public Double eval(Double lmbda) {
double c = 1.0 / (double) Math.sqrt(variance);
double sum = 0.0;
for (int i = 0; i < data.size(); i++) {
for (int k = 0; k < channels.length; k++) {
double pi = 0.0;
double pdi = 0.0;
for (Integer t : transcripts.keySet()) {
if (transcripts.get(t).contains(i)) {
double gammai = gammas[t][k];
double dit = delta(i, t);
double falloff = Math.exp(-lmbda * dit);
double pit = gammai * falloff;
double pdit = pit * dit;
pi += pit;
pdi += pdit;
}
}
double zi = Math.log(pi);
double err = data.values(i)[channels[k]] - zi;
double ratio = pdi / pi;
double termi = (err * ratio);
sum += termi;
}
}
return c * sum;
}
public void optimize() {
boolean iterating = true;
double eps = 0.01;
int iters = 0;
FunctionModel dllambda = new DLLambda();
while (iterating) {
iters += 1;
// System.out.print(String.format("%d:", iters));
iterating = false;
for (int t = 0; t < gammas.length; t++) {
for (int k = 0; k < gammas[t].length; k++) {
FunctionModel m = new DLGamma(t, k);
double z = findZero(m, 1.0, eps);
z = Math.max(z, 0.001);
double d = z - gammas[t][k];
iterating = iterating || Math.abs(d) >= eps;
gammas[t][k] = z;
// System.out.print(String.format(" g%d=%.5f (%.5f)", t, gammas[t], Math.log(gammas[t])));
}
}
double lz = findZero(dllambda, 1.0e-5, 1.0e-6);
double dz = lz - lambda;
lambda = lz;
// System.out.println(String.format(", lmbda=%f", lambda));
}
}
public Double eval(Double lmbda) {
double c1 = 0.0;
double c3 = -1.0 / (double) Math.sqrt(2.0 * variance);
double sum = 0.0;
double cpart = -0.5 * Math.log(Math.sqrt(2.0 * Math.PI * variance));
for (int i = 0; i < data.size(); i++) {
for (int k = 0; k < channels.length; k++) {
c1 += cpart;
double pi = 0.0;
for (Integer t : transcripts.keySet()) {
if (transcripts.get(t).contains(i)) {
double dit = delta(i, t);
double gammai = gammas[t][k];
double pit = gammai * Math.exp(-lmbda * dit);
pi += pit;
}
}
double zi = Math.log(pi);
double err = data.values(i)[channels[k]] - zi;
sum += (err * err);
}
}
return c1 + c3 * sum;
}
public Double eval(Double gamma) {
double c = 1.0 / (double) Math.sqrt(variance);
double sum = 0.0;
for (Integer i : transcripts.get(gammat)) {
double pi = 0.0;
for (int t = 0; t < fiveprime.length; t++) {
if (transcripts.get(t).contains(i)) {
double gammai = gammat == t ? gamma : gammas[t][gammak];
double dit = delta(i, t);
double pit = gammai * Math.exp(-lambda * dit);
pi += pit;
}
}
double zi = Math.log(pi);
double err = data.values(i)[channels[gammak]] - zi;
double ratio = (Math.exp(-lambda * delta(i, gammat))) / pi;
double termi = (err * ratio);
sum += termi;
}
return c * sum;
}
public Double eval(Double gamma) {
double c1 = 0.0;
double c3 = -1.0 / (double) Math.sqrt(2.0 * variance);
double sum = 0.0;
double cpart = -0.5 * Math.log(Math.sqrt(2.0 * Math.PI * variance));
for (Integer i : transcripts.get(gammat)) {
c1 += cpart;
double pi = 0.0;
for (int t = 0; t < fiveprime.length; t++) {
if (transcripts.get(t).contains(i)) {
double gammai = gammat == t ? gamma : gammas[t][gammak];
double dit = delta(i, t);
double pit = gammai * Math.exp(-lambda * dit);
pi += pit;
}
}
double zi = Math.log(pi);
double err = data.values(i)[channels[gammak]] - zi;
sum += (err * err);
}
return c1 + c3 * sum;
}
public double error() {
double sum = 0.0;
for (int i = 0; i < data.size(); i++) {
for (int k = 0; k < channels.length; k++) {
double pi = 0.0;
for (Integer t : transcripts.keySet()) {
if (transcripts.get(t).contains(i)) {
double gammai = gammas[t][k];
double dit = delta(i, t);
double pit = gammai * Math.exp(-lambda * dit);
pi += pit;
}
}
double zi = Math.log(pi);
double err = Math.abs(data.values(i)[channels[k]] - zi);
sum += err;
}
}
return sum;
}
public static double findZero(FunctionModel f, double start, double eps) {
double[] bounds = findZeroBrackets(f, start);
double lower = bounds[0], upper = bounds[1];
double ly = f.eval(lower), uy = f.eval(upper);
// System.out.println(String.format("Zero: [%f, %f] (%f, %f)", lower, upper, ly, uy));
boolean lsign = ly < 0.0;
boolean usign = uy <= 0.0;
while (Math.abs(upper - lower) > eps) {
double middle = (upper + lower) / 2.0;
double my = f.eval(middle);
boolean msign = my < 0.0;
if (my == 0.0) {
return middle;
} else if (msign == lsign) {
lower = middle;
ly = my;
lsign = msign;
// System.out.println(String.format("\tU: [%f, %f] (%f, %f)", lower, upper, ly, uy));
} else {
upper = middle;
uy = my;
usign = msign;
// System.out.println(String.format("\tL: [%f, %f] (%f, %f)", lower, upper, ly, uy));
}
}
double v = (lower + upper) / 2.0;
// System.out.println(String.format("\t-> %f", v));
return v;
}