int IPFP::runGEMA( ){
//Apply GEMA extensions of Iterative Proportional Fitting Procedure
int iter = 0;
targets_modified = false;
IPFP ipfp_copy(*this);
double diff = computeBeliefs();
std::vector<Message> desired_marginals, actual_marginals;
std::vector<Message> gema_marginals(cfg->dv_spectrum_depths.size());
computeMarginals( actual_marginals );
setDesiredMarginals( desired_marginals, actual_marginals );
while( !checkConvergence(false) && iter < MAX_IPFP_ITERATIONS ){
iter++;
//Re-initialise the GEMA target marginals
for( unsigned int idx = 0; idx < cfg->dv_spectrum_depths.size(); idx++ )
gema_marginals[idx].reset(actual_marginals[idx].size());
//Update the GEMA target marginals
for( unsigned int idx = 0; idx < cfg->dv_spectrum_depths.size(); idx++ ){
ipfp_copy = *this; //Create a copy of the IPFP instance so we don't change this one
std::vector<Message> tmp_marginals( actual_marginals );
ipfp_copy.applyIPFPstep( tmp_marginals, desired_marginals, idx );
for( unsigned int j = 0; j < cfg->dv_spectrum_depths.size(); j++ )
gema_marginals[j].addWeightedMessage(tmp_marginals[j], cfg->dv_spectrum_weights[idx]);
}
//Run standard IPFP for number of spectra iterations
for( unsigned int idx = 0; idx < cfg->dv_spectrum_depths.size(); idx++ )
applyIPFPstep( actual_marginals, gema_marginals, idx );
}
return iter;
}
void solve(Operator& opA, Vector& x, Vector& b, Comm& comm) const
{
Dune::InverseOperatorResult result;
// Parallel version is deactivated until we figure out how to do it properly.
#if HAVE_MPI
if (parallelInformation_.type() == typeid(ParallelISTLInformation))
{
const size_t size = opA.getmat().N();
const ParallelISTLInformation& info =
boost::any_cast<const ParallelISTLInformation&>( parallelInformation_);
// As we use a dune-istl with block size np the number of components
// per parallel is only one.
info.copyValuesTo(comm.indexSet(), comm.remoteIndices(),
size, 1);
// Construct operator, scalar product and vectors needed.
constructPreconditionerAndSolve<Dune::SolverCategory::overlapping>(opA, x, b, comm, result);
}
else
#endif
{
OPM_THROW(std::logic_error,"this method if for parallel solve only");
}
checkConvergence( result );
}
void solve(Operator& opA, Vector& x, Vector& b ) const
{
Dune::InverseOperatorResult result;
// Construct operator, scalar product and vectors needed.
Dune::Amg::SequentialInformation info;
constructPreconditionerAndSolve(opA, x, b, info, result);
checkConvergence( result );
}
void dd::ExpMax::maximization(const int &n_epoch, const int &n_sample_per_epoch, const double &stepsize,
const double &decay, const double reg_param, const double reg1_param, const bool is_quiet) {
//const double &decay, const double reg_param, const double reg1_param, const std::string meta_file, const bool is_quiet) {
//this->gibbs->learn(n_epoch, n_sample_per_epoch, stepsize,decay, reg_param, reg1_param, meta_file, is_quiet);
this->gibbs->learn(n_epoch, n_sample_per_epoch, stepsize,decay, reg_param, reg1_param, is_quiet);
resetEvidence();
iterationCount++;
if (check_convergence)
checkConvergence();
}
/// Ops to be performed after
/// an iteration
void IterativeSolverJacobi::postIterate()
{
// now, our current guess is updated to be
// what the iterating over rows above produced
*xGuess = *xNext ;
// Check if the solution
// is converging or diverging
checkConvergence() ;
if( solutionState == IsDiverging )
warning( "Solution actually diverging, iteration=%d, norm2=%f", iteration, norm2 ) ;
}
int IPFP::runIPFP( ){
//Apply Iterative Proportional Fitting Procedure
int iter = 0;
targets_modified = false;
double diff = computeBeliefs();
std::vector<Message> desired_marginals, actual_marginals;
computeMarginals( actual_marginals );
setDesiredMarginals( desired_marginals, actual_marginals );
while( !checkConvergence(false) && iter < MAX_IPFP_ITERATIONS ){
iter++;
for( unsigned int idx = 0; idx < cfg->dv_spectrum_depths.size(); idx++ )
applyIPFPstep( actual_marginals, desired_marginals, idx );
}
return iter;
}
/* ************************************************************************* */
void NonlinearOptimizer::defaultOptimize() {
const NonlinearOptimizerParams& params = this->_params();
double currentError = this->error();
// check if we're already close enough
if(currentError <= params.errorTol) {
if (params.verbosity >= NonlinearOptimizerParams::ERROR)
cout << "Exiting, as error = " << currentError << " < " << params.errorTol << endl;
return;
}
// Maybe show output
if (params.verbosity >= NonlinearOptimizerParams::VALUES) this->values().print("Initial values");
if (params.verbosity >= NonlinearOptimizerParams::ERROR) cout << "Initial error: " << currentError << endl;
// Return if we already have too many iterations
if(this->iterations() >= params.maxIterations)
return;
// Iterative loop
do {
// Do next iteration
currentError = this->error();
this->iterate();
// Maybe show output
if(params.verbosity >= NonlinearOptimizerParams::VALUES) this->values().print("newValues");
if(params.verbosity >= NonlinearOptimizerParams::ERROR) cout << "newError: " << this->error() << endl;
} while(this->iterations() < params.maxIterations &&
!checkConvergence(params.relativeErrorTol, params.absoluteErrorTol,
params.errorTol, currentError, this->error(), params.verbosity));
// Printing if verbose
if (params.verbosity >= NonlinearOptimizerParams::ERROR &&
this->iterations() >= params.maxIterations)
cout << "Terminating because reached maximum iterations" << endl;
}
// Coordinate descent for binomial models
SEXP cdfit_binomial(SEXP X_, SEXP y_, SEXP penalty_, SEXP lambda, SEXP eps_, SEXP max_iter_, SEXP gamma_, SEXP multiplier, SEXP alpha_, SEXP dfmax_, SEXP user_, SEXP warn_) {
// Declarations
int n = length(y_);
int p = length(X_)/n;
int L = length(lambda);
SEXP res, beta0, beta, Dev, iter;
PROTECT(beta0 = allocVector(REALSXP, L));
double *b0 = REAL(beta0);
for (int i=0; i<L; i++) b0[i] = 0;
PROTECT(beta = allocVector(REALSXP, L*p));
double *b = REAL(beta);
for (int j=0; j<(L*p); j++) b[j] = 0;
PROTECT(Dev = allocVector(REALSXP, L));
PROTECT(iter = allocVector(INTSXP, L));
for (int i=0; i<L; i++) INTEGER(iter)[i] = 0;
double *a = Calloc(p, double); // Beta from previous iteration
for (int j=0; j<p; j++) a[j] = 0;
double a0 = 0; // Beta0 from previous iteration
double *X = REAL(X_);
double *y = REAL(y_);
const char *penalty = CHAR(STRING_ELT(penalty_, 0));
double *lam = REAL(lambda);
double eps = REAL(eps_)[0];
int max_iter = INTEGER(max_iter_)[0];
double gamma = REAL(gamma_)[0];
double *m = REAL(multiplier);
double alpha = REAL(alpha_)[0];
int dfmax = INTEGER(dfmax_)[0];
int user = INTEGER(user_)[0];
int warn = INTEGER(warn_)[0];
double *r = Calloc(n, double);
double *w = Calloc(n, double);
double *s = Calloc(n, double);
double *z = Calloc(p, double);
double *eta = Calloc(n, double);
int *e1 = Calloc(p, int);
for (int j=0; j<p; j++) e1[j] = 0;
int *e2 = Calloc(p, int);
for (int j=0; j<p; j++) e2[j] = 0;
double xwr, xwx, pi, u, v, cutoff, l1, l2, shift, si;
int converged, lstart;
// Initialization
double ybar = sum(y, n)/n;
a0 = b0[0] = log(ybar/(1-ybar));
double nullDev = 0;
for (int i=0;i<n;i++) nullDev = nullDev - y[i]*log(ybar) - (1-y[i])*log(1-ybar);
for (int i=0; i<n; i++) s[i] = y[i] - ybar;
for (int i=0; i<n; i++) eta[i] = a0;
for (int j=0; j<p; j++) z[j] = crossprod(X, s, n, j)/n;
// If lam[0]=lam_max, skip lam[0] -- closed form sol'n available
if (user) {
lstart = 0;
} else {
lstart = 1;
REAL(Dev)[0] = nullDev;
}
// Path
for (int l=lstart; l<L; l++) {
if (l != 0) {
// Assign a, a0
a0 = b0[l-1];
for (int j=0; j<p; j++) a[j] = b[(l-1)*p+j];
// Check dfmax
int nv = 0;
for (int j=0; j<p; j++) {
if (a[j] != 0) nv++;
}
if (nv > dfmax) {
for (int ll=l; ll<L; ll++) INTEGER(iter)[ll] = NA_INTEGER;
res = cleanupB(s, w, a, r, e1, e2, z, eta, beta0, beta, Dev, iter);
return(res);
}
// Determine eligible set
if (strcmp(penalty, "lasso")==0) cutoff = 2*lam[l] - lam[l-1];
if (strcmp(penalty, "MCP")==0) cutoff = lam[l] + gamma/(gamma-1)*(lam[l] - lam[l-1]);
if (strcmp(penalty, "SCAD")==0) cutoff = lam[l] + gamma/(gamma-2)*(lam[l] - lam[l-1]);
for (int j=0; j<p; j++) if (fabs(z[j]) > (cutoff * alpha * m[j])) e2[j] = 1;
} else {
// Determine eligible set
double lmax = 0;
for (int j=0; j<p; j++) if (fabs(z[j]) > lmax) lmax = fabs(z[j]);
if (strcmp(penalty, "lasso")==0) cutoff = 2*lam[l] - lmax;
if (strcmp(penalty, "MCP")==0) cutoff = lam[l] + gamma/(gamma-1)*(lam[l] - lmax);
if (strcmp(penalty, "SCAD")==0) cutoff = lam[l] + gamma/(gamma-2)*(lam[l] - lmax);
for (int j=0; j<p; j++) if (fabs(z[j]) > (cutoff * alpha * m[j])) e2[j] = 1;
}
while (INTEGER(iter)[l] < max_iter) {
while (INTEGER(iter)[l] < max_iter) {
while (INTEGER(iter)[l] < max_iter) {
INTEGER(iter)[l]++;
REAL(Dev)[l] = 0;
for (int i=0;i<n;i++) {
if (eta[i] > 10) {
pi = 1;
w[i] = .0001;
} else if (eta[i] < -10) {
pi = 0;
w[i] = .0001;
} else {
pi = exp(eta[i])/(1+exp(eta[i]));
w[i] = pi*(1-pi);
}
s[i] = y[i] - pi;
r[i] = s[i]/w[i];
if (y[i]==1) REAL(Dev)[l] = REAL(Dev)[l] - log(pi);
if (y[i]==0) REAL(Dev)[l] = REAL(Dev)[l] - log(1-pi);
}
if (REAL(Dev)[l]/nullDev < .01) {
if (warn) warning("Model saturated; exiting...");
for (int ll=l; ll<L; ll++) INTEGER(iter)[ll] = NA_INTEGER;
res = cleanupB(s, w, a, r, e1, e2, z, eta, beta0, beta, Dev, iter);
return(res);
}
// Intercept
xwr = crossprod(w, r, n, 0);
xwx = sum(w, n);
b0[l] = xwr/xwx + a0;
for (int i=0; i<n; i++) {
si = b0[l] - a0;
r[i] -= si;
eta[i] += si;
}
// Covariates
for (int j=0; j<p; j++) {
if (e1[j]) {
// Calculate u, v
xwr = wcrossprod(X, r, w, n, j);
xwx = wsqsum(X, w, n, j);
u = xwr/n + (xwx/n)*a[j];
v = xwx/n;
// Update b_j
l1 = lam[l] * m[j] * alpha;
l2 = lam[l] * m[j] * (1-alpha);
if (strcmp(penalty,"MCP")==0) b[l*p+j] = MCP(u, l1, l2, gamma, v);
if (strcmp(penalty,"SCAD")==0) b[l*p+j] = SCAD(u, l1, l2, gamma, v);
if (strcmp(penalty,"lasso")==0) b[l*p+j] = lasso(u, l1, l2, v);
// Update r
shift = b[l*p+j] - a[j];
if (shift !=0) {
/* for (int i=0;i<n;i++) r[i] -= shift*X[j*n+i]; */
/* for (int i=0;i<n;i++) eta[i] += shift*X[j*n+i]; */
for (int i=0;i<n;i++) {
si = shift*X[j*n+i];
r[i] -= si;
eta[i] += si;
}
}
}
}
// Check for convergence
converged = checkConvergence(b, a, eps, l, p);
a0 = b0[l];
for (int j=0; j<p; j++) a[j] = b[l*p+j];
if (converged) break;
}
// Scan for violations in strong set
int violations = 0;
for (int j=0; j<p; j++) {
if (e1[j]==0 & e2[j]==1) {
z[j] = crossprod(X, s, n, j)/n;
l1 = lam[l] * m[j] * alpha;
if (fabs(z[j]) > l1) {
e1[j] = e2[j] = 1;
violations++;
}
}
}
if (violations==0) break;
}
// Scan for violations in rest
int violations = 0;
for (int j=0; j<p; j++) {
if (e2[j]==0) {
z[j] = crossprod(X, s, n, j)/n;
l1 = lam[l] * m[j] * alpha;
if (fabs(z[j]) > l1) {
e1[j] = e2[j] = 1;
violations++;
}
}
}
if (violations==0) break;
}
}
res = cleanupB(s, w, a, r, e1, e2, z, eta, beta0, beta, Dev, iter);
return(res);
}
int nasolver<nr_type_t>::solve_nonlinear (void)
{
qucs::exception * e;
int convergence, run = 0, MaxIterations, error = 0;
// fetch simulation properties
MaxIterations = getPropertyInteger ("MaxIter");
reltol = getPropertyDouble ("reltol");
abstol = getPropertyDouble ("abstol");
vntol = getPropertyDouble ("vntol");
updateMatrix = 1;
if (convHelper == CONV_GMinStepping)
{
// use the alternative non-linear solver solve_nonlinear_continuation_gMin
// instead of the basic solver provided by this function
iterations = 0;
error = solve_nonlinear_continuation_gMin ();
return error;
}
else if (convHelper == CONV_SourceStepping)
{
// use the alternative non-linear solver solve_nonlinear_continuation_Source
// instead of the basic solver provided by this function
iterations = 0;
error = solve_nonlinear_continuation_Source ();
return error;
}
// run solving loop until convergence is reached
do
{
error = solve_once ();
if (!error)
{
// convergence check
convergence = (run > 0) ? checkConvergence () : 0;
savePreviousIteration ();
run++;
// control fixpoint iterations
if (fixpoint)
{
if (convergence && !updateMatrix)
{
updateMatrix = 1;
convergence = 0;
}
else
{
updateMatrix = 0;
}
}
}
else
{
break;
}
}
while (!convergence &&
run < MaxIterations * (1 + convHelper ? 1 : 0));
if (run >= MaxIterations || error)
{
e = new qucs::exception (EXCEPTION_NO_CONVERGENCE);
e->setText ("no convergence in %s analysis after %d iterations",
desc.c_str(), run);
throw_exception (e);
error++;
}
iterations = run;
return error;
}
int nasolver<nr_type_t>::solve_nonlinear_continuation_Source (void)
{
qucs::exception * e;
int convergence, run = 0, MaxIterations, error = 0;
nr_double_t sStep, sPrev;
// fetch simulation properties
MaxIterations = getPropertyInteger ("MaxIter") / 4 + 1;
updateMatrix = 1;
fixpoint = 0;
// initialize the stepper
sPrev = srcFactor = 0;
sStep = 0.01;
srcFactor += sStep;
do
{
// run solving loop until convergence is reached
run = 0;
do
{
subnet->setSrcFactor (srcFactor);
error = solve_once ();
if (!error)
{
// convergence check
convergence = (run > 0) ? checkConvergence () : 0;
savePreviousIteration ();
run++;
}
else break;
}
while (!convergence && run < MaxIterations);
iterations += run;
// not yet converged, so decreased the source-step
if (run >= MaxIterations || error)
{
if (error)
sStep *= 0.1;
else
sStep *= 0.5;
restorePreviousIteration ();
saveSolution ();
// here the absolute minimum step checker
if (sStep < std::numeric_limits<nr_double_t>::epsilon())
{
error = 1;
e = new qucs::exception (EXCEPTION_NO_CONVERGENCE);
e->setText ("no convergence in %s analysis after %d sourceStepping "
"iterations", desc.c_str(), iterations);
throw_exception (e);
break;
}
srcFactor = std::min (sPrev + sStep, 1.0);
}
// converged, increased the source-step
else if (run < MaxIterations / 4)
{
sPrev = srcFactor;
srcFactor = std::min (srcFactor + sStep, 1.0);
sStep *= 1.5;
}
else
{
srcFactor = std::min (srcFactor + sStep, 1.0);
}
}
// continue until no source factor is necessary
while (sPrev < 1);
subnet->setSrcFactor (1);
return error;
}
int nasolver<nr_type_t>::solve_nonlinear_continuation_gMin (void)
{
qucs::exception * e;
int convergence, run = 0, MaxIterations, error = 0;
nr_double_t gStep, gPrev;
// fetch simulation properties
MaxIterations = getPropertyInteger ("MaxIter") / 4 + 1;
updateMatrix = 1;
fixpoint = 0;
// initialize the stepper
gPrev = gMin = 0.01;
gStep = gMin / 100;
gMin -= gStep;
do
{
// run solving loop until convergence is reached
run = 0;
do
{
error = solve_once ();
if (!error)
{
// convergence check
convergence = (run > 0) ? checkConvergence () : 0;
savePreviousIteration ();
run++;
}
else break;
}
while (!convergence && run < MaxIterations);
iterations += run;
// not yet converged, so decreased the gMin-step
if (run >= MaxIterations || error)
{
gStep /= 2;
// here the absolute minimum step checker
if (gStep < std::numeric_limits<nr_double_t>::epsilon())
{
error = 1;
e = new qucs::exception (EXCEPTION_NO_CONVERGENCE);
e->setText ("no convergence in %s analysis after %d gMinStepping "
"iterations", desc.c_str(), iterations);
throw_exception (e);
break;
}
gMin = MAX (gPrev - gStep, 0);
}
// converged, increased the gMin-step
else
{
gPrev = gMin;
gMin = MAX (gMin - gStep, 0);
gStep *= 2;
}
}
// continue until no additional resistances is necessary
while (gPrev > 0);
return error;
}
SEXP gdfit_gaussian(SEXP X_, SEXP y_, SEXP penalty_, SEXP K1_, SEXP K0_, SEXP lambda, SEXP alpha_, SEXP eps_, SEXP max_iter_, SEXP gamma_, SEXP group_multiplier, SEXP dfmax_, SEXP gmax_, SEXP user_) {
// Lengths/dimensions
int n = length(y_);
int L = length(lambda);
int J = length(K1_) - 1;
int p = length(X_)/n;
// Pointers
double *X = REAL(X_);
double *y = REAL(y_);
const char *penalty = CHAR(STRING_ELT(penalty_, 0));
int *K1 = INTEGER(K1_);
int K0 = INTEGER(K0_)[0];
double *lam = REAL(lambda);
double alpha = REAL(alpha_)[0];
double eps = REAL(eps_)[0];
int max_iter = INTEGER(max_iter_)[0];
double gamma = REAL(gamma_)[0];
double *m = REAL(group_multiplier);
int dfmax = INTEGER(dfmax_)[0];
int gmax = INTEGER(gmax_)[0];
int user = INTEGER(user_)[0];
// Outcome
SEXP res, beta, iter, df, loss;
PROTECT(beta = allocVector(REALSXP, L*p));
for (int j=0; j<(L*p); j++) REAL(beta)[j] = 0;
PROTECT(iter = allocVector(INTSXP, L));
for (int i=0; i<L; i++) INTEGER(iter)[i] = 0;
PROTECT(df = allocVector(REALSXP, L));
for (int i=0; i<L; i++) REAL(df)[i] = 0;
PROTECT(loss = allocVector(REALSXP, L));
for (int i=0; i<L; i++) REAL(loss)[i] = 0;
double *b = REAL(beta);
// Intermediate quantities
double *r = Calloc(n, double);
for (int i=0; i<n; i++) r[i] = y[i];
double *a = Calloc(p, double);
for (int j=0; j<p; j++) a[j] = 0;
int *e = Calloc(J, int);
for (int g=0; g<J; g++) e[g] = 0;
int converged, lstart, ng, nv, violations;
double shift, l1, l2;
// If lam[0]=lam_max, skip lam[0] -- closed form sol'n available
if (user) {
lstart = 0;
} else {
REAL(loss)[0] = gLoss(r,n);
lstart = 1;
}
// Path
for (int l=lstart; l<L; l++) {
R_CheckUserInterrupt();
if (l != 0) {
for (int j=0; j<p; j++) a[j] = b[(l-1)*p+j];
// Check dfmax, gmax
ng = 0;
nv = 0;
for (int g=0; g<J; g++) {
if (a[K1[g]] != 0) {
ng++;
nv = nv + (K1[g+1]-K1[g]);
}
}
if (ng > gmax | nv > dfmax) {
for (int ll=l; ll<L; ll++) INTEGER(iter)[ll] = NA_INTEGER;
res = cleanupG(a, r, e, beta, iter, df, loss);
return(res);
}
}
while (INTEGER(iter)[l] < max_iter) {
while (INTEGER(iter)[l] < max_iter) {
converged = 0;
INTEGER(iter)[l]++;
REAL(df)[l] = 0;
// Update unpenalized covariates
for (int j=0; j<K0; j++) {
shift = crossprod(X, r, n, j)/n;
b[l*p+j] = shift + a[j];
for (int i=0; i<n; i++) r[i] -= shift * X[n*j+i];
REAL(df)[l] += 1;
}
// Update penalized groups
for (int g=0; g<J; g++) {
l1 = lam[l] * m[g] * alpha;
l2 = lam[l] * m[g] * (1-alpha);
if (e[g]) gd_gaussian(b, X, r, g, K1, n, l, p, penalty, l1, l2, gamma, df, a);
}
// Check convergence
if (checkConvergence(b, a, eps, l, p)) {
converged = 1;
REAL(loss)[l] = gLoss(r,n);
break;
}
for (int j=0; j<p; j++) a[j] = b[l*p+j];
}
// Scan for violations
violations = 0;
for (int g=0; g<J; g++) {
if (e[g]==0) {
l1 = lam[l] * m[g] * alpha;
l2 = lam[l] * m[g] * (1-alpha);
gd_gaussian(b, X, r, g, K1, n, l, p, penalty, l1, l2, gamma, df, a);
if (b[l*p+K1[g]] != 0) {
e[g] = 1;
violations++;
}
}
}
if (violations==0) {
REAL(loss)[l] = gLoss(r, n);
break;
}
for (int j=0; j<p; j++) a[j] = b[l*p+j];
}
}
res = cleanupG(a, r, e, beta, iter, df, loss);
return(res);
}
/**
* main function
* divided to two brances for master & slave processors respectively
* @param argc commandline argument count
* @param argv array of commandline arguments
* @return 0 if success
*/
int main(int argc, char* argv[])
{
int rank;
int size;
int num_clusters;
int num_points;
int dex;
int job_size;
int job_done=0;
Point* centroids;
Point* points;
Point* received_points;
int * slave_clusters;
int * former_clusters;
int * latter_clusters;
MPI_Init(&argc, &argv);
MPI_Status status;
MPI_Comm_rank(MPI_COMM_WORLD, &rank);
MPI_Comm_size(MPI_COMM_WORLD, &size);
//creation of derived MPI structure
MPI_Datatype MPI_POINT;
MPI_Datatype type=MPI_DOUBLE;
int blocklen=2;
MPI_Aint disp=0;
MPI_Type_create_struct(1,&blocklen,&disp,&type,&MPI_POINT);
MPI_Type_commit(&MPI_POINT);
/******** MASTER PROCESSOR WORKS HERE******************************************************/
if(rank==MASTER)
{
//inputting from file
FILE *input;
input=fopen(argv[1],"r");
readHeaders(input,&num_clusters,&num_points);
points=(Point*)malloc(sizeof(Point)*num_points);
readPoints(input,points,num_points);
fclose(input);
//other needed memory locations
former_clusters=(int*)malloc(sizeof(int)*num_points);
latter_clusters=(int*)malloc(sizeof(int)*num_points);
job_size=num_points/(size-1);
centroids=malloc(sizeof(Point)*num_clusters);
//reseting and initializing to default behaviour
initialize(centroids,num_clusters);
resetData(former_clusters,num_points);
resetData(latter_clusters,num_points);
//Sending the essential data to slave processors
for(dex=1;dex<size;dex++)
{
printf("Sending to [%d]\n",dex);
MPI_Send(&job_size ,1 , MPI_INT ,dex,0,MPI_COMM_WORLD);
MPI_Send(&num_clusters ,1 , MPI_INT ,dex,0,MPI_COMM_WORLD);
MPI_Send(centroids ,num_clusters, MPI_POINT ,dex,0,MPI_COMM_WORLD);
MPI_Send(points+(dex-1)*job_size,job_size , MPI_POINT ,dex,0,MPI_COMM_WORLD);
}
printf("Sent!\n");
MPI_Barrier(MPI_COMM_WORLD);
//Main job of master processor is done here
while(1)
{
MPI_Barrier(MPI_COMM_WORLD);
printf("Master Receiving\n");
for(dex=1;dex<size;dex++)
MPI_Recv(latter_clusters+(job_size*(dex-1)),job_size,MPI_INT,dex,0,MPI_COMM_WORLD,&status);
printf("Master Received\n");
calculateNewCentroids(points,latter_clusters,centroids,num_clusters,num_points);
printf("New Centroids are done!\n");
if(checkConvergence(latter_clusters,former_clusters,num_points)==0)
{
printf("Converged!\n");
job_done=1;
}
else
{
printf("Not converged!\n");
for(dex=0;dex<num_points;dex++)
former_clusters[dex]=latter_clusters[dex];
}
//Informing slaves that no more job to be done
for(dex=1;dex<size;dex++)
MPI_Send(&job_done,1, MPI_INT,dex,0,MPI_COMM_WORLD);
MPI_Barrier(MPI_COMM_WORLD);
if(job_done==1)
break;
//Sending the recently created centroids
for(dex=1;dex<size;dex++)
MPI_Send(centroids,num_clusters, MPI_POINT,dex,0, MPI_COMM_WORLD);
MPI_Barrier(MPI_COMM_WORLD);
}
//Outputting to the output file
FILE* output=fopen(argv[2],"w");
fprintf(output,"%d\n",num_clusters);
fprintf(output,"%d\n",num_points);
for(dex=0;dex<num_clusters;dex++)
fprintf(output,"%lf,%lf\n",centroids[dex]._x,centroids[dex]._y);
for(dex=0;dex<num_points;dex++)
fprintf(output,"%lf,%lf,%d\n",points[dex]._x,points[dex]._y,latter_clusters[dex]+1);
fclose(output);
}
/*************END OF MASTER PROCESSOR'S BRANCH -- SLAVE PROCESSORS' JOB IS TO FOLLOW ************************/
else
{
//Receiving the essential data
printf("Receiving\n");
MPI_Recv(&job_size ,1 ,MPI_INT ,MASTER,0,MPI_COMM_WORLD,&status);
MPI_Recv(&num_clusters,1 ,MPI_INT ,MASTER,0,MPI_COMM_WORLD,&status);
centroids=malloc(sizeof(Point)*num_clusters);
MPI_Recv(centroids ,num_clusters,MPI_POINT,MASTER,0,MPI_COMM_WORLD,&status);
printf("part_size =%d\n",job_size);
received_points=(Point*)malloc(sizeof(Point)*job_size);
slave_clusters=(int*)malloc(sizeof(int)*job_size);
MPI_Recv(received_points,job_size,MPI_POINT ,MASTER,0,MPI_COMM_WORLD,&status);
printf("Received [%d]\n",rank);
MPI_Barrier(MPI_COMM_WORLD);
while(1)
{
printf("Calculation of new clusters [%d]\n",rank);
for(dex=0;dex<job_size;dex++)
{
slave_clusters[dex]=whoIsYourDaddy(received_points[dex],centroids,num_clusters);
}
printf("sending to master [%d]\n",rank);
MPI_Send(slave_clusters,job_size, MPI_INT,MASTER, 0, MPI_COMM_WORLD);
MPI_Barrier(MPI_COMM_WORLD);
MPI_Barrier(MPI_COMM_WORLD);
MPI_Recv(&job_done,1, MPI_INT,MASTER,0,MPI_COMM_WORLD,&status);
if(job_done==1) //No more work to be done
break;
//Receiving recently created centroids from master
MPI_Recv(centroids,num_clusters,MPI_POINT,MASTER,0, MPI_COMM_WORLD,&status);
MPI_Barrier(MPI_COMM_WORLD);
}
}
//End of all
MPI_Finalize();
return 0;
}
int IPFP::runIPFPwithOscAdjust( ){
//Apply Iterative Proportional Fitting Procedure - detecting and adjusting for oscillatory convergence
int iter = 0;
int reverse = 0;
targets_modified = false;
//Store a copy of the initial msgs
std::vector<Message> init_down_msgs = down_msgs;
std::vector<Message> init_up_msgs = up_msgs;
//Initialise the target marginals
std::vector<Message> desired_marginals, actual_marginals, reverse_marginals;
initialiseFactorProbsAndBeliefs();
double diff = computeBeliefs();
computeMarginals( actual_marginals );
setDesiredMarginals( desired_marginals, actual_marginals );
int retries = 0;
while( (retries == 0 || status == OSC_CONVERGE) && retries <= MAX_IPFP_OSC_RETRIES ){
//Run IPFP to convergence (oscillatory or otherwise) in the forward direction
iter = 0;
while( !checkConvergence(true) && iter < MAX_IPFP_ITERATIONS ){
iter++;
//for( int idx = cfg->dv_spectrum_depths.size()-1; idx >= 0; idx-- ){
for( unsigned int idx = 0; idx < cfg->dv_spectrum_depths.size(); idx++ )
applyIPFPstep( actual_marginals, desired_marginals, idx );
}
if( status != OSC_CONVERGE ) break;
//Oscillatory Convergence detected:
// std::cout << "Oscillatory convergence - modifying targets for retry after " << iter << " iterations (" << retries << " retry)" << std::endl;
//Re-Initialise msgs and factor transition/persistence probabilities
down_msgs = init_down_msgs;
up_msgs = init_up_msgs;
initialiseFactorProbsAndBeliefs();
diff = computeBeliefs();
computeMarginals( reverse_marginals );
for( unsigned int i = 0; i < diff_buf.size(); i++){
diff_buf[i] = 100.0;
prev_diff_buf[i] = 1000.0;
}
//Run IPFP to convergence (oscillatory or otherwise) in the reverse direction
iter = 0;
while( !checkConvergence(true) && iter < MAX_IPFP_ITERATIONS ){
iter++;
for( int idx = cfg->dv_spectrum_depths.size()-1; idx >= 0; idx-- )
applyIPFPstep( reverse_marginals, desired_marginals, idx );
}
//Set the target marginals to the average of the forward and reverse marginals
desired_marginals = actual_marginals;
for( unsigned int j = 0; j < cfg->dv_spectrum_depths.size(); j++ )
desired_marginals[j].addWeightedMessage(reverse_marginals[j], 1.0);
targets_modified = true;
//Re-Initialise everything ready to go again
down_msgs = init_down_msgs;
up_msgs = init_up_msgs;
initialiseFactorProbsAndBeliefs();
diff = computeBeliefs();
computeMarginals( actual_marginals );
for( unsigned int i = 0; i < diff_buf.size(); i++){
diff_buf[i] = 100.0;
prev_diff_buf[i] = 1000.0;
}
retries++;
}
return iter;
}
static void cdfit(double *x, double *y, double *omega, double *init, double lambda,
double kappa, double theta, char *penalty, double eps,
int max, int inmax, int n, int p, int *iter)
{
double *beta_old, *beta, *w, *ww, *re;
double z, r = 0, s = 0;
int i, j, itetime = 0, flag = 1, itetime2 = 0, flag2 = 1;
beta = vector(p);
beta_old = vector(p);
w = vector(p); /* p dimensional vector for X'WX. */
re = vector(n);
ww = vector(n); /* n dimensional weight vector for diag(W). */
for (i = 0; i < p; i++)
{
beta_old[i] = init[i];
beta[i] = init[i];
}
for (i = 0; i < n; i++)
{
s = 0;
for (j = 0; j < p; j++)
s += x[i + j * n] * beta[j];
re[i] = y[i] - s; /* re is the r vector. */
}
/* This is the MM layer. */
while (flag && itetime <= max)
{
if (itetime > 0) for (i = 0; i < p; i++) beta_old[i] = beta[i];
fww(beta, theta, x, y, omega, n, p, ww);
for (j = 0; j < p; j++)
{
s = 0;
for (i = 0; i < n; i++)
s += x[i + j * n] * ww[i] * x[i + j * n];
w[j] = s;
}
/* This is one coordinate descent layer. */
itetime2 = 0;
flag2 = 1;
while (flag2 && itetime2 < inmax)
{
for (j = 0; j < p; j++)
{
r = 0;
for (i = 0; i < n; i++) r += x[i + j * n] * ww[i] * re[i];
if (strcmp(penalty, "MCP") == 0) z = fmcp(lambda, kappa, beta[j], w[j], r);
if (strcmp(penalty, "LASSO") == 0) z = flasso(lambda, beta[j], w[j], r);
if (fabs(beta[j] - z) > eps) {
for (i = 0; i < n; i++) re[i] += x[i + j * n] * (beta[j] - z);}
beta[j] = z;
}
itetime2++;
flag2 = !checkConvergence(beta, beta_old, eps, p);
}
itetime++;
flag = !checkConvergence(beta, beta_old, eps, p);
}
for (i = 0; i < p; i++) init[i] = beta[i];
iter[0] = itetime;
free_vector(beta);
free_vector(beta_old);
free_vector(w);
free_vector(ww);
free_vector(re);
}
bool NOX::LineSearch::Polynomial::compute(Abstract::Group& newGrp,
double& step,
const Abstract::Vector& dir,
const Solver::Generic& s)
{
printOpeningRemarks();
int nNonlinearIters = s.getNumIterations();
if (useCounter)
counter.incrementNumLineSearches();
// Get the linear solve tolerance if doing ared/pred for conv criteria
std::string direction = const_cast<Teuchos::ParameterList&>(s.getList()).
sublist("Direction").get("Method", "Newton");
double eta = (suffDecrCond == AredPred) ?
const_cast<Teuchos::ParameterList&>(s.getList()).
sublist("Direction").sublist(direction).sublist("Linear Solver").
get("Tolerance", -1.0) : 0.0;
// Computations with old group
const Abstract::Group& oldGrp = s.getPreviousSolutionGroup();
double oldPhi = meritFuncPtr->computef(oldGrp); // \phi(0)
double oldValue = computeValue(oldGrp, oldPhi);
double oldSlope = meritFuncPtr->computeSlope(dir, oldGrp);
// Computations with new group
step = defaultStep;
updateGrp(newGrp, oldGrp, dir, step);
double newPhi = meritFuncPtr->computef(newGrp);
double newValue = computeValue(newGrp, newPhi);
bool isConverged = false;
bool isFailed = false;
int nIters = 1;
if (oldSlope >= 0.0)
{
printBadSlopeWarning(oldSlope);
isFailed = true;
}
else
isConverged = checkConvergence(newValue, oldValue, oldSlope, step,
eta, nIters, nNonlinearIters);
// Increment the number of newton steps requiring a line search
if ((useCounter) && (!isConverged))
counter.incrementNumNonTrivialLineSearches();
double prevPhi = 0.0; // \phi(\lambda_{k-1})
double prevPrevPhi = 0.0; // \phi(\lambda_{k-2})
double prevStep = 0.0; // \lambda_{k-1}
double prevPrevStep = 0.0; // \lambda_{k-2}
while ((!isConverged) && (!isFailed))
{
print.printStep(nIters, step, oldValue, newValue,
"", (suffDecrCond != AredPred));
if (nIters > maxIters)
{
isFailed = true;
break;
}
if (interpolationType == Quadratic3)
{
/* 3-Point Quadratic Interpolation */
prevPrevPhi = prevPhi;
prevPhi = newPhi;
prevPrevStep = prevStep;
prevStep = step;
if (nIters == 1)
{
step = 0.5 * step;
}
else
{
double c1 = prevStep * prevStep * (prevPrevPhi - oldPhi) -
prevPrevStep * prevPrevStep * (prevPhi - oldPhi);
double c2 = prevPrevStep * (prevPhi - oldPhi) -
prevStep * (prevPrevPhi - oldPhi);
if (c1 < 0)
step = -0.5 * c1 / c2;
}
}
else if ((nIters == 1) || (interpolationType == Quadratic))
{
/* Quadratic Interpolation */
prevPhi = newPhi;
prevStep = step;
step = - (oldSlope * prevStep * prevStep) /
(2.0 * (prevPhi - oldPhi - prevStep * oldSlope)) ;
}
else
{
/* Cubic Interpolation */
prevPrevPhi = prevPhi;
prevPhi = newPhi;
prevPrevStep = prevStep;
prevStep = step;
double term1 = prevPhi - oldPhi - prevStep * oldSlope ;
double term2 = prevPrevPhi - oldPhi - prevPrevStep * oldSlope ;
double a = 1.0 / (prevStep - prevPrevStep) *
(term1 / (prevStep * prevStep) - term2 /
(prevPrevStep * prevPrevStep)) ;
double b = 1.0 / (prevStep - prevPrevStep) *
(-1.0 * term1 * prevPrevStep / (prevStep * prevStep) +
term2 * prevStep / (prevPrevStep * prevPrevStep)) ;
double disc = b * b - 3.0 * a * oldSlope;
if (disc < 0)
{
isFailed = true;
break;
}
if (b > 0.0) // Check to prevent round off error (H. Walker)
{
step = -oldSlope / (b + sqrt(disc));
}
else
{
if (fabs(a) < 1.e-12) // check for when a is small
{
step = -oldSlope / (2.0 * b);
}
else
{
step = (-b + sqrt(disc))/ (3.0 * a);
}
}
}
// Apply bounds
if (step < minBoundFactor * prevStep)
step = minBoundFactor * prevStep;
else if (step > maxBoundFactor * prevStep)
step = maxBoundFactor * prevStep;
// Check that step isn't too small
if (step < minStep)
{
isFailed = true;
break;
}
// Update the new group and compute new measures
updateGrp(newGrp, oldGrp, dir, step);
newPhi = meritFuncPtr->computef(newGrp);
newValue = computeValue(newGrp, newPhi);
nIters ++;
if (useCounter)
counter.incrementNumIterations();
isConverged = checkConvergence(newValue, oldValue, oldSlope, step,
eta, nIters, nNonlinearIters);
} // End while loop
if (isFailed)
{
if (useCounter)
counter.incrementNumFailedLineSearches();
if (recoveryStepType == Constant)
step = recoveryStep;
if (step == 0.0)
{
newGrp = oldGrp;
newPhi = oldPhi;
newValue = oldValue;
}
else
{
updateGrp(newGrp, oldGrp, dir, step);
newPhi = meritFuncPtr->computef(newGrp);
newValue = computeValue(newGrp, newPhi);
}
}
std::string message = (isFailed) ? "(USING RECOVERY STEP!)" : "(STEP ACCEPTED!)";
print.printStep(nIters, step, oldValue, newValue, message, (suffDecrCond != AredPred));
paramsPtr->set("Adjusted Tolerance", 1.0 - step * (1.0 - eta));
if (useCounter)
counter.setValues(*paramsPtr);
return (!isFailed);
}
Mahalanobis InfTheoMetricLearner::learnMetric() {
computeConstraints();
int dim = getVectorDim();
Mahalanobis metric = getMetric();
metric.setM(M0);
int simConCount = simConstraints.getConstraintCount();
int disSimConCount = disSimConstraints.getConstraintCount();
vec x1;
vec x2;
double slack = 0.0;
double lambda = 0.0;
InfTheoConstraints* currentConstSet = NULL;
int currentIdx = 0;
int currentSimIdx = 0;
int currentDisSimIdx = 0;
double p = 0.0;
double delta = 0.0;
double alpha = 0.0;
double beta = 0.0;
int i = 0;
for(i = 0; !checkConvergence(metric.getM()) && (simConCount || disSimConCount); ++i) {
// choose sim constraint
if(i % 2 && simConCount) {
currentConstSet = &simConstraints;
currentIdx = currentSimIdx = (currentSimIdx + 1) % simConCount;
// line 3.3
delta = 1;
}
// choose dissim constraint
else if(!(i %2) && disSimConCount) {
currentConstSet = &disSimConstraints;
currentIdx = currentDisSimIdx = (currentDisSimIdx + 1) % disSimConCount;
// line 3.3
delta = -1;
}
// pick some constraint (line 3.1)
x1 = currentConstSet->getX1(currentIdx);
x2 = currentConstSet->getX2(currentIdx);
slack = currentConstSet->getSlack(currentIdx);
lambda = currentConstSet->getLambda(currentIdx);
// line 3.2
p = metric.computeSquaredDistance(x1, x2);
// ignore pairs with x1 == x2
if(p > 0) {
// line 3.4
alpha = min(lambda, delta / 2.0 * (1.0 / p - gamma / slack));
// line 3.5
beta = delta * alpha / (1.0 - delta * alpha * p);
/*
// prints debug information
cout << "p: " << p << endl;
cout << "alpha: " << alpha << endl;
cout << "1.0 / p: " << (1.0 / p) << endl;
cout << "gamma / slack: " << (gamma / slack) << endl;
cout << x1.t() << endl << x2.t() << endl;
cout << "delta / 2.0 * (1.0 / p - gamma / slack): " << (delta / 2.0 * (1.0 / p - gamma / slack)) << endl;
cout << "beta: " << beta << endl;
*/
// line 3.6
double nextSlack = gamma * slack / (gamma + delta * alpha * slack);
currentConstSet->setSlack(currentIdx, nextSlack);
// line 3.7
double nextLambda = lambda - alpha;
currentConstSet->setLambda(currentIdx, nextLambda);
// line 3.8
mat currentM = metric.getM();
currentM = currentM + beta * currentM * (x1 - x2) * (x1 - x2).t() * currentM;
metric.setM(currentM);
}
}
cout << "(InfTheoMetricLearner) metric learning converged in " << i << " iterations" << endl;
return metric;
}
