int randomEMinit(double **x, int n, int p, int nclass, double *pi,
double **Mu, double **LTSigma)
{
int *ordr,i,j,*clas,*nc;
/* This is a bug. Modified by Wei-Chen Chen on 2009/03/13.
MAKE_VECTOR(ordr,n);
*/
MAKE_VECTOR(ordr, nclass);
MAKE_VECTOR(clas, n);
MAKE_VECTOR(nc, nclass);
do {
/* This is a bug. Modified by Wei-Chen Chen on 2009/03/13.
i=srswor(n, n, ordr);
*/
i=srswor(n, nclass, ordr);
for(i=0;i<nclass;i++){
for(j=0;j<p;j++) Mu[i][j]=x[ordr[i]][j];
}
for(i=0;i<n;i++) clas[i]=assign_closest(x[i],p,nclass,Mu);
j=initials(x,n,p,nclass,nc,Mu,LTSigma,clas);
} while (j==0);
for(i=0;i<nclass;i++) pi[i]=1.*nc[i]/n;
FREE_VECTOR(nc);
FREE_VECTOR(clas);
FREE_VECTOR(ordr);
return 0;
}
/* This function is called by ss_shortems().
Mu[0, ..., labK-1] should be assigned before calling this function.
*/
void ss_randomEMinit(double **x, int n, int p, int nclass, double *pi,
double **Mu, double **LTSigma,
int *lab, int labK, int nonlab_total, int *lab_index){
int *ordr, i, j, *clas, *nc;
int new_nclass = nclass - labK;
double labMu[labK][p];
for(i = 0; i < labK; i++){
for(j = 0; j < p; j++) labMu[i][j] = Mu[i][j];
}
/* Initial centers for all other unknown clusters. */
MAKE_VECTOR(ordr, new_nclass);
MAKE_VECTOR(clas, n);
MAKE_VECTOR(nc, nclass);
do{
for(i = 0; i < labK; i++){
for(j = 0; j < p; j++) Mu[i][j] = labMu[i][j];
}
i = srswor(nonlab_total, new_nclass, ordr);
for(i = labK; i < nclass; i++){
for(j = 0; j < p; j++) Mu[i][j] = x[lab_index[ordr[i - labK]]][j];
}
for(i = 0; i < n; i++){
if(lab[i] == -1){
clas[i] = assign_closest(x[i], p, nclass, Mu);
} else{
clas[i] = lab[i];
}
}
j = initials(x, n, p, nclass, nc, Mu, LTSigma, clas);
} while(j == 0);
for(i = 0; i < nclass; i++) pi[i] = 1. * nc[i] / n;
FREE_VECTOR(nc);
FREE_VECTOR(clas);
FREE_VECTOR(ordr);
} /* End of ss_randomEMinit(). */
int Update_init_random_Mu_unique_label(em_phyclust_struct *empcs, Q_matrix_array *QA, em_control *EMC, em_fp *EMFP){
int init_iter = 0, ret_stop = 0;
int n_X, k, l, N_X = empcs->N_X, K = empcs->K, L = empcs->L,
N_X_unlabeled = empcs->N_X_unlabeled, K_labeled = empcs->K_labeled, K_unlabeled = K - K_labeled,
tmp_n, tmp_k;
int center_id[K], tmp_center_id[K], tmp_id;
int consensus_Mu[L];
double tmp, tmp_min, init_logL_observed = 0.0;
edist_struct *eds;
find_consensus_Mu(empcs->N_X_org, L, empcs->ncode, empcs->gap_index, empcs->X_org, consensus_Mu);
eds = initialize_edist_struct_UT(EMC->edist_model, N_X, L, empcs->X);
while(init_iter < EMC->max_init_iter){
init_iter++;
reset_Q_matrix_array(QA);
// reset_SE_P_matrix(empcs->SE_P);
/* Randomly pick centers from X. */
for(k = 0; k < K_labeled; k++){
tmp_n = 0;
for(n_X = 0; n_X < empcs->N_X_labeled; n_X++){
if(empcs->label_semi[n_X] == k){
tmp_n++;
}
}
srswor(tmp_n, 1, tmp_center_id);
tmp_n = -1;
for(n_X = 0; n_X < empcs->N_X_labeled; n_X++){
if(empcs->label_semi[n_X] == k){
tmp_n++;
if(tmp_n == tmp_center_id[0]){
break;
}
}
}
tmp_n = n_X;
for(n_X = 0; n_X < N_X; n_X++){
if(empcs->X[n_X] == empcs->X_labeled[tmp_n]){
center_id[k] = n_X;
break;
}
}
}
if(K_unlabeled > 0){
srswor(N_X_unlabeled, K_unlabeled, tmp_center_id);
for(k = 0; k < K_unlabeled; k++){
tmp_n = tmp_center_id[k];
tmp_k = k + K_labeled;
for(n_X = 0; n_X < N_X; n_X++){
if(empcs->X[n_X] == empcs->X_unlabeled[tmp_n]){
center_id[tmp_k] = n_X;
break;
}
}
}
}
/* Assign Mu by centers. */
for(k = 0; k < K; k++){
for(l = 0; l < L; l++){
empcs->Mu[k][l] = empcs->X[center_id[k]][l];
}
empcs->n_class[k] = 0;
}
/* Assign X to the nearest mu by distance, and recreate Z_normalized. */
for(n_X = 0; n_X < N_X; n_X++){
tmp_min = eds->get_pair_edist(eds, n_X, center_id[0]);
tmp_id = 0;
for(k = 1; k < K; k++){
tmp = eds->get_pair_edist(eds, n_X, center_id[k]);
if(tmp < tmp_min){
tmp_min = tmp;
tmp_id = k;
}
}
for(k = 0; k < K; k++){
empcs->Z_normalized[n_X][k] = 0.0;
}
empcs->Z_normalized[n_X][tmp_id] = 1.0;
empcs->n_class[tmp_id] += empcs->replication_X[n_X];
}
/* Replace gaps by the concensus. */
for(k = 0; k < K; k++){
for(l = 0; l < L; l++){
if(empcs->Mu[k][l] == empcs->gap_index || empcs->Mu[k][l] == MISSING_ALLELE){
empcs->Mu[k][l] = consensus_Mu[l];
}
}
}
if(check_all_min_n_class(K, empcs->n_class, EMC->min_n_class)){
ret_stop = init_m_step(empcs, QA, EMC, EMFP);
if(ret_stop > 0){
continue;
}
init_logL_observed = EMFP->LogL_observed(empcs, QA);
if(is_finite(init_logL_observed)){
break;
}
}
}
if(init_iter >= EMC->max_init_iter){
ret_stop = init_m_step(empcs, QA, EMC, EMFP);
if(ret_stop > 0){
#if PRINT_ERROR > 0
fprintf_stderr("PE: Initialization error. (%s)\n", INIT_METHOD[EMC->init_method]);
#endif
free_edist_struct(eds);
return(ret_stop);
}
init_logL_observed = EMFP->LogL_observed(empcs, QA);
if(!is_finite(init_logL_observed)){
#if PRINT_ERROR > 0
fprintf_stderr("PE: Initial logL_observed is not finit. (%s)\n",
INIT_METHOD[EMC->init_method]);
#endif
free_edist_struct(eds);
return(1);
}
}
free_edist_struct(eds);
return(ret_stop);
} /* End of Update_init_random_Mu_unique(). */
