void phyanimal_free(PhyAnimal *model) {
ListStr l;
char *name;
PhyAnimal m = *model;
if (*model==NULL) return;
free_temporaries(*model);
free_arrays(m);
/* Variable names */
if (m->fvar != NULL) {
l = m->fvar;
while (!list_str_empty(l)) {
list_str_pop_front(l,&name);
PM_MEM_FREE(name);
}
list_str_free(&l);
}
if (m->yvar != NULL) {
l = m->yvar;
while (!list_str_empty(l)) {
list_str_pop_front(l,&name);
PM_MEM_FREE(name);
}
list_str_free(&l);
}
PM_MEM_FREE(*model);
*model = NULL;
return;
}
int l1_logreg_train(dmatrix *X, double *b, double lambda, train_opts to,
double *initial_x, double *initial_t, double *sol,
int *total_ntiter, int *total_pcgiter)
{
/* problem data */
problem_data_t prob;
variables_t vars;
dmatrix *matX1; /* matX1 = diag(b)*X_std */
dmatrix *matX2; /* matX2 = X_std.^2 (only for pcg) */
double *ac, *ar;
double *avg_x, *std_x;
int m, n, ntiter, pcgiter, status;
double pobj, dobj, gap;
double t, s, maxAnu;
double *g, *h, *z, *expz, *expmz;
double *x, *v, *w, *u;
double *dx, *dv, *dw, *du;
double *gv, *gw, *gu, *gx;
double *d1, *d2, *Aw;
/* pcg variables */
pcg_status_t pcgstat;
adata_t adata;
mdata_t mdata;
double *precond;
/* temporary variables */
double *tm1, *tn1, *tn2, *tn3, *tn4, *tx1;
/* temporary variables for dense case (cholesky) */
dmatrix *B; /* m x n (or m x n) */
dmatrix *BB; /* n x n (or m x m) */
char format_buf[PRINT_BUF_SIZE];
#if INTERNAL_PLOT
dmatrix *internal_plot;
dmat_new_dense(&internal_plot, 3, MAX_NT_ITER);
memset(internal_plot->val,0,sizeof(double)*3*MAX_NT_ITER);
/* row 1: cum_nt_iter, row 2: cum_pcg_iter, row 3: duality gap */
#endif
p2func_progress print_progress = NULL;
/*
* INITIALIZATION
*/
s = 1.0;
pobj = DBL_MAX;
dobj = -DBL_MAX;
pcgiter = 0;
matX1 = NULL;
matX2 = NULL;
init_pcg_status(&pcgstat);
dmat_duplicate(X, &matX1);
dmat_copy(X, matX1);
m = matX1->m;
n = matX1->n;
if (to.sflag == TRUE)
{
/* standardize_data not only standardizes the data,
but also multiplies diag(b). */
standardize_data(matX1, b, &avg_x, &std_x, &ac, &ar);
}
else
{
/* matX1 = diag(b)*X */
dmat_diagscale(matX1, b, FALSE, NULL, TRUE);
avg_x = std_x = ac = ar = NULL;
}
if (matX1->nz >= 0) /* only for pcg */
{
dmat_elemAA(matX1, &matX2);
}
else
{
matX2 = NULL;
}
set_problem_data(&prob, matX1, matX2, ac, ar, b, lambda, avg_x, std_x);
create_variables(&vars, m, n);
get_variables(&vars, &x, &v, &w, &u, &dx, &dv, &dw, &du, &gx, &gv,
&gw, &gu, &g, &h, &z, &expz, &expmz, &d1, &d2, &Aw);
allocate_temporaries(m, n, (matX1->nz >= 0),
&tm1, &tn1, &tn2, &tn3, &tn4, &tx1, &precond, &B, &BB);
if (initial_x == NULL)
{
dmat_vset(1, 0.0, v);
dmat_vset(n, 0.0, w);
dmat_vset(n, 1.0, u);
dmat_vset(n+n+1, 0, dx);
t = min(max(1.0, 1.0 / lambda), 2.0 * n / ABSTOL);
}
else
{
dmat_vcopy(n+n+1, initial_x, x);
dmat_vset(n+n+1, 0, dx);
t = *initial_t;
}
set_adata(&adata, matX1, ac, ar, b, h, d1, d2);
set_mdata(&mdata, m, n, precond);
/* select printing function and format according to
verbose level and method type (pcg/direct) */
if (to.verbose_level>=2) init_progress((matX1->nz >= 0), to.verbose_level,
format_buf, &print_progress);
/*** MAIN LOOP ************************************************************/
for (ntiter = 0; ntiter < MAX_NT_ITER; ntiter++)
{
/*
* Sets v as the optimal value of the intercept.
*/
dmat_yAmpqx(matX1, ac, ar, w, Aw);
optimize_intercept(v, z, expz, expmz, tm1, b, Aw, m);
/*
* Constructs dual feasible point nu.
*/
fprimes(m, expz, expmz, g, h);
/* partially computes the gradient of phi.
the rest part of the gradient will be completed while computing
the search direction. */
gv[0] = dmat_dot(m, b, g); /* gv = b'*g */
dmat_yAmpqTx(matX1, ac, ar, g, gw); /* gw = A'*g */
dmat_waxpby(m, -1, g, 0, NULL, tm1); /* nu = -g */
maxAnu = dmat_norminf(n, gw); /* max(A'*nu) */
if (maxAnu > lambda)
dmat_waxpby(m, lambda / maxAnu, tm1, 0.0, NULL, tm1);
/*
* Evaluates duality gap.
*/
pobj = logistic_loss2(m,z,expz,expmz)/m + lambda*dmat_norm1(n,w);
dobj = max(nentropy(m, tm1) / m, dobj);
gap = pobj - dobj;
#if INTERNAL_PLOT
internal_plot->val[0*MAX_NT_ITER+ntiter] = (double)ntiter;
internal_plot->val[1*MAX_NT_ITER+ntiter] = (double)pcgiter;
internal_plot->val[2*MAX_NT_ITER+ntiter] = gap;
#endif
if (to.verbose_level>=2)
{
(*print_progress)(format_buf, ntiter, gap, pobj, dobj, s, t,
pcgstat.flag, pcgstat.relres, pcgstat.iter);
}
/*
* Quits if gap < tolerance.
*/
if (gap < to.tolerance ) /***********************************************/
{
if (sol != NULL)
{
/* trim solution */
int i;
double lambda_threshold;
lambda_threshold = to.ktolerance*lambda;
sol[0] = x[0];
for (i = 0; i < n; i++)
{
sol[i+1] = (fabs(gw[i])>lambda_threshold)? x[i+1] : 0.0;
}
/* if standardized, sol = coeff/std */
if (to.sflag == TRUE && to.cflag == FALSE)
{
dmat_elemdivi(n, sol+1, std_x, sol+1);
sol[0] -= dmat_dot(n, avg_x, sol+1);
}
}
if (initial_x != NULL)
{
dmat_vcopy(n+n+1, x, initial_x);
*initial_t = t;
}
if (total_pcgiter) *total_pcgiter = pcgiter;
if (total_ntiter ) *total_ntiter = ntiter;
/* free memory */
free_variables(&vars);
free_temporaries(tm1, tn1, tn2, tn3, tn4, tx1, precond, B, BB);
free_problem_data(&prob);
#if INTERNAL_PLOT
write_mm_matrix("internal_plot",internal_plot,"",TYPE_G);
#endif
return STATUS_SOLUTION_FOUND;
} /********************************************************************/
/*
* Updates t
*/
if (s >= 0.5)
{
t = max(min(2.0 * n * MU / gap, MU * t), t);
}
else if (s < 1e-5)
{
t = 1.1*t;
}
/*
* Computes search direction.
*/
if (matX1->nz >= 0)
{
/* pcg */
compute_searchdir_pcg(&prob, &vars, t, s, gap, &pcgstat, &adata,
&mdata, precond, tm1, tn1, tx1);
pcgiter += pcgstat.iter;
}
else
{
/* direct */
if (n > m)
{
/* direct method for n > m, SMW */
compute_searchdir_chol_fat(&prob, &vars, t, B, BB,
tm1, tn1, tn2, tn3, tn4);
}
else
{
/* direct method for n <= m */
compute_searchdir_chol_thin(&prob, &vars, t, B, BB,
tm1, tn1, tn2);
}
}
/*
* Backtracking linesearch & update x = (v,w,u) and z.
*/
s = backtracking_linesearch(&prob, &vars, t, tm1, tx1);
if (s < 0) break; /* BLS error */
}
/*** END OF MAIN LOOP *****************************************************/
/* Abnormal termination */
if (s < 0)
{
status = STATUS_MAX_LS_ITER_EXCEEDED;
}
else /* if (ntiter == MAX_NT_ITER) */
{
status = STATUS_MAX_NT_ITER_EXCEEDED;
}
if (sol != NULL)
{
/* trim solution */
int i;
double lambda_threshold;
lambda_threshold = to.ktolerance*lambda;
sol[0] = x[0];
for (i = 0; i < n; i++)
{
sol[i+1] = (fabs(gw[i])>lambda_threshold)? x[i+1] : 0.0;
}
/* if standardized, sol = coeff/std */
if (to.sflag == TRUE && to.cflag == FALSE)
{
dmat_elemdivi(n, sol+1, std_x, sol+1);
sol[0] -= dmat_dot(n, avg_x, sol+1);
}
}
if (initial_x != NULL)
{
dmat_vcopy(n+n+1, x, initial_x);
*initial_t = t;
}
if (total_pcgiter) *total_pcgiter = pcgiter;
if (total_ntiter ) *total_ntiter = ntiter;
/* free memory */
free_variables(&vars);
free_temporaries(tm1, tn1, tn2, tn3, tn4, tx1, precond, B, BB);
free_problem_data(&prob);
#if INTERNAL_PLOT
write_mm_matrix("internal_plot",internal_plot,"",TYPE_G);
#endif
return status;
}