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-rw-r--r--libs/qm-dsp/hmm/hmm.c242
1 files changed, 121 insertions, 121 deletions
diff --git a/libs/qm-dsp/hmm/hmm.c b/libs/qm-dsp/hmm/hmm.c
index 69eee02b66..6642e4e1db 100644
--- a/libs/qm-dsp/hmm/hmm.c
+++ b/libs/qm-dsp/hmm/hmm.c
@@ -46,11 +46,11 @@ model_t* hmm_init(double** x, int T, int L, int N)
{
int i, j, d, e, t;
double s, ss;
-
+
model_t* model;
model = (model_t*) malloc(sizeof(model_t));
model->N = N;
- model->L = L;
+ model->L = L;
model->p0 = (double*) malloc(N*sizeof(double));
model->a = (double**) malloc(N*sizeof(double*));
model->mu = (double**) malloc(N*sizeof(double*));
@@ -62,10 +62,10 @@ model_t* hmm_init(double** x, int T, int L, int N)
model->cov = (double**) malloc(L*sizeof(double*));
for (i = 0; i < L; i++)
model->cov[i] = (double*) malloc(L*sizeof(double));
-
+
srand(time(0));
double* global_mean = (double*) malloc(L*sizeof(double));
-
+
/* find global mean */
for (d = 0; d < L; d++)
{
@@ -74,7 +74,7 @@ model_t* hmm_init(double** x, int T, int L, int N)
global_mean[d] += x[t][d];
global_mean[d] /= T;
}
-
+
/* calculate global diagonal covariance */
for (d = 0; d < L; d++)
{
@@ -84,7 +84,7 @@ model_t* hmm_init(double** x, int T, int L, int N)
model->cov[d][d] += (x[t][d] - global_mean[d]) * (x[t][d] - global_mean[d]);
model->cov[d][d] /= T-1;
}
-
+
/* set all means close to global mean */
for (i = 0; i < N; i++)
{
@@ -94,8 +94,8 @@ model_t* hmm_init(double** x, int T, int L, int N)
/* ideally the random number would be Gaussian(0,1), as a hack we make it uniform on [-0.25,0.25] */
model->mu[i][d] = global_mean[d] + (0.5 * rand() / (double) RAND_MAX - 0.25) * sqrt(model->cov[d][d]);
}
- }
-
+ }
+
/* random intial and transition probs */
s = 0;
for (i = 0; i < N; i++)
@@ -115,16 +115,16 @@ model_t* hmm_init(double** x, int T, int L, int N)
}
for (i = 0; i < N; i++)
model->p0[i] /= s;
-
+
free(global_mean);
-
+
return model;
}
void hmm_close(model_t* model)
{
int i;
-
+
for (i = 0; i < model->N; i++)
{
free(model->a[i]);
@@ -134,23 +134,23 @@ void hmm_close(model_t* model)
free(model->mu);
for (i = 0; i < model->L; i++)
free(model->cov[i]);
- free(model->cov);
- free(model);
+ free(model->cov);
+ free(model);
}
void hmm_train(double** x, int T, model_t* model)
{
int i, t;
double loglik; /* overall log-likelihood at each iteration */
-
+
int N = model->N;
int L = model->L;
double* p0 = model->p0;
double** a = model->a;
double** mu = model->mu;
double** cov = model->cov;
-
- /* allocate memory */
+
+ /* allocate memory */
double** gamma = (double**) malloc(T*sizeof(double*));
double*** xi = (double***) malloc(T*sizeof(double**));
for (t = 0; t < T; t++)
@@ -160,45 +160,45 @@ void hmm_train(double** x, int T, model_t* model)
for (i = 0; i < N; i++)
xi[t][i] = (double*) malloc(N*sizeof(double));
}
-
+
/* temporary memory */
double* gauss_y = (double*) malloc(L*sizeof(double));
- double* gauss_z = (double*) malloc(L*sizeof(double));
-
+ double* gauss_z = (double*) malloc(L*sizeof(double));
+
/* obs probs P(j|{x}) */
double** b = (double**) malloc(T*sizeof(double*));
for (t = 0; t < T; t++)
b[t] = (double*) malloc(N*sizeof(double));
-
+
/* inverse covariance and its determinant */
double** icov = (double**) malloc(L*sizeof(double*));
for (i = 0; i < L; i++)
icov[i] = (double*) malloc(L*sizeof(double));
double detcov;
-
+
double thresh = 0.0001;
- int niter = 50;
+ int niter = 50;
int iter = 0;
double loglik1, loglik2;
int foundnan = 0;
- while (iter < niter && !foundnan && !(iter > 1 && (loglik - loglik1) < thresh * (loglik1 - loglik2)))
+ while (iter < niter && !foundnan && !(iter > 1 && (loglik - loglik1) < thresh * (loglik1 - loglik2)))
{
++iter;
-/*
+/*
fprintf(stderr, "calculating obsprobs...\n");
fflush(stderr);
-*/
+*/
/* precalculate obs probs */
invert(cov, L, icov, &detcov);
-
+
for (t = 0; t < T; t++)
{
//int allzero = 1;
for (i = 0; i < N; i++)
{
b[t][i] = exp(loggauss(x[t], L, mu[i], icov, detcov, gauss_y, gauss_z));
-
+
//if (b[t][i] != 0)
// allzero = 0;
}
@@ -213,13 +213,13 @@ void hmm_train(double** x, int T, model_t* model)
}
*/
}
-/*
+/*
fprintf(stderr, "forwards-backwards...\n");
fflush(stderr);
-*/
+*/
forward_backwards(xi, gamma, &loglik, &loglik1, &loglik2, iter, N, T, p0, a, b);
-/*
- fprintf(stderr, "iteration %d: loglik = %f\n", iter, loglik);
+/*
+ fprintf(stderr, "iteration %d: loglik = %f\n", iter, loglik);
fprintf(stderr, "re-estimation...\n");
fflush(stderr);
*/
@@ -227,9 +227,9 @@ void hmm_train(double** x, int T, model_t* model)
foundnan = 1;
continue;
}
-
+
baum_welch(p0, a, mu, cov, N, T, L, x, xi, gamma);
-
+
/*
printf("a:\n");
for (i = 0; i < model->N; i++)
@@ -242,7 +242,7 @@ void hmm_train(double** x, int T, model_t* model)
*/
//hmm_print(model);
}
-
+
/* deallocate memory */
for (t = 0; t < T; t++)
{
@@ -254,12 +254,12 @@ void hmm_train(double** x, int T, model_t* model)
}
free(gamma);
free(xi);
- free(b);
-
+ free(b);
+
for (i = 0; i < L; i++)
free(icov[i]);
free(icov);
-
+
free(gauss_y);
free(gauss_z);
}
@@ -267,27 +267,27 @@ void hmm_train(double** x, int T, model_t* model)
void mlss_reestimate(double* p0, double** a, double** mu, double** cov, int N, int T, int L, int* q, double** x)
{
/* fit a single Gaussian to observations in each state */
-
+
/* calculate the mean observation in each state */
-
+
/* calculate the overall covariance */
-
+
/* count transitions */
-
+
/* estimate initial probs from transitions (???) */
}
void baum_welch(double* p0, double** a, double** mu, double** cov, int N, int T, int L, double** x, double*** xi, double** gamma)
{
int i, j, t;
-
+
double* sum_gamma = (double*) malloc(N*sizeof(double));
-
+
/* temporary memory */
double* u = (double*) malloc(L*L*sizeof(double));
double* yy = (double*) malloc(T*L*sizeof(double));
- double* yy2 = (double*) malloc(T*L*sizeof(double));
-
+ double* yy2 = (double*) malloc(T*L*sizeof(double));
+
/* re-estimate transition probs */
for (i = 0; i < N; i++)
{
@@ -295,7 +295,7 @@ void baum_welch(double* p0, double** a, double** mu, double** cov, int N, int T,
for (t = 0; t < T-1; t++)
sum_gamma[i] += gamma[t][i];
}
-
+
for (i = 0; i < N; i++)
{
if (sum_gamma[i] == 0)
@@ -310,7 +310,7 @@ void baum_welch(double* p0, double** a, double** mu, double** cov, int N, int T,
for (t = 0; t < T-1; t++)
a[i][j] += xi[t][i][j];
//s += a[i][j];
- a[i][j] /= sum_gamma[i];
+ a[i][j] /= sum_gamma[i];
}
/*
for (j = 0; j < N; j++)
@@ -319,21 +319,21 @@ void baum_welch(double* p0, double** a, double** mu, double** cov, int N, int T,
}
*/
}
-
+
/* NB: now we need to sum gamma over all t */
for (i = 0; i < N; i++)
sum_gamma[i] += gamma[T-1][i];
-
+
/* re-estimate initial probs */
for (i = 0; i < N; i++)
p0[i] = gamma[0][i];
-
+
/* re-estimate covariance */
int d, e;
double sum_sum_gamma = 0;
for (i = 0; i < N; i++)
- sum_sum_gamma += sum_gamma[i];
-
+ sum_sum_gamma += sum_gamma[i];
+
/*
for (d = 0; d < L; d++)
{
@@ -343,9 +343,9 @@ void baum_welch(double* p0, double** a, double** mu, double** cov, int N, int T,
for (t = 0; t < T; t++)
for (j = 0; j < N; j++)
cov[d][e] += gamma[t][j] * (x[t][d] - mu[j][d]) * (x[t][e] - mu[j][e]);
-
+
cov[d][e] /= sum_sum_gamma;
-
+
if (ISNAN(cov[d][e]))
{
printf("cov[%d][%d] was nan\n", d, e);
@@ -365,12 +365,12 @@ void baum_welch(double* p0, double** a, double** mu, double** cov, int N, int T,
for (e = 0; e < d; e++)
cov[d][e] = cov[e][d];
*/
-
+
/* using BLAS */
for (d = 0; d < L; d++)
for (e = 0; e < L; e++)
cov[d][e] = 0;
-
+
for (j = 0; j < N; j++)
{
for (d = 0; d < L; d++)
@@ -379,20 +379,20 @@ void baum_welch(double* p0, double** a, double** mu, double** cov, int N, int T,
yy[d*T+t] = x[t][d] - mu[j][d];
yy2[d*T+t] = gamma[t][j] * (x[t][d] - mu[j][d]);
}
-
+
cblas_dgemm(CblasColMajor, CblasTrans, CblasNoTrans, L, L, T, 1.0, yy, T, yy2, T, 0, u, L);
-
+
for (e = 0; e < L; e++)
for (d = 0; d < L; d++)
cov[d][e] += u[e*L+d];
}
-
+
for (d = 0; d < L; d++)
for (e = 0; e < L; e++)
- cov[d][e] /= T; /* sum_sum_gamma; */
-
+ cov[d][e] /= T; /* sum_sum_gamma; */
+
//printf("sum_sum_gamma = %f\n", sum_sum_gamma); /* fine, = T IS THIS ALWAYS TRUE with pooled cov?? */
-
+
/* re-estimate means */
for (j = 0; j < N; j++)
{
@@ -404,7 +404,7 @@ void baum_welch(double* p0, double** a, double** mu, double** cov, int N, int T,
mu[j][d] /= sum_gamma[j];
}
}
-
+
/* deallocate memory */
free(sum_gamma);
free(yy);
@@ -416,7 +416,7 @@ void forward_backwards(double*** xi, double** gamma, double* loglik, double* log
{
/* forwards-backwards with scaling */
int i, j, t;
-
+
double** alpha = (double**) malloc(T*sizeof(double*));
double** beta = (double**) malloc(T*sizeof(double*));
for (t = 0; t < T; t++)
@@ -424,34 +424,34 @@ void forward_backwards(double*** xi, double** gamma, double* loglik, double* log
alpha[t] = (double*) malloc(N*sizeof(double));
beta[t] = (double*) malloc(N*sizeof(double));
}
-
+
/* scaling coefficients */
double* c = (double*) malloc(T*sizeof(double));
-
+
/* calculate forward probs and scale coefficients */
c[0] = 0;
for (i = 0; i < N; i++)
{
alpha[0][i] = p0[i] * b[0][i];
c[0] += alpha[0][i];
-
+
//printf("p0[%d] = %f, b[0][%d] = %f\n", i, p0[i], i, b[0][i]);
}
c[0] = 1 / c[0];
for (i = 0; i < N; i++)
{
- alpha[0][i] *= c[0];
-
+ alpha[0][i] *= c[0];
+
//printf("alpha[0][%d] = %f\n", i, alpha[0][i]); /* OK agrees with Matlab */
}
-
+
*loglik1 = *loglik;
*loglik = -log(c[0]);
if (iter == 2)
*loglik2 = *loglik;
-
+
for (t = 1; t < T; t++)
- {
+ {
c[t] = 0;
for (j = 0; j < N; j++)
{
@@ -459,10 +459,10 @@ void forward_backwards(double*** xi, double** gamma, double* loglik, double* log
for (i = 0; i < N; i++)
alpha[t][j] += alpha[t-1][i] * a[i][j];
alpha[t][j] *= b[t][j];
-
+
c[t] += alpha[t][j];
}
-
+
/*
if (c[t] == 0)
{
@@ -477,16 +477,16 @@ void forward_backwards(double*** xi, double** gamma, double* loglik, double* log
exit(-1);
}
*/
-
+
c[t] = 1 / c[t];
for (j = 0; j < N; j++)
alpha[t][j] *= c[t];
-
+
//printf("c[%d] = %e\n", t, c[t]);
-
+
*loglik -= log(c[t]);
}
-
+
/* calculate backwards probs using same coefficients */
for (i = 0; i < N; i++)
beta[T-1][i] = 1;
@@ -495,20 +495,20 @@ void forward_backwards(double*** xi, double** gamma, double* loglik, double* log
{
for (i = 0; i < N; i++)
beta[t][i] *= c[t];
-
+
if (t == 0)
break;
-
+
for (i = 0; i < N; i++)
{
beta[t-1][i] = 0;
for (j = 0; j < N; j++)
beta[t-1][i] += a[i][j] * b[t][j] * beta[t][j];
}
-
+
t--;
}
-
+
/*
printf("alpha:\n");
for (t = 0; t < T; t++)
@@ -526,7 +526,7 @@ void forward_backwards(double*** xi, double** gamma, double* loglik, double* log
}
printf("\n\n");
*/
-
+
/* calculate posterior probs */
double tot;
for (t = 0; t < T; t++)
@@ -539,12 +539,12 @@ void forward_backwards(double*** xi, double** gamma, double* loglik, double* log
}
for (i = 0; i < N; i++)
{
- gamma[t][i] /= tot;
-
- //printf("gamma[%d][%d] = %f\n", t, i, gamma[t][i]);
+ gamma[t][i] /= tot;
+
+ //printf("gamma[%d][%d] = %f\n", t, i, gamma[t][i]);
}
- }
-
+ }
+
for (t = 0; t < T-1; t++)
{
tot = 0;
@@ -560,7 +560,7 @@ void forward_backwards(double*** xi, double** gamma, double* loglik, double* log
for (j = 0; j < N; j++)
xi[t][i][j] /= tot;
}
-
+
/*
// CHECK - fine
// gamma[t][i] = \sum_j{xi[t][i][j]}
@@ -568,8 +568,8 @@ void forward_backwards(double*** xi, double** gamma, double* loglik, double* log
for (j = 0; j < N; j++)
tot += xi[3][1][j];
printf("gamma[3][1] = %f, sum_j(xi[3][1][j]) = %f\n", gamma[3][1], tot);
- */
-
+ */
+
for (t = 0; t < T; t++)
{
free(alpha[t]);
@@ -585,20 +585,20 @@ void viterbi_decode(double** x, int T, model_t* model, int* q)
int i, j, t;
double max;
int havemax;
-
+
int N = model->N;
int L = model->L;
double* p0 = model->p0;
double** a = model->a;
double** mu = model->mu;
double** cov = model->cov;
-
+
/* inverse covariance and its determinant */
double** icov = (double**) malloc(L*sizeof(double*));
for (i = 0; i < L; i++)
icov[i] = (double*) malloc(L*sizeof(double));
double detcov;
-
+
double** logb = (double**) malloc(T*sizeof(double*));
double** phi = (double**) malloc(T*sizeof(double*));
int** psi = (int**) malloc(T*sizeof(int*));
@@ -608,24 +608,24 @@ void viterbi_decode(double** x, int T, model_t* model, int* q)
phi[t] = (double*) malloc(N*sizeof(double));
psi[t] = (int*) malloc(N*sizeof(int));
}
-
+
/* temporary memory */
double* gauss_y = (double*) malloc(L*sizeof(double));
- double* gauss_z = (double*) malloc(L*sizeof(double));
-
+ double* gauss_z = (double*) malloc(L*sizeof(double));
+
/* calculate observation logprobs */
invert(cov, L, icov, &detcov);
for (t = 0; t < T; t++)
for (i = 0; i < N; i++)
logb[t][i] = loggauss(x[t], L, mu[i], icov, detcov, gauss_y, gauss_z);
-
+
/* initialise */
for (i = 0; i < N; i++)
{
phi[0][i] = log(p0[i]) + logb[0][i];
psi[0][i] = 0;
}
-
+
for (t = 1; t < T; t++)
{
for (j = 0; j < N; j++)
@@ -646,7 +646,7 @@ void viterbi_decode(double** x, int T, model_t* model, int* q)
}
}
}
-
+
/* find maximising state at time T-1 */
max = phi[T-1][0];
q[T-1] = 0;
@@ -659,7 +659,7 @@ void viterbi_decode(double** x, int T, model_t* model, int* q)
}
}
-
+
/* track back */
t = T - 2;
while (t >= 0)
@@ -667,7 +667,7 @@ void viterbi_decode(double** x, int T, model_t* model, int* q)
q[t] = psi[t+1][q[t+1]];
t--;
}
-
+
/* de-allocate memory */
for (i = 0; i < L; i++)
free(icov[i]);
@@ -681,7 +681,7 @@ void viterbi_decode(double** x, int T, model_t* model, int* q)
free(logb);
free(phi);
free(psi);
-
+
free(gauss_y);
free(gauss_z);
}
@@ -695,11 +695,11 @@ void invert(double** cov, int L, double** icov, double* detcov)
for(j=0; j < L; j++)
for (i=0; i < L; i++)
a[j*L+i] = cov[i][j];
-
- int M = (int) L;
+
+ int M = (int) L;
int* ipiv = (int *) malloc(L*L*sizeof(int));
int ret;
-
+
/* LU decomposition */
ret = dgetrf_(&M, &M, a, &M, ipiv, &ret); /* ret should be zero, negative if cov is singular */
if (ret < 0)
@@ -707,7 +707,7 @@ void invert(double** cov, int L, double** icov, double* detcov)
fprintf(stderr, "Covariance matrix was singular, couldn't invert\n");
exit(-1);
}
-
+
/* find determinant */
double det = 1;
for(i = 0; i < L; i++)
@@ -723,27 +723,27 @@ void invert(double** cov, int L, double** icov, double* detcov)
if (det < 0)
det = -det;
*detcov = det;
-
+
/* allocate required working storage */
#ifndef HAVE_ATLAS
int lwork = -1;
double lwbest = 0.0;
dgetri_(&M, a, &M, ipiv, &lwbest, &lwork, &ret);
- lwork = (int) lwbest;
+ lwork = (int) lwbest;
double* work = (double*) malloc(lwork*sizeof(double));
#endif
-
+
/* find inverse */
dgetri_(&M, a, &M, ipiv, work, &lwork, &ret);
for(j=0; j < L; j++)
for (i=0; i < L; i++)
- icov[i][j] = a[j*L+i];
-
-#ifndef HAVE_ATLAS
+ icov[i][j] = a[j*L+i];
+
+#ifndef HAVE_ATLAS
free(work);
#endif
- free(a);
+ free(a);
}
/* probability of multivariate Gaussian given mean, inverse and determinant of covariance */
@@ -762,8 +762,8 @@ double gauss(double* x, int L, double* mu, double** icov, double detcov, double*
}
s = cblas_ddot(L, z, 1, y, 1);
//for (i = 0; i < L; i++)
- // s += z[i] * y[i];
-
+ // s += z[i] * y[i];
+
return exp(-s/2.0) / (pow(2*PI, L/2.0) * sqrt(detcov));
}
@@ -784,10 +784,10 @@ double loggauss(double* x, int L, double* mu, double** icov, double detcov, doub
}
s = cblas_ddot(L, z, 1, y, 1);
//for (i = 0; i < L; i++)
- // s += z[i] * y[i];
-
+ // s += z[i] * y[i];
+
ret = -0.5 * (s + L * log(2*PI) + log(detcov));
-
+
/*
// TEST
if (ISINF(ret) > 0)
@@ -795,9 +795,9 @@ double loggauss(double* x, int L, double* mu, double** icov, double detcov, doub
if (ISINF(ret) < 0)
printf("loggauss returning -infinity\n");
if (ISNAN(ret))
- printf("loggauss returning nan\n");
+ printf("loggauss returning nan\n");
*/
-
+
return ret;
}
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