slightly simplifiy EMGLLF.c, check that C == R (code reading only)

diff --git a/pkg/R/EMGLLF_R.R b/pkg/R/EMGLLF_R.R
index 362d0dc..09ae2e3 100644 (file)
--- a/pkg/R/EMGLLF_R.R
+++ b/pkg/R/EMGLLF_R.R
@@ -17,7 +17,6 @@ EMGLLF_R = function(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,lambda,X,Y,ta
        gam = gamInit
        Gram2 = array(0, dim=c(p,p,k))
        ps2 = array(0, dim=c(p,m,k))
        gam = gamInit
        Gram2 = array(0, dim=c(p,p,k))
        ps2 = array(0, dim=c(p,m,k))

-       b = rep(0, k)

        X2 = array(0, dim=c(n,p,k))
        Y2 = array(0, dim=c(n,m,k))
        EPS = 1e-15
        X2 = array(0, dim=c(n,p,k))
        Y2 = array(0, dim=c(n,m,k))
        EPS = 1e-15


@@ -108,34 +107,34 @@ EMGLLF_R = function(phiInit,rhoInit,piInit,gamInit,mini,maxi,gamma,lambda,X,Y,ta
                #Etape E #
                ##########
 
                #Etape E #
                ##########
 

-               sumLogLLH2 = 0
+               # Precompute det(rho[,,r]) for r in 1...k
+               detRho = sapply(1:k, function(r) det(rho[,,r]))
+
+               sumLogLLH = 0

                for (i in 1:n)
                {
                        # Update gam[,]
                for (i in 1:n)
                {
                        # Update gam[,]

-                       sumLLH1 = 0

                        sumGamI = 0
                        for (r in 1:k)
                        {
                        sumGamI = 0
                        for (r in 1:k)
                        {

-                               gam[i,r] = pi[r] * exp(-0.5*sum( (Y[i,]%*%rho[,,r]-X[i,]%*%phi[,,r])^2 ))
-                                       * det(rho[,,r])
-                               sumLLH1 = sumLLH1 + gam[i,r] / (2*base::pi)^(m/2)
+                               gam[i,r] = pi[r]*exp(-0.5*sum((Y[i,]%*%rho[,,r]-X[i,]%*%phi[,,r])^2))*detRho[r]

                                sumGamI = sumGamI + gam[i,r]
                        }
                                sumGamI = sumGamI + gam[i,r]
                        }

-                       sumLogLLH2 = sumLogLLH2 + log(sumLLH1)
-                       if(sumGamI > EPS) #else: gam[i,] is already ~=0
+                       sumLogLLH = sumLogLLH + log(sumGamI) - log((2*base::pi)^(m/2))
+                       if (sumGamI > EPS) #else: gam[i,] is already ~=0

                                gam[i,] = gam[i,] / sumGamI
                }
 
                sumPen = sum(pi^gamma * b)
                last_llh = llh
                                gam[i,] = gam[i,] / sumGamI
                }
 
                sumPen = sum(pi^gamma * b)
                last_llh = llh

-               llh = -sumLogLLH2/n + lambda*sumPen
+               llh = -sumLogLLH/n + lambda*sumPen

                dist = ifelse( ite == 1, llh, (llh-last_llh) / (1+abs(llh)) )
                Dist1 = max( (abs(phi-Phi)) / (1+abs(phi)) )
                Dist2 = max( (abs(rho-Rho)) / (1+abs(rho)) )
                Dist3 = max( (abs(pi-Pi)) / (1+abs(Pi)) )
                dist2 = max(Dist1,Dist2,Dist3)
 
                dist = ifelse( ite == 1, llh, (llh-last_llh) / (1+abs(llh)) )
                Dist1 = max( (abs(phi-Phi)) / (1+abs(phi)) )
                Dist2 = max( (abs(rho-Rho)) / (1+abs(rho)) )
                Dist3 = max( (abs(pi-Pi)) / (1+abs(Pi)) )
                dist2 = max(Dist1,Dist2,Dist3)
 

-               if (ite>=mini && (dist>= tau || dist2 >= sqrt(tau)))
+               if (ite >= mini && (dist >= tau || dist2 >= sqrt(tau)))

                        break
        }
 
                        break
        }
 

diff --git a/pkg/src/sources/EMGLLF.c b/pkg/src/sources/EMGLLF.c
index e019588..4ceb3e3 100644 (file)
--- a/pkg/src/sources/EMGLLF.c
+++ b/pkg/src/sources/EMGLLF.c
@@ -1,9 +1,10 @@
 #include "utils.h"
 #include <stdlib.h>
 #include "utils.h"
 #include <stdlib.h>

+#include <math.h>

 #include <gsl/gsl_linalg.h>
 
 // TODO: don't recompute indexes ai(...) and mi(...) when possible
 #include <gsl/gsl_linalg.h>
 
 // TODO: don't recompute indexes ai(...) and mi(...) when possible

-void EMGLLF_core(
+void EMGLLH_core(

        // IN parameters
        const Real* phiInit, // parametre initial de moyenne renormalisé
        const Real* rhoInit, // parametre initial de variance renormalisé
        // IN parameters
        const Real* phiInit, // parametre initial de moyenne renormalisé
        const Real* rhoInit, // parametre initial de variance renormalisé


@@ -20,7 +21,8 @@ void EMGLLF_core(
        Real* phi, // parametre de moyenne renormalisé, calculé par l'EM
        Real* rho, // parametre de variance renormalisé, calculé par l'EM
        Real* pi, // parametre des proportions renormalisé, calculé par l'EM
        Real* phi, // parametre de moyenne renormalisé, calculé par l'EM
        Real* rho, // parametre de variance renormalisé, calculé par l'EM
        Real* pi, // parametre des proportions renormalisé, calculé par l'EM

-       Real* LLF, // log vraisemblance associée à cet échantillon, pour les valeurs estimées des paramètres
+       Real* llh, // (derniere) log vraisemblance associée à cet échantillon,
+                  // pour les valeurs estimées des paramètres

        Real* S,
        int* affec,
        // additional size parameters
        Real* S,
        int* affec,
        // additional size parameters


@@ -33,7 +35,6 @@ void EMGLLF_core(
        copyArray(phiInit, phi, p*m*k);
        copyArray(rhoInit, rho, m*m*k);
        copyArray(piInit, pi, k);
        copyArray(phiInit, phi, p*m*k);
        copyArray(rhoInit, rho, m*m*k);
        copyArray(piInit, pi, k);

-       zeroArray(LLF, maxi);

        //S is already allocated, and doesn't need to be 'zeroed'
 
        //Other local variables: same as in R
        //S is already allocated, and doesn't need to be 'zeroed'
 
        //Other local variables: same as in R


@@ -44,18 +45,13 @@ void EMGLLF_core(
        Real* b = (Real*)malloc(k*sizeof(Real));
        Real* X2 = (Real*)malloc(n*p*k*sizeof(Real));
        Real* Y2 = (Real*)malloc(n*m*k*sizeof(Real));
        Real* b = (Real*)malloc(k*sizeof(Real));
        Real* X2 = (Real*)malloc(n*p*k*sizeof(Real));
        Real* Y2 = (Real*)malloc(n*m*k*sizeof(Real));

-       Real dist = 0.;
-       Real dist2 = 0.;
-       int ite = 0;
+       *llh = -INFINITY;

        Real* pi2 = (Real*)malloc(k*sizeof(Real));
        Real* pi2 = (Real*)malloc(k*sizeof(Real));

-       Real* ps = (Real*)malloc(m*k*sizeof(Real));
-       Real* nY2 = (Real*)malloc(m*k*sizeof(Real));
-       Real* ps1 = (Real*)malloc(n*m*k*sizeof(Real));
-       Real* Gam = (Real*)malloc(n*k*sizeof(Real));

        const Real EPS = 1e-15;
        // Additional (not at this place, in R file)
        Real* gam2 = (Real*)malloc(k*sizeof(Real));
        Real* sqNorm2 = (Real*)malloc(k*sizeof(Real));
        const Real EPS = 1e-15;
        // Additional (not at this place, in R file)
        Real* gam2 = (Real*)malloc(k*sizeof(Real));
        Real* sqNorm2 = (Real*)malloc(k*sizeof(Real));

+       Real* detRho = (Real*)malloc(k*sizeof(Real));

        gsl_matrix* matrix = gsl_matrix_alloc(m, m);
        gsl_permutation* permutation = gsl_permutation_alloc(m);
        Real* YiRhoR = (Real*)malloc(m*sizeof(Real));
        gsl_matrix* matrix = gsl_matrix_alloc(m, m);
        gsl_permutation* permutation = gsl_permutation_alloc(m);
        Real* YiRhoR = (Real*)malloc(m*sizeof(Real));


@@ -65,7 +61,7 @@ void EMGLLF_core(
        Real* Rho = (Real*)malloc(m*m*k*sizeof(Real));
        Real* Pi = (Real*)malloc(k*sizeof(Real));
 
        Real* Rho = (Real*)malloc(m*m*k*sizeof(Real));
        Real* Pi = (Real*)malloc(k*sizeof(Real));
 

-       while (ite < mini || (ite < maxi && (dist >= tau || dist2 >= sqrt(tau))))
+       for (int ite=0; ite<maxi; ite++)

        {
                copyArray(phi, Phi, p*m*k);
                copyArray(rho, Rho, m*m*k);
        {
                copyArray(phi, Phi, p*m*k);
                copyArray(rho, Rho, m*m*k);


@@ -143,8 +139,8 @@ void EMGLLF_core(
                }
 
                //tant que les proportions sont negatives
                }
 
                //tant que les proportions sont negatives

-               int kk = 0;
-               int pi2AllPositive = 0;
+               int kk = 0,
+                       pi2AllPositive = 0;

                Real invN = 1./n;
                while (!pi2AllPositive)
                {
                Real invN = 1./n;
                while (!pi2AllPositive)
                {


@@ -209,28 +205,21 @@ void EMGLLF_core(
                {
                        for (int mm=0; mm<m; mm++)
                        {
                {
                        for (int mm=0; mm<m; mm++)
                        {

+                               Real ps = 0.,
+                                       nY2 = 0.;
+                               // Compute ps, and nY2 = sum(Y2[,mm,r]^2)

                                for (int i=0; i<n; i++)
                                {
                                        //< X2[i,,r] , phi[,mm,r] >
                                        Real dotProduct = 0.;
                                        for (int u=0; u<p; u++)
                                                dotProduct += X2[ai(i,u,r,n,p,k)] * phi[ai(u,mm,r,p,m,k)];
                                for (int i=0; i<n; i++)
                                {
                                        //< X2[i,,r] , phi[,mm,r] >
                                        Real dotProduct = 0.;
                                        for (int u=0; u<p; u++)
                                                dotProduct += X2[ai(i,u,r,n,p,k)] * phi[ai(u,mm,r,p,m,k)];

-                                       //ps1[i,mm,r] = Y2[i,mm,r] * sum(X2[i,,r] * phi[,mm,r])
-                                       ps1[ai(i,mm,r,n,m,k)] = Y2[ai(i,mm,r,n,m,k)] * dotProduct;
+                                       //ps = ps + Y2[i,mm,r] * sum(X2[i,,r] * phi[,mm,r])
+                                       ps += Y2[ai(i,mm,r,n,m,k)] * dotProduct;
+                                       nY2 += Y2[ai(i,mm,r,n,m,k)] * Y2[ai(i,mm,r,n,m,k)];

                                }
                                }

-                               //ps[mm,r] = sum(ps1[,mm,r])
-                               Real sumPs1 = 0.;
-                               for (int u=0; u<n; u++)
-                                       sumPs1 += ps1[ai(u,mm,r,n,m,k)];
-                               ps[mi(mm,r,m,k)] = sumPs1;
-                               //nY2[mm,r] = sum(Y2[,mm,r]^2)
-                               Real sumY2 = 0.;
-                               for (int u=0; u<n; u++)
-                                       sumY2 += Y2[ai(u,mm,r,n,m,k)] * Y2[ai(u,mm,r,n,m,k)];
-                               nY2[mi(mm,r,m,k)] = sumY2;
-                               //rho[mm,mm,r] = (ps[mm,r]+sqrt(ps[mm,r]^2+4*nY2[mm,r]*(gam2[r]))) / (2*nY2[mm,r])
-                               rho[ai(mm,mm,r,m,m,k)] = ( ps[mi(mm,r,m,k)] + sqrt( ps[mi(mm,r,m,k)]*ps[mi(mm,r,m,k)]
-                                       + 4*nY2[mi(mm,r,m,k)] * gam2[r] ) ) / (2*nY2[mi(mm,r,m,k)]);
+                               //rho[mm,mm,r] = (ps+sqrt(ps^2+4*nY2*gam2[r])) / (2*nY2)
+                               rho[ai(mm,mm,r,m,m,k)] = (ps + sqrt(ps*ps + 4*nY2 * gam2[r])) / (2*nY2);

                        }
                }
 
                        }
                }
 


@@ -240,7 +229,7 @@ void EMGLLF_core(
                        {
                                for (int mm=0; mm<m; mm++)
                                {
                        {
                                for (int mm=0; mm<m; mm++)
                                {

-                                       //sum(phi[-j,mm,r] * Gram2[j, setdiff(1:p,j),r])
+                                       //sum(phi[-j,mm,r] * Gram2[j,-j,r])

                                        Real phiDotGram2 = 0.;
                                        for (int u=0; u<p; u++)
                                        {
                                        Real phiDotGram2 = 0.;
                                        for (int u=0; u<p; u++)
                                        {


@@ -248,7 +237,8 @@ void EMGLLF_core(
                                                        phiDotGram2 += phi[ai(u,mm,r,p,m,k)] * Gram2[ai(j,u,r,p,p,k)];
                                        }
                                        //S[j,mm,r] = -rho[mm,mm,r]*ps2[j,mm,r] + sum(phi[-j,mm,r] * Gram2[j,-j,r])
                                                        phiDotGram2 += phi[ai(u,mm,r,p,m,k)] * Gram2[ai(j,u,r,p,p,k)];
                                        }
                                        //S[j,mm,r] = -rho[mm,mm,r]*ps2[j,mm,r] + sum(phi[-j,mm,r] * Gram2[j,-j,r])

-                                       S[ai(j,mm,r,p,m,k)] = -rho[ai(mm,mm,r,m,m,k)] * ps2[ai(j,mm,r,p,m,k)] + phiDotGram2;
+                                       S[ai(j,mm,r,p,m,k)] = -rho[ai(mm,mm,r,m,m,k)] * ps2[ai(j,mm,r,p,m,k)]
+                                               + phiDotGram2;

                                        Real pirPowGamma = pow(pi[r],gamma);
                                        if (fabs(S[ai(j,mm,r,p,m,k)]) <= n*lambda*pirPowGamma)
                                                phi[ai(j,mm,r,p,m,k)] = 0.;
                                        Real pirPowGamma = pow(pi[r],gamma);
                                        if (fabs(S[ai(j,mm,r,p,m,k)]) <= n*lambda*pirPowGamma)
                                                phi[ai(j,mm,r,p,m,k)] = 0.;


@@ -270,8 +260,20 @@ void EMGLLF_core(
                // Etape E //
                /////////////
 
                // Etape E //
                /////////////
 

+               // Precompute det(rho[,,r]) for r in 1...k
+               for (int r=0; r<k; r++)
+               {
+                       for (int u=0; u<m; u++)
+                       {
+                               for (int v=0; v<m; v++)
+                                       matrix->data[u*m+v] = rho[ai(u,v,r,m,m,k)];
+                       }
+                       gsl_linalg_LU_decomp(matrix, permutation, &signum);
+                       detRho[r] = gsl_linalg_LU_det(matrix, signum);
+               }
+

                int signum;
                int signum;

-               Real sumLogLLF2 = 0.;
+               Real sumLogLLH = 0.;

                for (int i=0; i<n; i++)
                {
                        for (int r=0; r<k; r++)
                for (int i=0; i<n; i++)
                {
                        for (int r=0; r<k; r++)


@@ -298,28 +300,18 @@ void EMGLLF_core(
                                        sqNorm2[r] += (YiRhoR[u]-XiPhiR[u]) * (YiRhoR[u]-XiPhiR[u]);
                        }
 
                                        sqNorm2[r] += (YiRhoR[u]-XiPhiR[u]) * (YiRhoR[u]-XiPhiR[u]);
                        }
 

-                       Real sumLLF1 = 0.;

                        Real sumGamI = 0.;
                        for (int r=0; r<k; r++)
                        {
                        Real sumGamI = 0.;
                        for (int r=0; r<k; r++)
                        {

-                               //compute det(rho[,,r]) [TODO: avoid re-computations]
-                               for (int u=0; u<m; u++)
-                               {
-                                       for (int v=0; v<m; v++)
-                                               matrix->data[u*m+v] = rho[ai(u,v,r,m,m,k)];
-                               }
-                               gsl_linalg_LU_decomp(matrix, permutation, &signum);
-                               Real detRhoR = gsl_linalg_LU_det(matrix, signum);
-                               Gam[mi(i,r,n,k)] = pi[r] * exp(-.5*sqNorm2[r]) * detRhoR;
-                               sumLLF1 += Gam[mi(i,r,n,k)] / gaussConstM;
-                               sumGamI += Gam[mi(i,r,n,k)];
+                               gam[mi(i,r,n,k)] = pi[r] * exp(-.5*sqNorm2[r]) * detRho[r];
+                               sumGamI += gam[mi(i,r,n,k)];

                        }
 
                        }
 

-                       sumLogLLF2 += log(sumLLF1);
-                       for (int r=0; r<k; r++)
+                       sumLogLLH += log(sumGamI) - log(gaussConstM);
+                       if (sumGamI > EPS) //else: gam[i,] is already ~=0

                        {
                        {

-                               //gam[i,] = Gam[i,] / sumGamI
-                               gam[mi(i,r,n,k)] = sumGamI > EPS ? Gam[mi(i,r,n,k)] / sumGamI : 0.;
+                               for (int r=0; r<k; r++)
+                                       gam[mi(i,r,n,k)] /= sumGamI;

                        }
                }
 
                        }
                }
 


@@ -327,9 +319,10 @@ void EMGLLF_core(
                Real sumPen = 0.;
                for (int r=0; r<k; r++)
                        sumPen += pow(pi[r],gamma) * b[r];
                Real sumPen = 0.;
                for (int r=0; r<k; r++)
                        sumPen += pow(pi[r],gamma) * b[r];

-               //LLF[ite] = -sumLogLLF2/n + lambda*sumPen
-               LLF[ite] = -invN * sumLogLLF2 + lambda * sumPen;
-               dist = ite==0 ? LLF[ite] : (LLF[ite] - LLF[ite-1]) / (1. + fabs(LLF[ite]));
+               Real last_llh = *llh;
+               //llh = -sumLogLLH/n + lambda*sumPen
+               *llh = -invN * sumLogLLH + lambda * sumPen;
+               Real dist = ite==0 ? *llh : (*llh - last_llh) / (1. + fabs(*llh));

 
                //Dist1 = max( abs(phi-Phi) / (1+abs(phi)) )
                Real Dist1 = 0.;
 
                //Dist1 = max( abs(phi-Phi) / (1+abs(phi)) )
                Real Dist1 = 0.;


@@ -373,13 +366,14 @@ void EMGLLF_core(
                        }
                }
                //dist2=max([max(Dist1),max(Dist2),max(Dist3)]);
                        }
                }
                //dist2=max([max(Dist1),max(Dist2),max(Dist3)]);

-               dist2 = Dist1;
+               Real dist2 = Dist1;

                if (Dist2 > dist2)
                        dist2 = Dist2;
                if (Dist3 > dist2)
                        dist2 = Dist3;
 
                if (Dist2 > dist2)
                        dist2 = Dist2;
                if (Dist3 > dist2)
                        dist2 = Dist3;
 

-               ite++;
+               if (ite >= mini && (dist >= tau || dist2 >= sqrt(tau)))
+                       break;

        }
 
        //affec = apply(gam, 1, which.max)
        }
 
        //affec = apply(gam, 1, which.max)


@@ -400,13 +394,9 @@ void EMGLLF_core(
        //free memory
        free(b);
        free(gam);
        //free memory
        free(b);
        free(gam);

-       free(Gam);

        free(Phi);
        free(Rho);
        free(Pi);
        free(Phi);
        free(Rho);
        free(Pi);

-       free(ps);
-       free(nY2);
-       free(ps1);

        free(Gram2);
        free(ps2);
        gsl_matrix_free(matrix);
        free(Gram2);
        free(ps2);
        gsl_matrix_free(matrix);