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demo-logistic.cpp
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demo-logistic.cpp
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/***
* Copyright (c) 2020-2022 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 Logistic Regression Approximation 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-logistic --SNPdir "../data" --SNPfilename "random_sample" --pvalue "pvalue.txt" --runtime "result.txt" --samplesize="200" --snps="16384"
*/
#include <getopt.h>
#include <numeric>
#include <cmath>
#include "openfhe.h"
using namespace std;
using namespace lbcrypto;
void RunLogReg(const string &SNPDir, const string &SNPFileName, const string &pValue,
const string &Runtime, const string &SampleSize, const string &SNPs);
Ciphertext<DCRTPoly> zExpand(const Ciphertext<DCRTPoly> p, const Ciphertext<DCRTPoly> y);
shared_ptr<std::vector<std::vector<Ciphertext<DCRTPoly>>>> MatrixInverse(const Ciphertext<DCRTPoly> m, size_t k, CiphertextImpl<DCRTPoly> &b, CiphertextImpl<DCRTPoly> &cd,
const std::map<usint, EvalKey<DCRTPoly>> &map, const std::map<usint, EvalKey<DCRTPoly>> &rotKeys,
const std::map<usint, EvalKey<DCRTPoly>> &evalSumRows);
Ciphertext<DCRTPoly> CloneCiphertext(const Ciphertext<DCRTPoly> ciphertext, size_t size,
const std::map<usint,EvalKey<DCRTPoly>> &rotKeys, const std::map<usint,EvalKey<DCRTPoly>> &evalSumRows);
shared_ptr<std::vector<Ciphertext<DCRTPoly>>> SplitIntoSingle(const Ciphertext<DCRTPoly> c, size_t N, size_t k,
const std::map<usint, EvalKey<DCRTPoly>> &rotKeys);
Ciphertext<DCRTPoly> BinaryTreeAdd(std::vector<Ciphertext<DCRTPoly>> &vector);
void CompressEvalKeys(std::map<usint, EvalKey<DCRTPoly>> &ek, size_t level);
void ReadSNPFile(vector<string>& headers, std::vector<std::vector<double>> & dataColumns,std::vector<std::vector<double>> &x, std::vector<double> &y,
string dataFileName, size_t N, size_t M);
Ciphertext<DCRTPoly> HoistedAutomorphism(const EvalKey<DCRTPoly> ek,
ConstCiphertext<DCRTPoly> cipherText, const shared_ptr<vector<DCRTPoly>> digits, const usint index);
double normalCFD(double value) { return 0.5 * erfc(-value * M_SQRT1_2); }
double sf(double value) { return 1 - normalCFD(value); }
double BS(double z) {
double y = exp(-z*z/2);
return sqrt(1-y) * (31*y/200 - 341*y*y/8000) / sqrt(M_PI);
}
int main(int argc, char **argv) {
int opt;
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);
}
}
RunLogReg(SNPDir, SNPFileName, pValue, Runtime, SampleSize, SNPs);
return 0;
}
std::vector<uint32_t> GenerateIndices2nComplexCols(uint32_t batchSize, uint32_t m) {
auto isize = static_cast<size_t>(std::ceil(std::log2(batchSize)));
std::vector<uint32_t> indices;
indices.reserve(isize);
uint32_t g = NativeInteger(5).ModInverse(m).ConvertToInt<uint32_t>();
for (size_t i = 0; i < isize; ++i) {
indices.push_back(g);
g = (g * g) % m;
}
return indices;
}
void RunLogReg(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 computation1Time(0.0);
double computation2Time(0.0);
double computation3Time(0.0);
double computation4Time(0.0);
double computation5Time(0.0);
double computation6Time(0.0);
double computation7Time(0.0);
double computation8Time(0.0);
double computationTime(0.0);
double decryptionTime(0.0);
double endToEndTime(0.0);
std::cout << "\n======LOGISTIC REGRESSION SOLUTION========\n" << std::endl;
vector<string> headers1;
vector<string> headersS;
std::vector<std::vector<double>> xData;
std::vector<double> yData;
std::vector<std::vector<double>> sData;
size_t N = std::stoi(SampleSize);
size_t M = std::stoi(SNPs);
double scalingFactor = 1e-1;
double scalingFactorD = 1e-2;
double scalingFactorN = 1e-2;
ReadSNPFile(headersS,sData,xData,yData,SNPDir + "/" + SNPFileName,N,M);
N = sData.size();
M = sData[0].size();
size_t k = xData[0].size();
usint m;
m = 65536;
size_t n = m/4;
usint init_size = 17;
usint dcrtBits = 50;
size_t k2 = k*k;
usint batchSize = k*k;
CCParams<CryptoContextCKKSRNS> parameters;
parameters.SetScalingModSize(dcrtBits);
parameters.SetMultiplicativeDepth(init_size-1);
parameters.SetRingDim(m/2);
parameters.SetScalingTechnique(FIXEDMANUAL);
parameters.SetKeySwitchTechnique(BV);
parameters.SetFirstModSize(dcrtBits);
parameters.SetBatchSize(k);
parameters.SetMaxRelinSkDeg(4);
CryptoContext<DCRTPoly> cc = GenCryptoContext(parameters);
cc->Enable(PKE);
cc->Enable(KEYSWITCH);
cc->Enable(LEVELEDSHE);
cc->Enable(ADVANCEDSHE);
std::cout << "\nNumber of Individuals = " << N << std::endl;
std::cout << "Number of SNPs = " << M << std::endl;
std::cerr << "Number of features = " << k << std::endl;
TIC(t);
auto keyPair = cc->KeyGen();
cc->EvalMultKeysGen(keyPair.secretKey);
// as we have introduced a new internal EvalAutomorphismKey map in OpenFHE which includes
// ALL EvalAutomorphism keys, we had to alter this code to make it work with the new map
cc->EvalSumKeyGen(keyPair.secretKey);
auto evalSum = cc->GetEvalSumKeyMap(keyPair.secretKey->GetKeyTag());
auto evalSumRows = cc->EvalSumRowsKeyGen(keyPair.secretKey, nullptr, k);
std::vector<uint32_t> indicesCols = GenerateIndices2nComplexCols(k, m);
auto evalSumCols = cc->GetScheme()->EvalAutomorphismKeyGen(keyPair.secretKey, indicesCols);
auto pubKeyS = PublicKey<DCRTPoly>(new PublicKeyImpl<DCRTPoly>(*keyPair.publicKey));
std::vector<DCRTPoly> pubElementsS = pubKeyS->GetPublicElements();
for (size_t i=0; i < pubElementsS.size(); i++)
pubElementsS[i].DropLastElements(10);
pubKeyS->SetPublicElements(pubElementsS);
auto pubKeyX = PublicKey<DCRTPoly>(new PublicKeyImpl<DCRTPoly>(*keyPair.publicKey));
auto pubElementsX = pubKeyX->GetPublicElements();
for (size_t i=0; i < pubElementsX.size(); i++)
pubElementsX[i].DropLastElements(11);
pubKeyX->SetPublicElements(pubElementsX);
std::vector<int32_t> indicesM;
for (size_t i = 3; i < k*k; i++) {
if (!((i == 4) || (i == 8)))
indicesM.push_back(i);
}
cc->SetKeyGenLevel(5);
auto rotKeysM = cc->GetScheme()->EvalAtIndexKeyGen(nullptr,keyPair.secretKey, indicesM);
std::vector<int32_t> indicesConv;
for (size_t i = 4; i < m/4; i=2*i)
indicesConv.push_back(m/4-i);
cc->SetKeyGenLevel(8);
auto rotKeysConv = cc->GetScheme()->EvalAtIndexKeyGen(nullptr,keyPair.secretKey, indicesConv);
keyGenTime = TOC(t);
TIC(t);
uint32_t numCt = (uint32_t)std::ceil((double)(N*k*k)/(double)(n));
std::cerr << "Number of ciphertexts: " << numCt << std::endl;
size_t Nfull = n/k2;
std::vector<std::vector<std::complex<double>>> x;
for (size_t r = 0; r < numCt; r++) {
std::vector<std::complex<double>> xTemp;
size_t N1;
if ((r+1)*n < N*k2)
N1 = n/(k2);
else
N1 = N - r*n/k2;
for (size_t j = 0; j < N1; j++)
for (size_t i = 0; i < k; i++)
for (size_t p = 0; p < k; p++)
xTemp.push_back(xData[j+r*Nfull][p]);
x.push_back(xTemp);
}
std::vector<std::vector<std::complex<double>>> xt;
for (size_t r = 0; r < numCt; r++) {
std::vector<std::complex<double>> xTemp;
size_t N1;
if ((r+1)*n < N*k2)
N1 = n/(k2);
else
N1 = N - r*n/k2;
for (size_t j = 0; j < N1; j++)
for (size_t i = 0; i < k; i++)
for (size_t p = 0; p < k; p++)
xTemp.push_back(xData[j+r*Nfull][i]);
xt.push_back(xTemp);
}
std::vector<std::vector<std::complex<double>>> y;
for (size_t r = 0; r < numCt; r++) {
size_t N1;
if ((r+1)*n < N*k2)
N1 = n/(k2);
else
N1 = N - r*n/k2;
std::vector<std::complex<double>> yTemp;
for (size_t j = 0; j < N1; j++)
for (size_t i = 0; i < k*k; i++) {
{
yTemp.push_back(yData[j+r*Nfull]);
}
}
y.push_back(yTemp);
}
vector<Plaintext> X(numCt);
vector<Plaintext> XT(numCt);
vector<Plaintext> Y(numCt);
for (size_t r = 0; r < numCt; r++) {
X[r] = cc->MakeCKKSPackedPlaintext(x[r],1,0,nullptr,m/4);
XT[r] = cc->MakeCKKSPackedPlaintext(xt[r],1,0,nullptr,m/4);
Y[r] = cc->MakeCKKSPackedPlaintext(y[r],1,0,nullptr,m/4);
}
std::vector<vector<Ciphertext<DCRTPoly>>> cX1(N);
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>>(m/4);
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)] = scalingFactor*sData[i][j];
}
}
std::vector<std::vector<Ciphertext<DCRTPoly>>> S(sizeS);
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],1,10,pubElementsS[0].GetParams(),m/4);
S[s][i] = cc->Encrypt(pubKeyS, sTemp);
}
std::vector<Ciphertext<DCRTPoly>> x1Temp;
for (size_t j=0; j<k; j++){
std::vector<std::complex<double>> xVector(m/4,xData[i][j]);
Plaintext xTemp = cc->MakeCKKSPackedPlaintext(xVector,1,11,pubElementsX[0].GetParams(),m/4);
x1Temp.push_back(cc->Encrypt(pubKeyX, xTemp));
}
cX1[i] = x1Temp;
}
vector<Ciphertext<DCRTPoly>> cX(numCt);
vector<Ciphertext<DCRTPoly>> cXT(numCt);
vector<Ciphertext<DCRTPoly>> cY(numCt);
for (size_t r=0; r<numCt; r++){
cX[r] = cc->Encrypt(keyPair.publicKey, X[r]);
cXT[r] = cc->Encrypt(keyPair.publicKey, XT[r]);
cY[r] = cc->Encrypt(keyPair.publicKey, Y[r]);
}
encryptionTime = TOC(t);
TIC(t);
double alpha = 0.00358;
// Compute p1 = X^T (y - 0.5)
Ciphertext<DCRTPoly> cP1Sum, cP1;
for (size_t r=0; r<numCt; r++){
cP1 = cc->EvalMult(cX[r],cc->EvalSub(cc->EvalSub(cY[r],double(0.25)),double(0.25)));
cP1 = cc->EvalSumRows(cP1,k*k,*evalSumRows);
//cP1 = cc->ModReduce(cP1);
if (r==0)
cP1Sum = cP1;
else
cP1Sum = cc->EvalAdd(cP1Sum,cP1);
}
cP1Sum = cc->ModReduce(cP1Sum);
// Compute p2 = 0.15625*alpha*X
vector<Ciphertext<DCRTPoly>> cP2Arr(numCt);
for (size_t r=0; r<numCt; r++){
auto cP2 = cc->EvalMult(cX[r],double(0.15625*alpha));
cP2Arr[r] = cc->ModReduce(cP2);
}
//Compute p3 = p1*p2
vector<Ciphertext<DCRTPoly>> cP3Arr(numCt);
for (size_t r=0; r<numCt; r++){
auto cP3 = cc->EvalMult(cP1Sum,cP2Arr[r]);
cP3 = cc->EvalSumCols(cP3,k,*evalSumCols);
cP3 = cc->ModReduce(cP3);
cP3Arr[r] = cc->ModReduce(cP3);
}
//Compute p = p3 + 0.5
vector<Ciphertext<DCRTPoly>> cPArr(numCt);
for (size_t r=0; r<numCt; r++){
//auto cP = cc->EvalSub(cP3Arr[r],cP6Arr[r]);
auto cP = cc->EvalAdd(cP3Arr[r],double(0.25));
cPArr[r] = cc->EvalAdd(cP,double(0.25));
}
// Compute p^2
vector<Ciphertext<DCRTPoly>> cPSquareArr(numCt);
for (size_t r=0; r<numCt; r++){
auto cPSquare = cc->EvalMult(cPArr[r],cPArr[r]);
cPSquareArr[r] = cc->ModReduce(cPSquare);
}
// Compute w = p - p^2
vector<Ciphertext<DCRTPoly>> cWArr(numCt);
for (size_t r=0; r<numCt; r++){
auto cPReduced = cc->LevelReduce(cPArr[r],nullptr);
cWArr[r] = cc->EvalSub(cPReduced,cPSquareArr[r]);
}
// Computes zExpand
vector<Ciphertext<DCRTPoly>> cZArr(numCt);
for (size_t r=0; r<numCt; r++){
cZArr[r] = zExpand(cPArr[r], cY[r]);
}
// Compute x^T diag(w)
vector<Ciphertext<DCRTPoly>> cM1Arr(numCt);
for (size_t r=0; r<numCt; r++){
auto cXTNReduced = cc->LevelReduce(cXT[r],nullptr,4);
auto cM1 = cc->EvalMult(cXTNReduced,cWArr[r]);
cM1Arr[r] = cc->ModReduce(cM1); // Level 5
}
CompressEvalKeys(*evalSumRows,5);
//Compute M = (x^T diag(w)) X
Ciphertext<DCRTPoly> cMSum, cM;
vector<Ciphertext<DCRTPoly>> cXReducedArr(numCt);
for (size_t r=0; r<numCt; r++){
cXReducedArr[r] = cc->LevelReduce(cX[r],nullptr,5); //Level 5
cM = cc->EvalMult(cM1Arr[r],cXReducedArr[r]);
cM = cc->EvalSumRows(cM,k*k,*evalSumRows);
if (r==0)
cMSum = cM;
else
cMSum = cc->EvalAdd(cMSum,cM);
}
computation1Time = TOC(t);
TIC(t);
Ciphertext<DCRTPoly> cB(new CiphertextImpl<DCRTPoly>(cc));
Ciphertext<DCRTPoly> cd(new CiphertextImpl<DCRTPoly>(cc));
CompressEvalKeys(evalSum,5);
auto cB1 = MatrixInverse(cMSum,k,*cB,*cd, evalSum, *rotKeysM, *evalSumRows);
computation2Time = TOC(t);
TIC(t);
cMSum = cc->ModReduce(cMSum);
for (size_t r=0; r<numCt; r++){
cM1Arr[r] = cc->LevelReduce(cM1Arr[r],nullptr,2); //Level 7
}
// Compute (X^T diag(w)) z
Ciphertext<DCRTPoly> cztr1Sum, cztr1;
for (size_t r=0; r<numCt; r++){
cztr1 = cc->EvalMult(cM1Arr[r],cZArr[r]);
cztr1 = cc->EvalSumRows(cztr1,k*k,*evalSumRows);
//cztr1 = cc->ModReduce(cztr1); // Level 8
if (r==0)
cztr1Sum = cztr1;
else
cztr1Sum = cc->EvalAdd(cztr1Sum,cztr1);
}
cztr1Sum = cc->ModReduce(cztr1Sum);
// Compute XB
vector<Ciphertext<DCRTPoly>> cztr2Arr(numCt);
for (size_t r=0; r<numCt; r++){
cXReducedArr[r] = cc->LevelReduce(cXReducedArr[r],nullptr,4); //Level 9
auto cztr2 = cc->EvalMult(cXReducedArr[r],cB);
cztr2 = cc->EvalSumCols(cztr2,k,*evalSumCols);
cztr2 = cc->ModReduce(cztr2);
cztr2Arr[r] = cc->ModReduce(cztr2); //Level 11
}
CompressEvalKeys(*rotKeysM,6);
CompressEvalKeys(*evalSumRows,6);
// Compute the product of (XB) and (X^T diag(w)) z
vector<Ciphertext<DCRTPoly>> cztr3Arr(numCt);
cztr1Sum = cc->LevelReduce(cztr1Sum,nullptr,3); //Level 11
for (size_t r=0; r<numCt; r++){
auto cztr3 = cc->EvalMult(cztr1Sum,cztr2Arr[r]);
auto cztr4 = cc->EvalAdd(cztr3,cc->GetScheme()->EvalAtIndex(cztr3,4,*evalSumRows));
auto cztr5 = cc->EvalAdd(cc->GetScheme()->EvalAtIndex(cztr3,8,*evalSumRows),cc->GetScheme()->EvalAtIndex(cztr3,12,*rotKeysM));
auto cztr6 = cc->EvalAdd(cztr4,cztr5);
cztr6 = cc->ModReduce(cztr6); //Level 12
std::vector<std::complex<double>> mask(m/4);
size_t N1;
if ((r+1)*n < N*k2)
N1 = n/(k2);
else
N1 = N - r*n/k2;
size_t NPow2cur = 1<<(size_t)std::ceil(log2(N1));
for (size_t i = 0; i < NPow2cur*k*k; i++)
{
if ((i % batchSize == 0) || (i % batchSize == 1) || (i % batchSize == 2) || (i % batchSize == 3))
mask[i] = 1;
else
mask[i] = 0;
}
Plaintext plaintextMask = cc->MakeCKKSPackedPlaintext(mask,1,0,nullptr,m/4);
auto cMask = cc->EvalMult(cztr6,plaintextMask);
cztr4 = cc->EvalAdd(cMask,cc->GetScheme()->EvalAtIndex(cMask,m/4-4,*rotKeysConv));
cztr3Arr[r] = cc->EvalAdd(cztr4,cc->GetScheme()->EvalAtIndex(cztr4,m/4-8,*rotKeysConv));
}
rotKeysM->clear();
evalSumRows->clear();
//Compute d*z
auto cdDen = cc->LevelReduce(cd,nullptr,1); //Level 10
cd = cc->LevelReduce(cd,nullptr,3); //Level 12
vector<Ciphertext<DCRTPoly>> cztr4Arr(numCt);
for (size_t r=0; r<numCt; r++){
cZArr[r] = cc->LevelReduce(cZArr[r],nullptr,5); //Level 12
cztr4Arr[r] = cc->EvalMult(cZArr[r],cd);
}
//Computer ztr
vector<Ciphertext<DCRTPoly>> cztrArr(numCt);
for (size_t r=0; r<numCt; r++){
auto cztr = cc->EvalSub(cztr4Arr[r],cztr3Arr[r]);
cztrArr[r] = cc->ModReduce(cztr); //Level 13
}
computation3Time = TOC(t);
TIC(t);
vector<Ciphertext<DCRTPoly>> cWConvArr(numCt);
for (size_t r=0; r<numCt; r++){
cWArr[r] = cc->LevelReduce(cWArr[r],nullptr,4); //Level 8
size_t N1;
if ((r+1)*n < N*k2)
N1 = n/(k2);
else
N1 = N - r*n/k2;
size_t NPow2cur = 1<<(size_t)std::ceil(log2(N1));
std::vector<std::complex<double>> maskW(m/4);
for (size_t v = 0; v < NPow2cur*k*k; v++)
maskW[v] = 1;
for (size_t v = NPow2cur*k*k; v < m/4; v++)
maskW[v] = 0;
Plaintext plaintextW = cc->MakeCKKSPackedPlaintext(maskW,1,0,nullptr,m/4);
auto cWConv = cc->EvalMult(cWArr[r],plaintextW);
for (size_t j = NPow2cur*k*k; j < m/4; j=j*2 ) {
cWConv = cc->EvalAdd(cWConv,cc->GetScheme()->EvalAtIndex(cWConv,m/4-j,*rotKeysConv));
}
cWConvArr[r] = cc->ModReduce(cWConv); //Level 9
}
CompressEvalKeys(*rotKeysConv,1);
vector<Ciphertext<DCRTPoly>> cWVector;
for (size_t r=0; r<numCt; r++){
size_t N1;
if ((r+1)*n < N*k2)
N1 = n/(k2);
else
N1 = N - r*n/k2;
auto temp = SplitIntoSingle(cWConvArr[r], N1, k, *rotKeysConv); //Level 10
cWVector.insert(cWVector.end(),temp->begin(),temp->end()); //Level 10
cWArr[r] = cc->LevelReduce(cWArr[r],nullptr,1); //Level 9
}
computation4Time = TOC(t);
TIC(t);
std::vector<std::vector<Ciphertext<DCRTPoly>>> strVector1(sizeS);
for (size_t i = 0; i < sizeS; i++)
strVector1[i] = std::vector<Ciphertext<DCRTPoly>>(N);
// Compute diag(w) S
for (size_t s = 0; s < sizeS; s++) {
#pragma omp parallel for
for (size_t i = 0; i < N; i++)
{
strVector1[s][i] = cc->EvalMultNoRelin(cWVector[i],S[s][i]);
strVector1[s][i] = cc->ModReduce(strVector1[s][i]); // Level 11
}
}
// Compute X^T (diag(w) S)
std::vector<std::vector<Ciphertext<DCRTPoly>>> strVector2(sizeS);
for (size_t s = 0; s < sizeS; s++) {
strVector2[s] = std::vector<Ciphertext<DCRTPoly>>(k);
}
for (size_t j = 0; j < k; j++)
{
for (size_t s = 0; s < sizeS; s++) {
std::vector<Ciphertext<DCRTPoly>> tempVector(N);
#pragma omp parallel for
for (size_t i = 0; i < N; i++)
{
tempVector[i] = cc->EvalMultNoRelin(strVector1[s][i],cX1[i][j]);
}
//std::cerr << "passed mult" << std::endl;
strVector2[s][j] = BinaryTreeAdd(tempVector);
tempVector.clear();
//std::cerr << "passed binary tree" << std::endl;
strVector2[s][j] = cc->ModReduce(strVector2[s][j]); //Level 12
}
}
// Compute B X^T (diag(w) S)
std::vector<std::vector<Ciphertext<DCRTPoly>>> strVector3(sizeS);
for (size_t s = 0; s < sizeS; s++)
strVector3[s] = std::vector<Ciphertext<DCRTPoly>>(k);
#pragma omp parallel for
for(size_t i = 0; i < k; i++) {
(*cB1)[i][0] = cc->LevelReduce((*cB1)[i][0],nullptr,3);
for(size_t j=1; j < k; j++) {
(*cB1)[i][j] = cc->LevelReduce((*cB1)[i][j],nullptr,3);
}
}
for (size_t s = 0; s < sizeS; s++) {
#pragma omp parallel for
for(size_t i = 0; i < k; i++) {
auto temp = cc->EvalMultAndRelinearize((*cB1)[i][0],strVector2[s][0]);
for(size_t j=1; j < k; j++) {
temp = cc->EvalAdd(temp,cc->EvalMultAndRelinearize((*cB1)[i][j],strVector2[s][j]));
}
temp = cc->ModReduce(temp); //Level 13
strVector3[s][i] = temp;
}
}
#pragma omp parallel for
for(size_t i = 0; i < N; i++) {
cX1[i][0] = cc->LevelReduce(cX1[i][0],nullptr,2);
for(size_t j=1; j < k; j++) {
cX1[i][j] = cc->LevelReduce(cX1[i][j],nullptr,2);
}
}
// Compute X B X^T (diag(w) S)
for (size_t s = 0; s < sizeS; s++) {
#pragma omp parallel for
for(size_t i = 0; i < N; i++) {
auto temp = cc->EvalMultNoRelin(cX1[i][0],strVector3[s][0]);
for(size_t j=1; j < k; j++) {
temp = cc->EvalAdd(temp,cc->EvalMultNoRelin(cX1[i][j],strVector3[s][j]));
}
strVector1[s][i] = temp;
}
}
// Compute d S - X B X^T (diag(w) S)
//auto cd12 = cd;
cd = cc->LevelReduce(cd,nullptr,1); //Level 13
for (size_t s = 0; s < sizeS; s++) {
#pragma omp parallel for
for (size_t i = 0; i < N; i++)
{
S[s][i] = cc->LevelReduce(S[s][i],nullptr,3);
strVector1[s][i] = cc->EvalSub(cc->EvalMultNoRelin(cd,S[s][i]),strVector1[s][i]); // Level 13
strVector1[s][i] = cc->ModReduce(strVector1[s][i]); // Level 14
}
}
for (size_t i = 0; i < S.size(); i++)
S.clear();
S.clear();
for (size_t i = 0; i < cX1.size(); i++)
cX1.clear();
cX1.clear();
computation5Time = TOC(t);
TIC(t);
// Compute str * str
std::vector<std::vector<Ciphertext<DCRTPoly>>> invVarD(sizeS);
for (size_t s = 0; s < sizeS; s++)
invVarD[s] = std::vector<Ciphertext<DCRTPoly>>(N);
for (size_t s = 0; s < sizeS; s++) {
#pragma omp parallel for
for (size_t i = 0; i < N; i++)
{
invVarD[s][i] = cc->EvalMultNoRelin(strVector1[s][i],strVector1[s][i]); // Level 14
//invVarD[i] = cc->ModReduce(invVarD[i]); // Level 15
}
}
// Compute d*d
auto cd12 = cc->LevelReduce(cd,nullptr,1); // Level 14
auto cd2 = cc->EvalMult(cd12,cd12);
cd2 = cc->ModReduce(cd2); // Level 15
// Compute (w^T) (str*str)
#pragma omp parallel for
for (size_t i = 0; i < N; i++)
{
cWVector[i] = cc->LevelReduce(cWVector[i],nullptr,3); // Level 14
//scaling down
auto temp = cc->EvalMult(cWVector[i],double(scalingFactorD));
temp = cc->ModReduce(temp); // Level 15
//auto temp = cc->EvalMultNoRelin(cd2,cWVector[i]);
for (size_t s = 0; s < sizeS; s++) {
invVarD[s][i] = cc->EvalMultNoRelin(temp,invVarD[s][i]);
}
}
std::vector<Ciphertext<DCRTPoly>> invVar(sizeS);
for (size_t s = 0; s < sizeS; s++)
invVar[s] = BinaryTreeAdd(invVarD[s]);
for (size_t s = 0; s < sizeS; s++)
invVarD[s].clear();
invVarD.clear();
computation6Time = TOC(t);
TIC(t);
CompressEvalKeys(*rotKeysConv,4);
// Compute w*ztr
vector<Ciphertext<DCRTPoly>> beta1Arr(numCt);
for (size_t r=0; r<numCt; r++){
cWArr[r] = cc->LevelReduce(cWArr[r],nullptr,3); //Level 12
size_t N1;
if ((r+1)*n < N*k2)
N1 = n/(k2);
else
N1 = N - r*n/k2;
size_t NPow2cur = 1<<(size_t)std::ceil(log2(N1));
// clears the mask to prepare for the conversion
std::vector<std::complex<double>> maskW2(m/4);
for (size_t v = 0; v < NPow2cur*k*k; v++)
maskW2[v] = scalingFactorN;
for (size_t v = NPow2cur*k*k; v < m/4; v++)
maskW2[v] = 0;
Plaintext plaintextW2 = cc->MakeCKKSPackedPlaintext(maskW2,1,0,nullptr,m/4);
auto cWConv2 = cc->EvalMult(cWArr[r],plaintextW2);
cWConv2 = cc->ModReduce(cWConv2);//Level 13
auto beta1 = cc->EvalMult(cWConv2,cztrArr[r]);
for (size_t j = NPow2cur*k*k; j < m/4; j=j*2 ) {
beta1 = cc->EvalAdd(beta1,cc->GetScheme()->EvalAtIndex(beta1,m/4-j,*rotKeysConv));
}
beta1Arr[r] = cc->ModReduce(beta1); //Level 14
}
CompressEvalKeys(*rotKeysConv,1);
//CompressEvalKeys(*rotKeysBabyGiant,6);
vector<Ciphertext<DCRTPoly>> betaVector;
for (size_t r=0; r<numCt; r++){
size_t N1;
if ((r+1)*n < N*k2)
N1 = n/(k2);
else
N1 = N - r*n/k2;
auto temp = SplitIntoSingle(beta1Arr[r], N1, k, *rotKeysConv); //Level 15
betaVector.insert(betaVector.end(),temp->begin(),temp->end());
}
rotKeysConv->clear();
computation7Time = TOC(t);
TIC(t);
// Compute (w*ztr)^T str
for (size_t s = 0; s < sizeS; s++) {
#pragma omp parallel for
for (size_t i = 0; i < N; i++)
{
strVector1[s][i] = cc->LevelReduce(strVector1[s][i],nullptr,1);// Level 15
strVector1[s][i] = cc->EvalMultNoRelin(betaVector[i],strVector1[s][i]);
}
}
betaVector.clear();
std::vector<Ciphertext<DCRTPoly>> beta(sizeS);
for (size_t s = 0; s < sizeS; s++)
beta[s] = BinaryTreeAdd(strVector1[s]);
for (size_t s = 0; s < sizeS; s++)
strVector1[s].clear();
strVector1.clear();
computation8Time = TOC(t);
std::vector<Plaintext> pInvVar(sizeS);
std::vector<Plaintext> pBeta(sizeS);
Plaintext pD;
TIC(t);
cc->Decrypt(keyPair.secretKey, cd2 , &pD);
for (size_t s = 0; s < sizeS; s++) {
cc->Decrypt(keyPair.secretKey, invVar[s] , &(pInvVar[s]));
cc->Decrypt(keyPair.secretKey, beta[s] , &(pBeta[s]));
}
decryptionTime = TOC(t);
std::vector<double> zval(headersS.size());
std::vector<double> pval(headersS.size());
std::vector<double> betaval(headersS.size());
std::vector<std::complex<double>> num(headersS.size());
std::vector<std::complex<double>> den(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()) {
num[s*m/4 + i] = pow(scalingFactor,-1)*pow(scalingFactorN,-1)*pBeta[s]->GetCKKSPackedValue()[i];
den[s*m/4 + i] = pow(scalingFactor,-2)*pow(scalingFactorD,-1)*pInvVar[s]->GetCKKSPackedValue()[i];
betaval[s*m/4 + i] = num[s*m/4 + i].real()/den[s*m/4 + i].real();
zval[s*m/4 + i] = num[s*m/4 + i].real()/sqrt(den[s*m/4 + i].real()*pD->GetCKKSPackedValue()[0].real());
pval[s*m/4 + i] = 2*sf(abs(zval[s*m/4 + i]));
if (pval[s*m/4 + i] == 0)
pval[s*m/4 + i] = BS(zval[s*m/4 + i]);
}
}
}
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 myfilez;
myfilez.open(SNPDir + "/" + "zvalue.txt");
myfilez.precision(10);
for(uint32_t i = 0; i < headersS.size(); i++) {
myfilez << headersS[i] << "\t" << zval[i] << std::endl;
}
myfilez.close();
ofstream myfileb;
myfileb.open(SNPDir + "/" + "betavalue.txt");
myfileb.precision(10);
for(uint32_t i = 0; i < headersS.size(); i++) {
myfileb << headersS[i] << "\t" << betaval[i] << std::endl;
}
myfileb.close();
ofstream myfilenum;
myfilenum.open(SNPDir + "/" + "num.txt");
myfilenum.precision(10);
for(uint32_t i = 0; i < headersS.size(); i++) {
myfilenum << headersS[i] << "\t" << num[i] << std::endl;
}
myfilenum.close();
ofstream myfileden;
myfileden.open(SNPDir + "/" + "den.txt");
myfileden.precision(10);
for(uint32_t i = 0; i < headersS.size(); i++) {
myfileden << headersS[i] << "\t" << den[i] << std::endl;
}
myfileden.close();
computationTime = computation1Time + computation2Time + computation3Time + computation4Time +
computation5Time + computation6Time + computation7Time + computation8Time;
std::cout << "\nKey Generation Time: \t\t" << keyGenTime/1000 << " s" << std::endl;
std::cout << "Encoding and Encryption Time: \t" << encryptionTime/1000 << " s" << std::endl;
std::cout << "Computation Time: \t\t" << computationTime/1000 << " s" << std::endl;
std::cout << "Decryption & Decoding Time: \t" << decryptionTime/1000 << " s" << std::endl;
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> zExpand(const Ciphertext<DCRTPoly> p, const Ciphertext<DCRTPoly> y) {
CryptoContext<DCRTPoly> cc = p->GetCryptoContext();
//Compute p-0.5
auto pAdj = cc->EvalSub(p,double(0.25));
pAdj = cc->EvalSub(pAdj,double(0.25));
//Compute (p-0.5)^2; level 4
auto p2 = cc->EvalMult(pAdj,pAdj);
p2 = cc->ModReduce(p2);
//Compute (p-0.5)^3; level 5
auto p1 = cc->LevelReduce(pAdj,nullptr);
auto p3 = cc->EvalMult(p2,p1);
p3 = cc->ModReduce(p3);
//Compute (p-0.5)^4; level 5
auto p4 = cc->EvalMult(p2,p2);
p4 = cc->ModReduce(p4);
//Compute (p-0.5)^5; level 6
p1 = cc->LevelReduce(p1,nullptr);
auto p5 = cc->EvalMult(p4,p1);
p5 = cc->ModReduce(p5);
//Compute (p-0.5)^6; level 6
p2 = cc->LevelReduce(p2,nullptr);
auto p6 = cc->EvalMult(p4,p2);
p6 = cc->ModReduce(p6);
//Compute (p-0.5)^7; level 6
auto p7 = cc->EvalMult(p4,p3);
p7 = cc->ModReduce(p7);
//Compute (p-0.5)^8; level 6
auto p8 = cc->EvalMult(p4,p4);
p8 = cc->ModReduce(p8);
//Compute -2 + 4y
auto factor = cc->EvalMult(y,4);
factor = cc->ModReduce(factor); //level 1
factor = cc->EvalSub(factor,2);
auto t0 = cc->LevelReduce(factor,nullptr,6); //level 7
//Compute (-8 + 16y)*(p-0.5)^2
auto t1 = cc->EvalMult(factor,4);
t1 = cc->ModReduce(t1); // level 2