// [[Rcpp::export]]
arma::mat BeQTL2(const arma::mat & A, const arma::mat & B, const arma::umat & Bootmat){
int bsi= Bootmat.n_rows;
arma::mat C(A.n_cols*B.n_cols,Bootmat.n_rows);
arma::mat tC(A.n_rows,B.n_rows);
for(int i=0; i<bsi; i++){
tC = cor(A.rows(Bootmat.row(i)),B.rows(Bootmat.row(i)));
C.col(i) = vectorise(tC,0);
}
C.elem(find_nonfinite(C)).zeros();
return reshape(median(C,1),A.n_cols,B.n_cols);
}
//Script that takes two matrices, performs bootstrapped correlation, and returns the median
// [[Rcpp::export]]
arma::mat BeQTL(const arma::mat & A, const arma::mat & B, const arma::umat & Bootmat){
int bsi= Bootmat.n_rows;
Rcpp::Rcout<<"Starting Bootstrap!"<<std::endl;
arma::mat C(A.n_cols*B.n_cols,Bootmat.n_rows);
arma::mat tA(A.n_rows,A.n_cols);
arma::mat tB(B.n_rows,B.n_cols);
arma::mat tC(A.n_rows,B.n_rows);
for(int i=0; i<bsi; i++){
tA = A.rows(Bootmat.row(i));
tB = B.rows(Bootmat.row(i));
tC = cor(tA,tB);
C.col(i) = vectorise(tC,0);
}
C.elem(find_nonfinite(C)).zeros();
return reshape(median(C,1),A.n_cols,B.n_cols);
}
List objectivex(const arma::mat& transition, const arma::cube& emission,
const arma::vec& init, const arma::ucube& obs, const arma::umat& ANZ,
const arma::ucube& BNZ, const arma::uvec& INZ, const arma::uvec& nSymbols,
const arma::mat& coef, const arma::mat& X, arma::uvec& numberOfStates,
unsigned int threads) {
unsigned int q = coef.n_rows;
arma::vec grad(
arma::accu(ANZ) + arma::accu(BNZ) + arma::accu(INZ) + (numberOfStates.n_elem- 1) * q,
arma::fill::zeros);
arma::mat weights = exp(X * coef).t();
if (!weights.is_finite()) {
grad.fill(-arma::datum::inf);
return List::create(Named("objective") = arma::datum::inf, Named("gradient") = wrap(grad));
}
weights.each_row() /= sum(weights, 0);
arma::mat initk(emission.n_rows, obs.n_slices);
for (unsigned int k = 0; k < obs.n_slices; k++) {
initk.col(k) = init % reparma(weights.col(k), numberOfStates);
}
arma::uvec cumsumstate = arma::cumsum(numberOfStates);
unsigned int error = 0;
double ll = 0;
#pragma omp parallel for if(obs.n_slices >= threads) schedule(static) reduction(+:ll) num_threads(threads) \
default(none) shared(q, grad, nSymbols, ANZ, BNZ, INZ, \
numberOfStates, cumsumstate, obs, init, initk, X, weights, transition, emission, error)
for (unsigned int k = 0; k < obs.n_slices; k++) {
if (error == 0) {
arma::mat alpha(emission.n_rows, obs.n_cols); //m,n
arma::vec scales(obs.n_cols); //n
arma::sp_mat sp_trans(transition);
uvForward(sp_trans.t(), emission, initk.col(k), obs.slice(k), alpha, scales);
arma::mat beta(emission.n_rows, obs.n_cols); //m,n
uvBackward(sp_trans, emission, obs.slice(k), beta, scales);
int countgrad = 0;
arma::vec grad_k(grad.n_elem, arma::fill::zeros);
// transitionMatrix
if (arma::accu(ANZ) > 0) {
for (unsigned int jj = 0; jj < numberOfStates.n_elem; jj++) {
arma::vec gradArow(numberOfStates(jj));
arma::mat gradA(numberOfStates(jj), numberOfStates(jj));
int ind_jj = cumsumstate(jj) - numberOfStates(jj);
for (unsigned int i = 0; i < numberOfStates(jj); i++) {
arma::uvec ind = arma::find(ANZ.row(ind_jj + i).subvec(ind_jj, cumsumstate(jj) - 1));
if (ind.n_elem > 0) {
gradArow.zeros();
gradA.eye();
gradA.each_row() -= transition.row(ind_jj + i).subvec(ind_jj, cumsumstate(jj) - 1);
gradA.each_col() %= transition.row(ind_jj + i).subvec(ind_jj, cumsumstate(jj) - 1).t();
for (unsigned int j = 0; j < numberOfStates(jj); j++) {
for (unsigned int t = 0; t < (obs.n_cols - 1); t++) {
double tmp = alpha(ind_jj + i, t);
for (unsigned int r = 0; r < obs.n_rows; r++) {
tmp *= emission(ind_jj + j, obs(r, t + 1, k), r);
}
gradArow(j) += tmp * beta(ind_jj + j, t + 1);
}
}
gradArow = gradA * gradArow;
grad_k.subvec(countgrad, countgrad + ind.n_elem - 1) = gradArow.rows(ind);
countgrad += ind.n_elem;
}
}
}
}
if (arma::accu(BNZ) > 0) {
// emissionMatrix
for (unsigned int r = 0; r < obs.n_rows; r++) {
arma::vec gradBrow(nSymbols(r));
arma::mat gradB(nSymbols(r), nSymbols(r));
for (unsigned int i = 0; i < emission.n_rows; i++) {
arma::uvec ind = arma::find(BNZ.slice(r).row(i));
if (ind.n_elem > 0) {
gradBrow.zeros();
gradB.eye();
gradB.each_row() -= emission.slice(r).row(i).subvec(0, nSymbols(r) - 1);
gradB.each_col() %= emission.slice(r).row(i).subvec(0, nSymbols(r) - 1).t();
for (unsigned int j = 0; j < nSymbols(r); j++) {
if (obs(r, 0, k) == j) {
double tmp = initk(i, k);
for (unsigned int r2 = 0; r2 < obs.n_rows; r2++) {
if (r2 != r) {
tmp *= emission(i, obs(r2, 0, k), r2);
}
}
gradBrow(j) += tmp * beta(i, 0);
}
for (unsigned int t = 0; t < (obs.n_cols - 1); t++) {
if (obs(r, t + 1, k) == j) {
double tmp = beta(i, t + 1);
for (unsigned int r2 = 0; r2 < obs.n_rows; r2++) {
if (r2 != r) {
tmp *= emission(i, obs(r2, t + 1, k), r2);
}
}
gradBrow(j) += arma::dot(alpha.col(t), transition.col(i)) * tmp;
}
}
}
gradBrow = gradB * gradBrow;
grad_k.subvec(countgrad, countgrad + ind.n_elem - 1) = gradBrow.rows(ind);
countgrad += ind.n_elem;
}
}
}
}
if (arma::accu(INZ) > 0) {
for (unsigned int i = 0; i < numberOfStates.n_elem; i++) {
int ind_i = cumsumstate(i) - numberOfStates(i);
arma::uvec ind = arma::find(
INZ.subvec(ind_i, cumsumstate(i) - 1));
if (ind.n_elem > 0) {
arma::vec gradIrow(numberOfStates(i), arma::fill::zeros);
for (unsigned int j = 0; j < numberOfStates(i); j++) {
double tmp = weights(i, k);
for (unsigned int r = 0; r < obs.n_rows; r++) {
tmp *= emission(ind_i + j, obs(r, 0, k), r);
}
gradIrow(j) += tmp * beta(ind_i + j, 0);
}
arma::mat gradI(numberOfStates(i), numberOfStates(i), arma::fill::zeros);
gradI.eye();
gradI.each_row() -= init.subvec(ind_i, cumsumstate(i) - 1).t();
gradI.each_col() %= init.subvec(ind_i, cumsumstate(i) - 1);
gradIrow = gradI * gradIrow;
grad_k.subvec(countgrad, countgrad + ind.n_elem - 1) = gradIrow.rows(ind);
countgrad += ind.n_elem;
}
}
}
for (unsigned int jj = 1; jj < numberOfStates.n_elem; jj++) {
unsigned int ind_jj = (cumsumstate(jj) - numberOfStates(jj));
for (unsigned int j = 0; j < emission.n_rows; j++) {
double tmp = 1.0;
for (unsigned int r = 0; r < obs.n_rows; r++) {
tmp *= emission(j, obs(r, 0, k), r);
}
if ((j >= ind_jj) & (j < cumsumstate(jj))) {
grad_k.subvec(countgrad + q * (jj - 1), countgrad + q * jj - 1) += tmp
* beta(j, 0) * initk(j, k) * X.row(k).t() * (1.0 - weights(jj, k));
} else {
grad_k.subvec(countgrad + q * (jj - 1), countgrad + q * jj - 1) -= tmp
* beta(j, 0) * initk(j, k) * X.row(k).t() * weights(jj, k);
}
}
}
if (!scales.is_finite() || !beta.is_finite()) {
#pragma omp atomic
error++;
} else {
ll -= arma::sum(log(scales));
#pragma omp critical
grad += grad_k;
}
}
}
if(error > 0){
ll = -arma::datum::inf;
grad.fill(-arma::datum::inf);
}
return List::create(Named("objective") = -ll, Named("gradient") = wrap(-grad));
}
// [[Rcpp::export]]
Rcpp::List objective(const arma::mat& transition, const arma::cube& emission,
const arma::vec& init, arma::ucube& obs, const arma::umat& ANZ,
const arma::ucube& BNZ, const arma::uvec& INZ, const arma::uvec& nSymbols, unsigned int threads) {
arma::vec grad(arma::accu(ANZ) + arma::accu(BNZ) + arma::accu(INZ), arma::fill::zeros);
unsigned int error = 0;
double ll = 0;
#pragma omp parallel for if(obs.n_slices >= threads) schedule(static) reduction(+:ll) num_threads(threads) \
default(shared) //shared(grad, nSymbols, ANZ, BNZ, INZ, obs, init, transition, emission, error, arma::fill::zeros)
for (unsigned int k = 0; k < obs.n_slices; k++) {
if (error == 0) {
arma::mat alpha(emission.n_rows, obs.n_cols); //m,n
arma::vec scales(obs.n_cols); //n
arma::sp_mat sp_trans(transition);
uvForward(sp_trans.t(), emission, init, obs.slice(k), alpha, scales);
arma::mat beta(emission.n_rows, obs.n_cols); //m,n
uvBackward(sp_trans, emission, obs.slice(k), beta, scales);
int countgrad = 0;
arma::vec grad_k(grad.n_elem, arma::fill::zeros);
// transitionMatrix
arma::vec gradArow(emission.n_rows);
arma::mat gradA(emission.n_rows, emission.n_rows);
for (unsigned int i = 0; i < emission.n_rows; i++) {
arma::uvec ind = arma::find(ANZ.row(i));
if (ind.n_elem > 0) {
gradArow.zeros();
gradA.eye();
gradA.each_row() -= transition.row(i);
gradA.each_col() %= transition.row(i).t();
for (unsigned int t = 0; t < (obs.n_cols - 1); t++) {
for (unsigned int j = 0; j < emission.n_rows; j++) {
double tmp = 1.0;
for (unsigned int r = 0; r < obs.n_rows; r++) {
tmp *= emission(j, obs(r, t + 1, k), r);
}
gradArow(j) += alpha(i, t) * tmp * beta(j, t + 1);
}
}
gradArow = gradA * gradArow;
grad_k.subvec(countgrad, countgrad + ind.n_elem - 1) = gradArow.rows(ind);
countgrad += ind.n_elem;
}
}
// emissionMatrix
for (unsigned int r = 0; r < obs.n_rows; r++) {
arma::vec gradBrow(nSymbols(r));
arma::mat gradB(nSymbols(r), nSymbols(r));
for (unsigned int i = 0; i < emission.n_rows; i++) {
arma::uvec ind = arma::find(BNZ.slice(r).row(i));
if (ind.n_elem > 0) {
gradBrow.zeros();
gradB.eye();
gradB.each_row() -= emission.slice(r).row(i).subvec(0, nSymbols(r) - 1);
gradB.each_col() %= emission.slice(r).row(i).subvec(0, nSymbols(r) - 1).t();
for (unsigned int j = 0; j < nSymbols(r); j++) {
if (obs(r, 0, k) == j) {
double tmp = 1.0;
for (unsigned int r2 = 0; r2 < obs.n_rows; r2++) {
if (r2 != r) {
tmp *= emission(i, obs(r2, 0, k), r2);
}
}
gradBrow(j) += init(i) * tmp * beta(i, 0);
}
for (unsigned int t = 0; t < (obs.n_cols - 1); t++) {
if (obs(r, t + 1, k) == j) {
double tmp = 1.0;
for (unsigned int r2 = 0; r2 < obs.n_rows; r2++) {
if (r2 != r) {
tmp *= emission(i, obs(r2, t + 1, k), r2);
}
}
gradBrow(j) += arma::dot(alpha.col(t), transition.col(i)) * tmp
* beta(i, t + 1);
}
}
}
gradBrow = gradB * gradBrow;
grad_k.subvec(countgrad, countgrad + ind.n_elem - 1) = gradBrow.rows(ind);
countgrad += ind.n_elem;
}
}
}
// InitProbs
arma::uvec ind = arma::find(INZ);
if (ind.n_elem > 0) {
arma::vec gradIrow(emission.n_rows);
arma::mat gradI(emission.n_rows, emission.n_rows);
gradIrow.zeros();
gradI.zeros();
gradI.eye();
gradI.each_row() -= init.t();
gradI.each_col() %= init;
for (unsigned int j = 0; j < emission.n_rows; j++) {
double tmp = 1.0;
for (unsigned int r = 0; r < obs.n_rows; r++) {
tmp *= emission(j, obs(r, 0, k), r);
}
gradIrow(j) += tmp * beta(j, 0);
}
gradIrow = gradI * gradIrow;
grad_k.subvec(countgrad, countgrad + ind.n_elem - 1) = gradIrow.rows(ind);
countgrad += ind.n_elem;
}
if (!scales.is_finite() || !beta.is_finite()) {
#pragma omp atomic
error++;
} else {
ll -= arma::sum(log(scales));
#pragma omp critical
grad += grad_k;
// gradmat.col(k) = grad_k;
}
// for (unsigned int ii = 0; ii < grad_k.n_elem; ii++) {
// #pragma omp atomic
// grad(ii) += grad_k(ii);
// }
}
}
if(error > 0){
ll = -arma::datum::inf;
grad.fill(-arma::datum::inf);
}
// } else {
// grad = sum(gradmat, 1);
// }
return Rcpp::List::create(Rcpp::Named("objective") = -ll, Rcpp::Named("gradient") = Rcpp::wrap(-grad));
}