gmm_t * gmm_learn (int di, int ni, int ki, int niter,
const float * v, int nt, int seed, int nredo,
int flags)
{
long d=di,k=ki,n=ni;
int iter, iter_tot = 0;
double old_key, key = 666;
niter = (niter == 0 ? 10000 : niter);
/* the GMM parameters */
float * p = fvec_new_0 (n * k); /* p(ci|x) for all i */
gmm_t * g = gmm_new (d, k);
/* initialize the GMM: k-means + variance estimation */
int * nassign = ivec_new (n); /* not useful -> to be removed when debugged */
float * dis = fvec_new (n);
kmeans (d, n, k, niter, v, nt, seed, nredo, g->mu, dis, NULL, nassign);
fflush (stderr);
fprintf (stderr, "assign = ");
ivec_print (nassign, k);
fprintf (stderr, "\n");
free (nassign);
/* initialization of the GMM parameters assuming a diagonal matrix */
fvec_set (g->w, k, 1.0 / k);
double sig = fvec_sum (dis, n) / n;
printf ("sigma at initialization = %.3f\n", sig);
fvec_set (g->sigma, k * d, sig);
free (dis);
/* start the EM algorithm */
fprintf (stdout, "<><><><> GMM <><><><><>\n");
if(flags & GMM_FLAGS_PURE_KMEANS) niter=0;
for (iter = 1 ; iter <= niter ; iter++) {
gmm_compute_p_thread (n, v, g, p, flags, nt);
fflush(stdout);
gmm_handle_empty(n, v, g, p);
gmm_compute_params (n, v, p, g, flags, nt);
fflush(stdout);
iter_tot++;
/* convergence reached -> leave */
old_key = key;
key = fvec_sum (g->mu, k * d);
printf ("keys %5d: %.6f -> %.6f\n", iter, old_key, key);
fflush(stdout);
if (key == old_key)
break;
}
fprintf (stderr, "\n");
free(p);
return g;
}
void ahc_clustering(DyArray *ahct, int bf, int rho, const fDataSet *ds){
ASSERTINFO(ahct == NULL || bf <= 0 || rho <= 0 || ds == NULL, "IPP");
int n = ds->n;
int d = ds->d;
Cluster _clu, clu, *pclu = NULL, *p0clu = NULL;
int i;
float qerror;
int iclu, bfi, ni, ichild, ori_id; // the pointer, branch factor and volume of the i-th cluster
int *nassign = ivec_new_set(bf, 0);
int *assign = NULL;
float *cent = fvec_new(d*bf);
float *mem_points = NULL;
DyArray *member = (DyArray*)malloc(sizeof(DyArray)*bf);
/* initialize the first cluster (root) to add it to the ahc tree */
Cluster_init(&clu, n);
for(i = 0; i < n; i++){
clu.idx[i] = i;
}
clu.type = ClusterType_Root;
DyArray_add(ahct, (void*)&clu, 1);
/* begin the loop of adaptive hierarchical clustering */
iclu = 0;
while(iclu < ahct->count){
/* deal with the i-th cluster */
// figure out the adaptive branch factor of the i-th cluster
pclu = (Cluster*)DyArray_get(ahct, iclu, 1);
ni = pclu->npts;
bfi = i_min(bf, (int)round(ni / (float)rho));
// deal with the cluster according to its size
if(bfi < 2){
/*
* this is a leaf cluster
* - mark it, release the children
* * not necessary to store real data points
*/
pclu->type = ClusterType_Leaf;
}else{
printf("----------------- cluster %d, bfi-%d:\n", iclu, bfi);
/*
* this is an inner cluster
* - divide it
*/
memcpy(&_clu, pclu, sizeof(Cluster));
// extract data points from the original dataset according to the idx
mem_points = fvec_new(ni * d);
for(i = 0; i < ni; i++){
memcpy(mem_points+i*d, ds->data+_clu.idx[i]*d, d);
}
// divide this cluster
assign = ivec_new(ni);
if(iclu == 30){
int _a = 1;
_a++;
ivec_print(_clu.idx, _clu.npts);
}
qerror = kmeans( d, ni, bfi, CLUSTERING_NITER, mem_points,
CLUSTERING_NTHREAD | KMEANS_QUIET | KMEANS_INIT_BERKELEY, CLUSTERING_SEED, CLUSTERING_NREDO,
cent, NULL, assign, nassign);
// prepare space for members' ids
for(i = 0; i < bfi; i++){
DyArray_init(&member[i], sizeof(int), nassign[i]);
}
// extract member points' ids for each children cluster
for(i = 0; i < ni; i++){
ori_id = _clu.idx[i];
DyArray_add(&member[assign[i]], (void*)&ori_id, 1);
}
// fulfill the type, centroids and the children of this cluster, add them to the ahct
_clu.type = ClusterType_Inner;
_clu.cents = fvec_new(d * bfi);
memcpy(_clu.cents, cent, sizeof(float)*d*bfi);
DyArray_init(&_clu.children, sizeof(int), bfi);
for(i = 0; i < bfi; i++){
Cluster_init(&clu, nassign[i]);
memcpy(clu.idx, (int*)member[i].elem, sizeof(int)*nassign[i]);
DyArray_add(&_clu.children, (void*)&ahct->count, 1); /* the i-th child's position */
DyArray_add(ahct, (void*)&clu, 1); /* add the i-th child to the ahct */
}
/* as per the elems of ahct may change when expanding the space
* we decide to get the brand new address of the element
*/
pclu = (Cluster*)DyArray_get(ahct, iclu, 1);
memcpy(pclu, &_clu, sizeof(Cluster));
/* report */
ivec_print(nassign, bfi);
ivec_print((int*)_clu.children.elem, _clu.children.count);
/* unset or release */
FREE(mem_points);
FREE(assign);
for(i = 0; i < bfi; i++){
DyArray_unset(&member[i]);
}
}
// move to next cluster
iclu++;
}
FREE(nassign);
FREE(cent);
FREE(member);
pclu = NULL;
}