "" FORCE)

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Code/Duality_Technologies/palisade-gwas-demos-master/README.md
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GWAS Research Prototypes using Homomorphic Encryption
=====================================
This gitlab repository includes the implementation of Logistic Regression Approximation (LRA) and Chi-Square GWAS protocols described in
"Secure large-scale genome-wide association studies using homomorphic encryption"
by Marcelo Blatt, Alexander Gusev, Yuriy Polyakov, and Shafi Goldwasser.
The repo includes the following files:
* demo-logistic.cpp - research prototype for the LRA protocol.
* demo-chi2.cpp - research prototype for the Chi-Square protocol.
* data/random_sample.csv - an artificial random data set including 3 features, 200 individuals, and 16,384 SNPs (provided solely for demonstration purposes).
Notes on Compatibility with Different Versions of PALISADE
=====================================
The code in the master branch works in PALISADE v1.7 - 1.9. If you need to run this code in v1.10 and later, please use the branch called `updated-to-v1.10`.
How to Build and Run the Prototypes
=====================================
1. Install PALISADE v1.7 - 1.9, e.g., v1.9.1 from [PALISADE Development Repository](https://gitlab.com/palisade/palisade-development/-/tree/release-v1.9.1). Follow the instructions provided in [README.md](https://gitlab.com/palisade/palisade-development/-/blob/release-v1.9.1/README.md).
2. Clone this repository to a local directory and switch to this directory.
3. Create a directory where the binaries will be built. The typical choice is a subfolder "build". In this case, run the following commands:
```
mkdir build
cd build
cmake ..
make
```
4. Run the following command to execute the LRA prototype (change sample size and number of SNPs as needed):
```
./demo-logistic --SNPdir "../data" --SNPfilename "random_sample" --pvalue "pvalue.txt" --runtime "result.txt" --samplesize="200" --snps="16384"
```
or
Run the following command to execute the Chi-Square prototype (change sample size and number of SNPs as needed):
```
./demo-chi2 --SNPdir "../data" --SNPfilename "random_sample" --pvalue "pvalue.txt" --runtime "result.txt" --samplesize="200" --snps="16384"
```
5. The results will be written to the "data" folder. The following output files will be created for both prototypes:
* pvalue.txt - p-values for each SNP
* result.txt - runtime metrics
Additional files with outputs of protocol-specific statistics will also be created.

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#!/bin/bash
#
./demo-chi2 --SNPdir "../data" --SNPfilename "random_sample" --pvalue "pvalue.txt" --runtime "result.txt" --samplesize="200" --snps="16384"

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Key Generation Time: 0.022 s
Encoding and Encryption Time: 5.388 s
Computation Time: 1.613 s
Decryption & Decoding Time: 0.101 s
End-to-end Runtime: 7.54 s

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/***
* Copyright (c) 2020 Duality Technologies, Inc.
* Licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License <https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode>
* See the LICENSE.md file for the full text of the license.
* If you share the Licensed Material (including in modified form) you must include the above attribution in the copy you share.
***/
/*
Implementation for the Chi-Square GWAS solution described in
"Secure large-scale genome-wide association studies using homomorphic encryption"
by Marcelo Blatt, Alexander Gusev, Yuriy Polyakov, and Shafi Goldwasser
Command to execute the prototype
./demo-chi2 --SNPdir "../data" --SNPfilename "random_sample" --pvalue "pvalue.txt" --runtime "result.txt" --samplesize="200" --snps="16384"
*/
#include <getopt.h>
#include <numeric>
#include <cmath>
#include "palisade.h"
using namespace std;
using namespace lbcrypto;
const double EPSILON = 1.0E-08;
void RunChi2(const string &SNPDir, const string &SNPFileName,
const string &pValue, const string &Runtime, const string &SampleSize, const string &SNPs);
Ciphertext<DCRTPoly> BinaryTreeAdd(std::vector<Ciphertext<DCRTPoly>> &vector);
void ReadSNPFile(vector<string>& headers, std::vector<std::vector<double>> & dataColumns, std::vector<double> &y, string dataFileName, size_t N, size_t M);
double BS(double z) {
double y = exp(-z*z/2);
return sqrt(1-y) * (31*y/200 - 341*y*y/8000) / sqrt(M_PI);
}
double normalCFD(double value) { return 0.5 * erfc(-value * M_SQRT1_2); }
double sf(double value) { return 1 - normalCFD(value); }
static bool Equal(double a, double b) { return (EPSILON > fabs(a-b)); }
static bool Less(double a, double b) { return ((a-b) < (-EPSILON)); }
static bool Greater(double a, double b) { return ((a-b) > EPSILON); }
double IncompleteGamma(double val, double p);
int main(int argc, char **argv) {
int opt;
PalisadeParallelControls.Enable();
static struct option long_options[] =
{
/* These options dont set a flag.
We distinguish them by their indices. */
{"SNPdir", required_argument, 0, 'S'},
{"SNPfilename", required_argument, 0, 's'},
{"pvalue", required_argument, 0, 'p'},
{"runtime", required_argument, 0, 'r'},
{"samplesize", required_argument, 0, 'N'},
{"snps", required_argument, 0, 'M'},
{0, 0, 0, 0}
};
/* getopt_long stores the option index here. */
int option_index = 0;
string SNPDir;
string SNPFileName;
string pValue;
string Runtime;
string SampleSize;
string SNPs;
while ((opt = getopt_long(argc, argv, "S:s:p:r:N:M", long_options, &option_index)) != -1) {
switch (opt)
{
case 'S':
SNPDir = optarg;
break;
case 's':
SNPFileName = optarg;
break;
case 'p':
pValue = optarg;
break;
case 'r':
Runtime = optarg;
break;
case 'N':
SampleSize = optarg;
break;
case 'M':
SNPs = optarg;
break;
default: /* '?' */
std::cerr<< "Usage: "<<argv[0]<<" <arguments> " <<std::endl
<< "arguments:" <<std::endl
<< " -S --SNPdir SNP file directory" <<std::endl
<< " -s --SNPfilename SNP file name" <<std::endl
<< " -o --pvalue p-values file" <<std::endl
<< " -r --runtime runtime output file name" <<std::endl
<< " -N --samplesize number of individuals" <<std::endl
<< " -M --snps number of SNPs" <<std::endl;
exit(EXIT_FAILURE);
}
}
RunChi2(SNPDir, SNPFileName, pValue, Runtime, SampleSize, SNPs);
return 0;
}
void RunChi2(const string &SNPDir,
const string &SNPFileName, const string &pValue, const string &Runtime, const string &SampleSize, const string &SNPs) {
TimeVar t;
TimeVar tAll;
TIC(tAll);
double keyGenTime(0.0);
double encryptionTime(0.0);
double computationTime(0.0);
double decryptionTime(0.0);
double endToEndTime(0.0);
std::cout << "\n======CHI-SQUARE SOLUTION========\n" << std::endl;
vector<string> headers1;
vector<string> headersS;
std::vector<double> yData;
std::vector<std::vector<double>> sData;
size_t N = std::stoi(SampleSize);
size_t M = std::stoi(SNPs);
ReadSNPFile(headersS,sData,yData,SNPDir + "/" + SNPFileName,N,M);
//usint m = 16384;
usint m = 65536;
usint init_size = 4;
usint dcrtBits = 54;
double scalingFactor = 2.5e-6;
CryptoContext<DCRTPoly> cc =
CryptoContextFactory<DCRTPoly>::genCryptoContextCKKS(
init_size-1,
dcrtBits,
0,
HEStd_128_classic,
m/2, /*ringDimension*/
APPROXRESCALE,
BV,
3, /*numLargeDigits*/
2, /*maxDepth*/
dcrtBits, /*firstMod*/
0,
OPTIMIZED);
cc->Enable(ENCRYPTION);
cc->Enable(SHE);
cc->Enable(LEVELEDSHE);
std::cout << "\nNumber of Individuals = " << sData.size() << std::endl;
std::cout << "Number of SNPs = " << sData[0].size() << std::endl;
TIC(t);
auto keyPair = cc->KeyGen();
keyGenTime = TOC(t);
std::cout << "\nKey Generation Time: \t\t" << keyGenTime/1000 << " s" << std::endl;
TIC(t);
size_t sizeS = (size_t)std::ceil((double)sData[0].size()/(m/4));
std::vector<std::vector<std::vector<std::complex<double>>>> sDataArray(sizeS);
for(size_t s = 0; s < sizeS; s++)
sDataArray[s] = std::vector<std::vector<std::complex<double>>>(sData.size());
for (size_t i=0; i < sData.size(); i++){
for(size_t s = 0; s < sizeS; s++)
sDataArray[s][i] = std::vector<std::complex<double>>(sData[i].size());
size_t counter = 0;
for (size_t j=0; j<sData[i].size(); j++) {
if ((j>0) && (j%(m/4)==0))
counter++;
sDataArray[counter][i][j%(m/4)] = sData[i][j];
}
}
//std::cerr << " sData = " << sDataArray << std::endl;
std::vector<std::vector<Ciphertext<DCRTPoly>>> S(sizeS);
std::vector<Ciphertext<DCRTPoly>> Y(N);
for (size_t i = 0; i < sizeS; i++)
S[i] = std::vector<Ciphertext<DCRTPoly>>(N);
//Encryption of single-integer ciphertexts
#pragma omp parallel for
for (size_t i=0; i<N; i++){
for (size_t s=0; s < sizeS; s++){
Plaintext sTemp = cc->MakeCKKSPackedPlaintext(sDataArray[s][i]);
S[s][i] = cc->Encrypt(keyPair.publicKey, sTemp);
}
Plaintext sTemp2 = cc->MakeCKKSPackedPlaintext(std::vector<std::complex<double>>(m/4,yData[i]));
Y[i] = cc->Encrypt(keyPair.publicKey, sTemp2);
}
encryptionTime = TOC(t);
std::cout << "Encoding and Encryption Time: \t" << encryptionTime/1000 << " s" << std::endl;
TIC(t);
Plaintext d = cc->MakeCKKSPackedPlaintext(std::vector<std::complex<double>>(m/4,2*N));
d->SetFormat(EVALUATION);
Plaintext dScaled = cc->MakeCKKSPackedPlaintext(std::vector<std::complex<double>>(m/4,2*N*scalingFactor));
dScaled->SetFormat(EVALUATION);
std::vector<Ciphertext<DCRTPoly>> ySum = Y;
auto yU = BinaryTreeAdd(ySum);
std::vector<Ciphertext<DCRTPoly>> chiD(sizeS);
std::vector<Ciphertext<DCRTPoly>> chiN(sizeS);
std::vector<Ciphertext<DCRTPoly>> orD(sizeS);
std::vector<Ciphertext<DCRTPoly>> orN(sizeS);
for (size_t s = 0; s < sizeS; s++) {
std::vector<Ciphertext<DCRTPoly>> ySMult(N);
#pragma omp parallel for
for(size_t i = 0; i < N; i++) {
ySMult[i] = cc->EvalMultNoRelin(S[s][i],Y[i]);
}
auto n11 = BinaryTreeAdd(ySMult);
n11 = cc->ModReduce(n11);
auto c1 = BinaryTreeAdd(S[s]);
auto r1 = cc->EvalAdd(yU,yU);
auto r1Scaled = cc->EvalMult(r1,scalingFactor);
r1Scaled = cc->ModReduce(r1Scaled);
auto c1Scaled = cc->EvalMult(c1,scalingFactor);
c1Scaled = cc->ModReduce(c1Scaled);
r1 = cc->LevelReduce(r1,nullptr);
c1 = cc->LevelReduce(c1,nullptr);
// Chi2 computation
// numerator
auto mult1 = cc->EvalMult(n11,dScaled);
auto mult2 = cc->EvalMultNoRelin(c1,r1Scaled);
auto chiN1 = cc->EvalSub(mult1,mult2);
chiN1 = cc->ModReduce(chiN1);
chiN[s] = cc->EvalMultNoRelin(chiN1,chiN1);
// denominator
auto chiD1 = cc->EvalMultNoRelin(c1,cc->EvalSub(dScaled,c1Scaled));
chiD1 = cc->ModReduce(chiD1);
auto chiD2 = cc->EvalMultNoRelin(r1,cc->EvalSub(dScaled,r1Scaled));
chiD2 = cc->ModReduce(chiD2);
chiD[s] = cc->EvalMultNoRelin(chiD1,chiD2);
// Odds Ratio Computation
auto n11Scaled = cc->EvalMult(n11,scalingFactor);
n11Scaled = cc->ModReduce(n11Scaled);
// denominator
auto or2 = cc->EvalSub(c1,n11);
or2 = cc->LevelReduce(or2,nullptr);
r1Scaled = cc->LevelReduce(r1Scaled,nullptr);
auto or3 = cc->EvalSub(r1Scaled,n11Scaled);
orD[s] = cc->EvalMultNoRelin(or2,or3);
// numerator
auto or1 = cc->EvalSub(n11Scaled,r1Scaled);
c1Scaled = cc->LevelReduce(c1Scaled,nullptr);
or1 = cc->EvalSub(or1,c1Scaled);
or1 = cc->EvalAdd(or1,dScaled);
n11 = cc->LevelReduce(n11,nullptr);
orN[s] = cc->EvalMultNoRelin(n11,or1);
}
computationTime = TOC(t);
std::cout << "Computation Time: \t\t" << computationTime/1000 << " s" << std::endl;
TIC(t);
std::vector<Plaintext> pN(sizeS);
std::vector<Plaintext> pD(sizeS);
std::vector<Plaintext> oddN(sizeS);
std::vector<Plaintext> oddD(sizeS);
for (size_t s = 0; s < sizeS; s++) {
cc->Decrypt(keyPair.secretKey, chiN[s] , &(pN[s]));
cc->Decrypt(keyPair.secretKey, chiD[s] , &(pD[s]));
cc->Decrypt(keyPair.secretKey, orN[s] , &(oddN[s]));
cc->Decrypt(keyPair.secretKey, orD[s] , &(oddD[s]));
}
decryptionTime = TOC(t);
std::cout << "Decryption & Decoding Time: \t" << decryptionTime/1000 << " s" << std::endl;
std::vector<double> chival(headersS.size());
std::vector<double> pval(headersS.size());
std::vector<double> odds(headersS.size());
for (size_t s = 0; s < sizeS; s++) {
for (size_t i = 0; i < m/4; i++) {
if (s*m/4 + i < headersS.size()) {
chival[s*m/4 + i] = pN[s]->GetCKKSPackedValue()[i].real()*2*N/pD[s]->GetCKKSPackedValue()[i].real();
if (chival[s*m/4 + i] < 0)
chival[s*m/4 + i] = 0;
pval[s*m/4 + i] = (double)1-IncompleteGamma(chival[s*m/4 + i]/2,0.5);
if (pval[s*m/4 + i] < 0)
pval[s*m/4 + i] = 1e-15;
else
if (pval[s*m/4 + i]==0)
pval[s*m/4 + i] = BS(sqrt(chival[s*m/4 + i]));
odds[s*m/4 + i] = oddN[s]->GetCKKSPackedValue()[i].real()/oddD[s]->GetCKKSPackedValue()[i].real();
}
}
}
ofstream myfile;
myfile.open(SNPDir + "/" + pValue);
myfile.precision(10);
for(uint32_t i = 0; i < headersS.size(); i++) {
myfile << headersS[i] << "\t" << pval[i] << std::endl;
}
myfile.close();
ofstream myfile2;
myfile2.open(SNPDir + "/" + "odds.txt");
myfile2.precision(10);
for(uint32_t i = 0; i < headersS.size(); i++) {
myfile2 << headersS[i] << "\t" << odds[i] << std::endl;
}
myfile2.close();
ofstream myfile3;
myfile3.open(SNPDir + "/" + "chi2.txt");
myfile3.precision(10);
for(uint32_t i = 0; i < headersS.size(); i++) {
myfile3 << headersS[i] << "\t" << chival[i] << std::endl;
}
myfile3.close();
endToEndTime = TOC(tAll);
std::cout << "\nEnd-to-end Runtime: \t\t" << endToEndTime/1000 << " s" << std::endl;
ofstream myfileRuntime;
myfileRuntime.open(SNPDir + "/" + Runtime);
myfileRuntime << "Key Generation Time: \t\t" << keyGenTime/1000 << " s" << std::endl;
myfileRuntime << "Encoding and Encryption Time: \t" << encryptionTime/1000 << " s" << std::endl;
myfileRuntime << "Computation Time: \t\t" << computationTime/1000 << " s" << std::endl;
myfileRuntime << "Decryption & Decoding Time: \t" << decryptionTime/1000 << " s" << std::endl;
myfileRuntime << "End-to-end Runtime: \t\t" << endToEndTime/1000 << " s" << std::endl;
myfileRuntime.close();
}
Ciphertext<DCRTPoly> BinaryTreeAdd(std::vector<Ciphertext<DCRTPoly>> &vector) {
auto cc = vector[0]->GetCryptoContext();
for(size_t j = 1; j < vector.size(); j=j*2) {
for(size_t i = 0; i<vector.size(); i = i + 2*j) {
if ((i+j)<vector.size())
vector[i] = cc->EvalAdd(vector[i],vector[i+j]);
}
}
Ciphertext<DCRTPoly> result(new CiphertextImpl<DCRTPoly>(*(vector[0])));
return result;
}
double IncompleteGamma(double val, double p)
{
if( !Greater(val, 0) || !Greater(p, 0) )
return 0;
double expValue = p*log(val) - val - lgamma(p);
if( Less(expValue, log(1.0E-37)) ) // undeflow
return 0;
double factor = exp(expValue);
if( !Greater(val, 1) || Less(val, p) )
{
double igamma = 1;
double term = 1;
for( int i = 1; Greater(term, EPSILON); ++i )
{
term *= (val/(p+i));
igamma += term;
}
return (igamma*factor/p);
}
double pn[6] = { 1, val, val+1, val*(2+val-p) };
double upperIncGamma = pn[2]/pn[3];
for( int j = 1; ; ++j )
{
double a = (j+1)*2 + val- p;
double b = (1 + j - p)*j;
pn[4] = a*pn[2] - b*pn[0];
pn[5] = a*pn[3] - b*pn[1];
if( !Equal(pn[5], 0) )
{
double rn = pn[4]/pn[5];
double diff = fabs(upperIncGamma - rn);
if( !Greater(diff, EPSILON) && !Greater(diff, (EPSILON*rn)) )
return (1 - factor*upperIncGamma);
upperIncGamma = rn;
}
for( int i = 0; i < 4; i++ )
pn[i] = pn[i+2];
if( !Greater(1.0E+37, fabs(pn[4])) ) // overflow
{
for( int i = 0; i < 4; i++ )
pn[i] = pn[i] / 1.0E+37;
}
}
return 0;
}
void ReadSNPFile(vector<string>& headers, std::vector<std::vector<double>> & dataColumns, std::vector<double> &y,
string dataFileName, size_t N, size_t M)
{
uint32_t cols = 0;
string fileName = dataFileName + ".csv";
std::cerr << "file name = " << fileName << std::endl;
ifstream file(fileName);
string line, value;
if(file.good()) {
getline(file, line);
cols = std::count(line.begin(), line.end(), ',') + 1;
stringstream ss(line);
vector<string> result;
size_t tempcounter = 0;
for(uint32_t i = 0; i < cols; i++) {
string substr;
getline(ss, substr, ',');
if ((substr != "") && (i>4) && (i<M+5)) {
headers.push_back(substr);
tempcounter++;
}
}
cols = tempcounter;
}
size_t counter = 0;
while((file.good()) && (counter < N)) {
getline(file, line);
uint32_t curCols = std::count(line.begin(), line.end(), ',') + 1;
if (curCols > 2) {
stringstream ss(line);
for(uint32_t i = 0; i < 5; i++) {
string substr;
getline(ss, substr, ',');
if ((i==1))
y.push_back(std::stod(substr));
}
std::vector<double> row(cols);
for(uint32_t i = 5; i < cols + 5; i++) {
string substr;
getline(ss, substr, ',');
if (i < M+5)
{
double val;
val = std::stod(substr);
row[i-5] = val;
}
}
dataColumns.push_back(row);
}
counter++;
}
file.close();
std::cout << "Read in data: ";
std::cout << dataFileName << std::endl;
}

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Code/Duality_Technologies/palisade-gwas-demos-master/demo-logistic.cpp
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