int main()
{
HMM hmm_initial;
/*
HMM hmms[5];
load_models( "modellist.txt", hmms, 5);
dump_models( hmms, 5);
*/
loadHMM( &hmm_initial, "model_init.txt" );
dumpHMM( stderr, &hmm_initial );
printf("%f\n", log(1.5) ); // make sure the math library is included
return 0;
}
int main(int argc, char* argv[]) {
int seq[10000][50];
char tmp[52];
int i=0, j=0, k=0;
FILE *fp = fopen(argv[3], "r");
while (fscanf(fp, "%s", tmp) != EOF) {
for (i=0; i<50; i++)
seq[j][i] = tmp[i]-'A';
j++;
}
fclose (fp);
int iter = atoi(argv[1]);
HMM hmm;
loadHMM (&hmm, argv[2]);
double alpha[50][hmm.state_num], beta[50][hmm.state_num], gamma[50][hmm.state_num], gamma_sum[hmm.observ_num][hmm.state_num], epsilon[49][hmm.state_num][hmm.state_num];
while (iter--) {
//initialize
memset (gamma, 0, sizeof(gamma[0][0])*50*hmm.state_num);
memset (gamma_sum, 0, sizeof(gamma_sum[0][0])*hmm.observ_num*hmm.state_num);
memset (epsilon, 0, sizeof(epsilon[0][0][0])*49*hmm.state_num*hmm.state_num);
for (int it=0; it<10000; it++) {
//alpha
for (i=0; i<hmm.state_num; i++)
alpha[0][i] = hmm.initial[i]*hmm.observation[seq[it][0]][i];
for (i=0; i<49; i++) {
for (j=0; j<hmm.state_num; j++) {
double sum=0;
for (k=0; k<hmm.state_num; k++)
sum += alpha[i][k]*hmm.transition[k][j];
alpha[i+1][j] = sum*hmm.observation[seq[it][i+1]][j];
}
}
//beta
for (i=0; i<hmm.state_num; i++)
beta[49][i] = 1;
for (i=48; i>=0; i--) {
for (j=0; j<hmm.state_num; j++)
for (beta[i][j]=0, k=0; k<hmm.state_num; k++)
beta[i][j] += hmm.transition[j][k] * hmm.observation[seq[it][i+1]][k]*beta[i+1][k];
}
//gamma
for (i=0; i<50; i++) {
double sum=0;
for (j=0; j<hmm.state_num; j++)
sum += alpha[i][j]*beta[i][j];
for (j=0; j<hmm.state_num; j++) {
gamma[i][j] += alpha[i][j]*beta[i][j]/sum;
gamma_sum[seq[it][i]][j] += alpha[i][j]*beta[i][j]/sum;
}
}
//epsilon
for (j=0; j<49; j++) {
double sum=0;
for (k=0; k<hmm.state_num; k++)
for (i=0; i<hmm.state_num; i++)
sum += alpha[j][i]*hmm.transition[i][k]*hmm.observation[seq[it][j+1]][k]*beta[j+1][k];
for (k=0; k<hmm.state_num; k++)
for (i=0; i<hmm.state_num; i++)
epsilon[j][k][i] += alpha[j][k]*hmm.transition[k][i]*hmm.observation[seq[it][j+1]][i]*beta[j+1][i]/sum;
}
}
//pi
for (i=0; i<hmm.state_num; i++)
hmm.initial[i] = gamma[0][i]/10000;
//a
for (i=0; i<hmm.state_num; i++) {
double sum=0;
for (j=0; j<49; j++)
sum += gamma[j][i];
for (j=0; j<hmm.state_num; j++) {
double tmp=0;
for (k=0; k<49; k++)
tmp += epsilon[k][i][j];
hmm.transition[i][j] = tmp/sum;
}
}
//b
for (i=0; i<hmm.observ_num; i++) {
for (j=0; j<hmm.state_num; j++) {
double sum=0;
for (k=0; k<50; k++)
sum += gamma[k][j];
hmm.observation[i][j] = gamma_sum[i][j]/sum;
}
}
}
dumpHMM (fopen(argv[4], "w"), &hmm);
return 0;
}
