/* HMM_logL -
* Given an HMM and a vector of log likelihoods for states assigned to
* data vectors in the sequence, returns the log likelihood of the data
* given the HMM.
*/
Real HMM_logL(Hmm *m, RVec *logL)
{ int u, tt = VLENGTH(logL[0]);
Real l = NEGATIVE_INFINITY;
/* P(sequence|m) = sum(u = 1 ... m->uu, alpha[u][tt]) */
HMM_calcAlphas(m, logL);
for (u = 0; u<m->uu; u++) l = add_exp(l, MATRIX(g_alpha)[u][tt-1]);
return l;}
/* HMM_calcGammas computes gammas, which are the probabilities that
* each frame is in each state
*/
void HMM_calcGammas(Hmm *m, RVec *logL, RVec *gamma) {
int t, u, v, tt = VLENGTH(logL[0]);
Real **a = MATRIX(m->logA), **al, **be;
Real like;
assert(VLENGTH(logL[0])==VLENGTH(gamma[0]));
HMM_initGlobals(m->uu, tt);
al = MATRIX(g_alpha);
be = MATRIX(g_beta);
/* calculate alpha's */
HMM_calcAlphas(m, logL);
/* calculate beta's -
* beta[u][tt] = 1
* beta[u][t] = sum(v = 1 ... m->uu, a[u][v]*beta[v][t+1]*logL[v][t+1])
*/
for (u = 0; u<m->uu; u++) be[u][tt-1] = 0.0;
for (t = tt-2; t>=0; t--)
{ for (u = 0; u<m->uu; u++)
{ be[u][t] = NEGATIVE_INFINITY;
for (v = 0; v<m->uu; v++)
{ be[u][t] =
add_exp(be[u][t], a[u][v]+be[v][t+1]+VECTOR(logL[v])[t+1]);}}}
/* calculate logL of sequence -
* P(sequence|m) = sum(u = 1 ... m->uu, alpha[u][tt])
*/
like = NEGATIVE_INFINITY;
for (u = 0; u<m->uu; u++) like = add_exp(like, al[u][tt-1]);
/* calculate responsibilities
* alpha[u][t]*beta[u][t]
* gamma[u][t] = ----------------------
* P(data|model)
*/
for (t = 0; t<tt; t++)
{ for (u = 0; u<m->uu; u++) VECTOR(gamma[u])[t] = al[u][t]+be[u][t]-like;}}
/* HMM_updateModel -
* Given an HMM and a vector of log likelihoods for states in the sequences,
* calculates the responsibilities of each state in the HMM for each symbol
* in the sequences, and maximises the model parameters based on the
* assigned log likelihoods.
*/
Real HMM_updateModel(Hmm *m, Hmm *new_m, RVec *logL, RVec *gamma, Real log_D,
Real postpC, int c, int c_ls,
enum training_mode training_mode) {
int t, u, v, tt = VLENGTH(logL[0]);
Real **a = MATRIX(m->logA), *b = VECTOR(m->logB), **al, **be, ***ps;
Real logD = 0, like, dtf;
int Sc = (c==c_ls);
switch (training_mode) {
case HMM_ML:
assert(postpC==0.0);
logD = NEGATIVE_INFINITY;
break;
case HMM_DT:
assert(c>=0&&c_ls>=0);
logD = log_D;
break;
default: panic("unrecognized training mode");
}
assert(VLENGTH(logL[0])==VLENGTH(gamma[0]));
HMM_initGlobals(m->uu, tt);
al = MATRIX(g_alpha);
be = MATRIX(g_beta);
ps = MATRIX(g_psi);
/* calculate alpha's */
HMM_calcAlphas(m, logL);
/* calculate beta's -
* beta[u][tt] = 1
* beta[u][t] = sum(v = 1 ... m->uu, a[u][v]*beta[v][t+1]*logL[v][t+1])
*/
for (u = 0; u<m->uu; u++) be[u][tt-1] = 0.0;
for (t = tt-2; t>=0; t--)
{ for (u = 0; u<m->uu; u++)
{ be[u][t] = NEGATIVE_INFINITY;
for (v = 0; v<m->uu; v++)
{ be[u][t] =
add_exp(be[u][t], a[u][v]+be[v][t+1]+VECTOR(logL[v])[t+1]);}}}
/* calculate logL of sequence -
* P(sequence|m) = sum(u = 1 ... m->uu, alpha[u][tt])
*/
like = NEGATIVE_INFINITY;
for (u = 0; u<m->uu; u++)
like = add_exp(like, al[u][tt-1]);
/* A sample that can NEVER belong to this category */
if(like == NEGATIVE_INFINITY){
assert(postpC == 0.0);
assert(Sc==0);
}
/* calculate responsibilities
* alpha[u][t]*beta[u][t]
* gamma[u][t] = ----------------------
* P(data|model)
*/
for (t = 0; t<tt; t++){
for (u = 0; u<m->uu; u++){
if(like!=NEGATIVE_INFINITY)
VECTOR(gamma[u])[t] = al[u][t]+be[u][t]-like;
else
VECTOR(gamma[u])[t] = NEGATIVE_INFINITY;
}
}
/* calculate time-indexed transition probabilities
* alpha[u][t]*a[u][v]*logL[v][t+1]*beta[v][t+1]
* psi[u][v][t] = ---------------------------------------------
* P(data|model)
*/
for (u = 0; u<m->uu; u++){
for (v = 0; v<m->uu; v++){
for (t = 0; t<tt-1; t++){
if(like!=NEGATIVE_INFINITY)
ps[u][v][t] = al[u][t]+a[u][v]+VECTOR(logL[v])[t+1]+be[v][t+1]-like;
else
ps[u][v][t] = NEGATIVE_INFINITY;
}
}
}
/* Update new model. The model may have been partly updated by some training
samples. */
a = MATRIX(new_m->logA);
b = VECTOR(new_m->logB);
/* calculate B
b[u] = gamma[u][1]
- added scaling by sum of gammas to catch any numerical accuracy problems
not log space here
*/
for (u = 0; u<m->uu; u++) {
/* This may be negative */
b[u] += (Sc-postpC)*my_exp(VECTOR(gamma[u])[0])
+my_exp(logD+VECTOR(m->logB)[u]);
}
/* calculate A matrix
* sum(t = 1 ... tt-1, psi[u][v][t])
* a[u][v] = -------------------------------------------------------
* sum(t = 1 ... tt-1, sum(w = 1 ... m->uu, psi[u][w][t]))
* see note above about log space
*/
for (u = 0; u<m->uu; u++) {
for (v = 0; v<m->uu; v++) {
/* This may be negative */
dtf = 0.0;
for(t = 0; t<tt-1; t++)
dtf += my_exp(ps[u][v][t])*(Sc-postpC) + my_exp(logD+MATRIX(m->logA)[u][v]);
a[u][v] += dtf;
}
}
for (t = 0; t<tt; t++) {
for (u = 0; u<m->uu; u++) VECTOR(gamma[u])[t] = my_exp(VECTOR(gamma[u])[t]);
}
return like;
}
