predictor.cpp
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#include <vector>
#include <iterator>
#include <functional>
#include <utility>
#include <algorithm>
#include <string>
#include <cctype>
#include <iostream>
#include <float.h>
#include <math.h>
#include <numeric>
#include <map>
#include <optional>
#include <string.h>
#include "predictor.h"
#include "IP/ipcomp.h"
#include "utils.h"
//#define _DEBUG
//#define _DEBUG_UPDATE
// Parameters for BOSHLIB-W instances
const int Lo = 4;
const int Lmax = 4;
const unsigned int phi = 7;
Predictor::Predictor( const std::vector < unsigned int > &v,
const std::vector < float > &vWCt,
const std::vector < float > &vWP,
const std::vector < float > &vWE,
const std::vector < std::vector < unsigned int > > &Nvs,
const std::vector < std::vector < unsigned int > > &NvBs,
const std::vector < std::vector < unsigned int > > &G2vertices,
const std::vector < std::vector < std::vector < unsigned int > > > &G2Nv,
const std::vector < std::vector < unsigned int > > &G2G1correspondance)
: vertices(v), verticesWCt(vWCt), verticesWP(vWP), verticesWE(vWE), Nv(Nvs),
NvB(NvBs), G2vertices(G2vertices), G2Nv(G2Nv), G2G1correspondance(G2G1correspondance)
{
tabu = std::vector < unsigned int > (uint(verticesWCt.size()), 0); // Record number of iteration for each vertice
L = Lo; // 0.1*float(vertices.size());
fc.push_back(-1); // Max user constraint weight
fc.push_back(FLT_MAX); // Min energy weight
fc.push_back(-1); // Max probing weight
w = 0; // Counter for consecutive non-improving local optima
}
Predictor::~Predictor()
{
}
void Predictor::predict(unsigned int T,
float alphas,
float alphar,
float Po,
unsigned int pseudoknotLevel,
unsigned int I,
unsigned int seed,
unsigned int nbHardCT)
{
//-----------------BLS-----------------
// Initialize random seed
srand(seed);
// Generate initial solution
int r = rand() % int(vertices.size());
unsigned int vertex = vertices[ulong(r)];
std::vector < unsigned int > nv, intersec,intersec2;
size_t i, size, j, size2;
// Take randomly one vertex
C.push_back(vertex);
fc[0] = verticesWCt[vertex];
fc[1] = verticesWE[vertex];
fc[2] = verticesWP[vertex];
#ifdef _DEBUG
std::cout << "INITIALIZATION" << std::endl;
std::cout << "\tC (initial) : ";
printVector(1);
#endif
// Update PA OM
std::map < uint, std::optional < uint > > omUpdate;
std::vector < uint >::iterator NvIt, NvEnd;
std::map < uint, std::optional < uint > >::iterator omUpdateIt;
std::vector < float > weights;
PA = Nv[C[0]];
for(j = 0; vertices[j] != C[0]; j++) {
weights = { verticesWCt[vertices[j]] - verticesWCt[C[0]],
verticesWE[vertices[j]] - verticesWE[C[0]],
verticesWP[vertices[j]] - verticesWP[C[0]] };
OM.push_back(std::make_tuple(vertices[j], C[0],weights));
}
j++;
for(size = vertices.size(); j != size; j++) {
weights = { verticesWCt[vertices[j]] - verticesWCt[C[0]],
verticesWE[vertices[j]] - verticesWE[C[0]],
verticesWP[vertices[j]] - verticesWP[C[0]] };
OM.push_back(std::make_tuple(vertices[j], C[0],weights));
}
Cbest.push_back(C); // Best solution found so far
fbest.push_back(fc); // Best objective value reached so far
Cp = C; // Last local optimum
#ifdef _DEBUG
std::cout << "\t--> Cbest (initial) :\n";
printVector(3);
printVector(4);
printVector(5);
std::cout << std::endl;
#endif
int m = -1, id = -1, sum = 0, dom = 0;
std::vector < float > delta = {FLT_MIN, FLT_MAX, FLT_MIN}, score, condition, alphaFc;
std::vector < unsigned int > PA1, verticesToPairs, newC, tabuUpdate, toRemove, G2, colors, givenColors, neighborColors;
unsigned int k, iter = 0, del, add;
size_t l, size3;
uint paretoSetUnchanged = 0;
while( !( (paretoSetUnchanged >= 2*T and paretoRespectHardCT(nbHardCT)) or iter >= 100000)){
#ifdef _DEBUG
std::cout << std::endl;
std::cout << "####################################################################################################\n" << std::endl;
std::cout << std::endl;
std::cout << "LOCAL SEARCH" << std::endl;
#endif
#ifdef _DEBUG_UPDATE
std::cout << std::endl;
std::cout << "####################################################################################################\n" << std::endl;
#endif
delta = {-1, FLT_MAX, -1};
m = -1;
id = -1;
// m1
for (i = 0, size = PA.size(); i != size; i++) {
weights = {verticesWCt[PA[i]],
verticesWE[PA[i]],
verticesWP[PA[i]]};
if(dominate(weights, delta) == 1 /*and findPseudoknotLevel(C, PA[i], -1) <= pseudoknotLevel*/) {
delta = weights;
m = 1;
id = int(i);
}
}
// m2
for (i = 0, size = OM.size(); i != size; i++) {
weights = std::get<2>(OM[i]);
if(dominate(weights, delta) == 1 /*and findPseudoknotLevel(C, std::get<0>(OM[i]), std::get<1>(OM[i])) <= pseudoknotLevel*/) {
delta = std::get<2>(OM[i]);
m = 2;
id = int(i);
}
}
#ifdef _DEBUG
std::cout << "\tMOVE : m = " << m;
if (m == 1) {
std::cout << " ; vertex = " << PA[id] << std::endl;
}
else if (m == 2) {
std::cout << " ; vertex = " << std::get<0>(OM[id]) << std::endl;
}
else {
std::cout << std::endl;
}
#endif
condition = {fc[0] + delta[0],
fc[1] + delta[1],
fc[2] + delta[2]};
while(dominate(condition, fc) == 1 and m != -1) {
// Perform the best move
if(m == 1) {
add = PA[ulong(id)];
C.push_back(add);
std::sort(C.begin(), C.end());
// Update PA, OM and OC
PA1 = PA;
// OM
for(i = 0, size = OM.size(); i != size; i++) {
if (std::find(Nv[add].begin(), Nv[add].end(), std::get<0>(OM[i])) == Nv[add].end()) {
OM.erase(OM.begin() + i);
i--;
size--;
}
}
verticesToPairs.clear();
std::set_intersection(NvB[add].begin(), NvB[add].end(), PA.begin(), PA.end(), std::back_inserter(verticesToPairs));
for(i = 0, size = verticesToPairs.size(); i != size; i++) {
weights = {verticesWCt[verticesToPairs[i]] - verticesWCt[add],
verticesWE[verticesToPairs[i]] - verticesWE[add],
verticesWP[verticesToPairs[i]] - verticesWP[add]};
OM.push_back(std::make_tuple(verticesToPairs[i], add, weights));
}
// PA
PA.clear();
std::set_intersection(Nv[add].begin(), Nv[add].end(), PA1.begin(), PA1.end(), std::back_inserter(PA));
// Update fc
fc[0] += delta[0];
fc[1] += delta[1];
fc[2] += delta[2];
// Update tabu list
for(i = 0, size = tabu.size(); i != size; i++) {
tabu[i] >= 1 ? tabu[i]-- : tabu[i] = 0;
}
} else if (m == 2) {
add = std::get<0>(OM[ulong(id)]);
del = std::get<1>(OM[ulong(id)]);
C.erase(std::find(C.begin(), C.end(), del));
C.push_back(add);
std::sort(C.begin(), C.end());
// Update PA OM
PA.clear();
OM.clear();
omUpdate.clear(); // omUpdate is a hash table where the key is a vertex and the associated element is
// either nothing : the vertex is linked to all the vertices of the clique
// or another vertex : the key vertex is linked to all the vertices of the clique except to the associated vertex
if (C.size() > 1) {
// Initial first hash
for(j = 0, size = Nv[C[0]].size(); j != size; j++) {
omUpdate[Nv[C[0]][j]] = std::nullopt;
}
j = 1;
NvIt = Nv[C[j]].begin();
NvEnd = Nv[C[j]].end();
omUpdateIt = omUpdate.begin();
while (omUpdateIt != omUpdate.end()) {
if (NvIt == NvEnd) {
break;
}
if (*NvIt < omUpdateIt->first) {
omUpdate[*NvIt] = C[0];
++NvIt;
} else if (*NvIt > omUpdateIt->first){
omUpdateIt->second = C[j];
++omUpdateIt;
} else {
++omUpdateIt;
++NvIt;
}
}
while (NvIt != NvEnd) {
omUpdate[*NvIt] = C[0];
NvIt++;
}
while (omUpdateIt != omUpdate.end()) {
omUpdateIt->second = C[j];
++omUpdateIt;
}
if (C.size() > 2) {
for(j = 2, size = C.size(); j != size; j++) {
NvIt = Nv[C[j]].begin();
NvEnd = Nv[C[j]].end();
omUpdateIt = omUpdate.begin();
while (NvIt != NvEnd) {
if (omUpdateIt == omUpdate.end()) {
break;
}
if (*NvIt < omUpdateIt->first) {
++NvIt;
} else if (*NvIt > omUpdateIt->first){
if(omUpdateIt->second.has_value()) {
omUpdateIt = omUpdate.erase(omUpdateIt);
} else {
omUpdateIt->second = C[j];
++omUpdateIt;
}
} else {
++omUpdateIt;
++NvIt;
}
}
while (omUpdateIt != omUpdate.end()) {
if(omUpdateIt->second.has_value()) {
omUpdateIt = omUpdate.erase(omUpdateIt);
} else {
omUpdateIt->second = C[j];
++omUpdateIt;
}
}
}
}
omUpdateIt = omUpdate.begin();
for(;omUpdateIt != omUpdate.end(); omUpdateIt++) {
if (omUpdateIt->second.has_value()){
if(omUpdateIt->first != omUpdateIt->second.value()) {
weights = {verticesWCt[omUpdateIt->first] - verticesWCt[omUpdateIt->second.value()],
verticesWE[omUpdateIt->first] - verticesWE[omUpdateIt->second.value()],
verticesWP[omUpdateIt->first] - verticesWP[omUpdateIt->second.value()]};
OM.push_back(std::make_tuple(omUpdateIt->first, omUpdateIt->second.value(),
weights));
}
} else {
PA.push_back(omUpdateIt->first);
}
}
} else if (int(C.size()) == 1) {
for(j = 0; vertices[j] != C[0]; j++) {
weights = { verticesWCt[vertices[j]] - verticesWCt[C[0]],
verticesWE[vertices[j]] - verticesWE[C[0]],
verticesWP[vertices[j]] - verticesWP[C[0]] };
OM.push_back(std::make_tuple(vertices[j], C[0],weights));
}
j++;
for(size = vertices.size(); j != size; j++) {
weights = { verticesWCt[vertices[j]] - verticesWCt[C[0]],
verticesWE[vertices[j]] - verticesWE[C[0]],
verticesWP[vertices[j]] - verticesWP[C[0]] };
OM.push_back(std::make_tuple(vertices[j], C[0],weights));
}
PA = Nv[C[0]];
}
// Update fc
fc[0] += delta[0];
fc[1] += delta[1];
fc[2] += delta[2];
// Update tabu list
for(i = 0, size = tabu.size(); i != size; i++) {
tabu[i] >= 1 ? tabu[i]-- : tabu[i] = 0;
}
if( OM.empty())
tabu[del] = phi;
else
tabu[del] = phi + rand() % int(OM.size()) + 1;
}
#ifdef _DEBUG
std::cout << "\tBEST MOVE PERFORMED : ";
std::cout << "C : ";
printVector(1);
printVector(4);
printVector(5);
#endif
delta = {-1, FLT_MAX, -1};
m = -1;
id = -1;
// m1
for (i = 0, size = PA.size(); i != size; i++) {
weights = {verticesWCt[PA[i]],
verticesWE[PA[i]],
verticesWP[PA[i]]};
if(dominate(weights, delta) == 1 /*and findPseudoknotLevel(C, PA[i], -1) <= pseudoknotLevel*/) {
delta = weights;
m = 1;
id = int(i);
}
}
// m2
for (i = 0, size = OM.size(); i != size; i++) {
weights = std::get<2>(OM[i]);
if(dominate(weights, delta) == 1 /*and findPseudoknotLevel(C, std::get<0>(OM[i]), std::get<1>(OM[i])) <= pseudoknotLevel*/) {
delta = std::get<2>(OM[i]);
m = 2;
id = int(i);
}
}
#ifdef _DEBUG
std::cout << "\tMOVE : m = " << m;
if (m == 1) {
std::cout << " ; vertex = " << PA[id] << std::endl;
}
else if (m == 2) {
std::cout << " ; vertex = " << std::get<0>(OM[id]) << std::endl;
}
else {
std::cout << std::endl;
}
#endif
condition = {fc[0] + delta[0],
fc[1] + delta[1],
fc[2] + delta[2]};
}
#ifdef _DEBUG
std::cout << "END OF LOCAL SEARCH" << std::endl;
std::cout << std::endl;
#endif
#ifdef _DEBUG_UPDATE
std::cout << "CBEST UPDATE" << std::endl;
std::cout << "\tCbest (before update) :\n";
printVector(3);
std::cout << "\tC (candidate) : ";
printVector(1);
#endif
dom = 0;
bool exists = false;
toRemove.clear();
for(i = 0, size = fbest.size(); i < size and dom != -1 and !exists; i++) {
if (Cbest[i].size() == C.size()) {
exists = true;
for(j = 0, size2 = Cbest[i].size(); j < size2 and exists; j++) {
if (Cbest[i][j] != C[j])
exists = false;
}
}
dom = dominate(fc, fbest[i]);
if (dom == 1) {
#ifdef _DEBUG_UPDATE
std::cout << "\tCandidate dominate clique " << i << std::endl;
#endif
toRemove.push_back(uint(i));
}
#ifdef _DEBUG_UPDATE
if (dom == -1) {
std::cout << "\tCandidate is dominated by clique " << i << std::endl;
}
if (dom == 0) {
std::cout << "\tNo dominanceship between candidate and clique " << i << std::endl;
}
#endif
}
if(dom != -1 and !exists) {
#ifdef _DEBUG
std::cout << "\t--> dom != -1 and !exists" << std::endl;
std::cout << "\tsum = " << sum << " ; fbest.size() = " << int(fbest.size()) << std::endl;
#endif
// Remove the dominated solution
if(sum != int(fbest.size())) {
#ifdef _DEBUG
std::cout << "\t--> sum != int(fbest.size()))" << std::endl;
std::cout << "\ttoRemove.size = " << toRemove.size() << std::endl;
#endif
for(int size = int(toRemove.size())-1; size >= 0; size--) {
fbest.erase(fbest.begin() + toRemove[ulong(size)]);
Cbest.erase(Cbest.begin() + toRemove[ulong(size)]);
}
}
Cbest.push_back(C);
fbest.push_back(fc);
w = 0;
paretoSetUnchanged = 0;
} else {
w++;
paretoSetUnchanged++;
}
#ifdef _DEBUG
std::cout << "\t--> Cbest :\n";
printVector(3);
#endif
#ifdef _DEBUG_UPDATE
std::cout << "END OF CBEST UPDATE" << std::endl;
#endif
#ifdef _DEBUG
std::cout << std::endl;
std::cout << "PERTURBATION" << std::endl;
#endif
// Find the pertubation strength
if (w > T) {
L = Lmax;
w = 0;
}
else if ( C.size() == Cp.size() and std::equal(C.begin(), C.end(), Cp.begin()) )
L++;
else
L = Lo;
Cp = C;
// Pertubation of C
if(w == 0 or
( exp(-float(w)/float(T)) > Po ?
exp(-float(w)/float(T)) * 100 - rand() % 100 + 1 < 0.0 :
Po * 100 - rand() % 100 + 1 < 0.0 ) ) {
#ifdef _DEBUG
std::cout << "--> RANDOM PERTURBATION" << std::endl;
std::cout << "\tL = " << L << std::endl;
#endif
float alpha = alphas;
if ( w != 0 )
alpha = alphar;
for(k = 1; k <= L; k++) {
// Select a random move among M4
newC.clear();
tabuUpdate.clear();
std::sort(C.begin(), C.end());
// Choose randomly a move among M4
std::vector < uint > OC;
std::set_difference(vertices.begin(), vertices.end(), C.begin(), C.end(), std::back_inserter(OC));
score = {alpha * fc[0]-1,
alpha * fc[1]+1,
alpha * fc[2]-1};
alphaFc = {alpha * fc[0],
alpha * fc[1],
alpha * fc[2]};
while(int(OC.size()) > 0 and (dominate(score, alphaFc) == -1 /*or findPseudoknotLevel(newC, -1, -1) > pseudoknotLevel*/)) {
newC.clear();
score = {0, 0, 0};
r = rand() % int(OC.size());
add = OC[ulong(r)];
std::set_intersection(Nv[add].begin(), Nv[add].end(), C.begin(), C.end(), std::back_inserter(newC));
newC.push_back(add);
for(j = 0, size2 = newC.size(); j != size2; j++) {
score[0] += verticesWCt[newC[j]];
score[1] += verticesWE[newC[j]];
score[2] += verticesWP[newC[j]];
}
OC.erase(OC.begin() + r);
}
// Update tabu list
std::set_difference(C.begin(), C.end(), newC.begin(), newC.end(), std::back_inserter(tabuUpdate));
C = newC;
std::sort(C.begin(), C.end());
fc = score;
#ifdef _DEBUG
std::cout << "\tNEW C" << std::endl;
std::cout << "\t\tC : ";
printVector(1);
#endif
// Update PA OM
PA.clear();
OM.clear();
omUpdate.clear(); // omUpdate is a hash table where the key is a vertex and the associated element is
// either nothing : the vertex is linked to all the vertices of the clique
// or another vertex : the key vertex is linked to all the vertices of the clique except to the associated vertex
if (C.size() > 1) {
// initial first hash
for(j = 0, size = Nv[C[0]].size(); j != size; j++) {
omUpdate[Nv[C[0]][j]] = std::nullopt;
}
j = 1;
NvIt = Nv[C[j]].begin();
NvEnd = Nv[C[j]].end();
omUpdateIt = omUpdate.begin();
while (omUpdateIt != omUpdate.end()) {
if (NvIt == NvEnd) {
break;
}
if (*NvIt < omUpdateIt->first) {
omUpdate[*NvIt] = C[0];
++NvIt;
} else if (*NvIt > omUpdateIt->first){
omUpdateIt->second = C[j];
++omUpdateIt;
} else {
++omUpdateIt;
++NvIt;
}
}
while (NvIt != NvEnd) {
omUpdate[*NvIt] = C[0];
NvIt++;
}
while (omUpdateIt != omUpdate.end()) {
omUpdateIt->second = C[j];
++omUpdateIt;
}
if (C.size() > 2) {
for(j = 2, size = C.size(); j != size; j++) {
NvIt = Nv[C[j]].begin();
NvEnd = Nv[C[j]].end();
omUpdateIt = omUpdate.begin();
while (NvIt != NvEnd) {
if (omUpdateIt == omUpdate.end()) {
break;
}
if (*NvIt < omUpdateIt->first) {
++NvIt;
} else if (*NvIt > omUpdateIt->first){
if(omUpdateIt->second.has_value()) {
omUpdateIt = omUpdate.erase(omUpdateIt);
} else {
omUpdateIt->second = C[j];
++omUpdateIt;
}
} else {
++omUpdateIt;
++NvIt;
}
}
while (omUpdateIt != omUpdate.end()) {
if(omUpdateIt->second.has_value()) {
omUpdateIt = omUpdate.erase(omUpdateIt);
} else {
omUpdateIt->second = C[j];
++omUpdateIt;
}
}
}
}
omUpdateIt = omUpdate.begin();
for(;omUpdateIt != omUpdate.end(); omUpdateIt++) {
if (omUpdateIt->second.has_value()){
if(omUpdateIt->first != omUpdateIt->second.value()) {
weights = {verticesWCt[omUpdateIt->first] - verticesWCt[omUpdateIt->second.value()],
verticesWE[omUpdateIt->first] - verticesWE[omUpdateIt->second.value()],
verticesWP[omUpdateIt->first] - verticesWP[omUpdateIt->second.value()]};
OM.push_back(std::make_tuple(omUpdateIt->first, omUpdateIt->second.value(),
weights));
}
} else {
PA.push_back(omUpdateIt->first);
}
}
} else if (int(C.size()) == 1) {
for(j = 0; vertices[j] != C[0]; j++) {
weights = { verticesWCt[vertices[j]] - verticesWCt[C[0]],
verticesWE[vertices[j]] - verticesWE[C[0]],
verticesWP[vertices[j]] - verticesWP[C[0]] };
OM.push_back(std::make_tuple(vertices[j], C[0],weights));
}
j++;
for(size = vertices.size(); j != size; j++) {
weights = { verticesWCt[vertices[j]] - verticesWCt[C[0]],
verticesWE[vertices[j]] - verticesWE[C[0]],
verticesWP[vertices[j]] - verticesWP[C[0]] };
OM.push_back(std::make_tuple(vertices[j], C[0],weights));
}
PA = Nv[C[0]];
}
// Update tabu list
for( j = 0, size = tabu.size(); j != size; j++) {
tabu[j] >= 1 ? tabu[j]-- : tabu[j] = 0;
}
if( OM.empty())
for( j = 0, size = tabuUpdate.size(); j != size; j++) {
tabu[tabuUpdate[j]] = phi;
}
else
for( j = 0, size = tabuUpdate.size(); j != size; j++) {
tabu[tabuUpdate[j]] = phi + rand() % (int(OM.size()) + 1);
}
iter++;
}
} else {
#ifdef _DEBUG
std::cout << "--> PERTURBATION A" << std::endl;
std::cout << "\tL = " << L << std::endl;
printVector(4);
printVector(5);
#endif
m = 0;
for( k = 1; k <= L and m != -1 ; k++) {
// Select a random move among M4
delta = {-1, FLT_MAX, -1}; // Change of the score function
id = -1; // ID of the selected vertex
m = -1; // Movement to perform
#ifdef _DEBUG
std::cout << "\tM1 ?" << std::endl;
#endif
// m1
for ( j = 0, size = PA.size(); j != size; j++) {
weights = {verticesWCt[PA[j]],
verticesWE[PA[j]],
verticesWP[PA[j]]};
dom = 0;
for(l = 0, size3 = fbest.size(); l < size3 and dom != -1; l++) {
dom = dominate({verticesWCt[PA[j]] + fc[0],
verticesWE[PA[j]] + fc[1],
verticesWP[PA[j]] + fc[2]},
fbest[l]);
}
#ifdef _DEBUG
std::cout << "\t\tdominate(weigths, delta) = " << dominate(weights, delta) << " ; dom = " << dom << " ; tabu[PA[j]] = " << tabu[PA[j]] << std::endl;
#endif
if(dominate(weights, delta) == 1
and (tabu[PA[j]] == 0 or dom == 1)
/*and findPseudoknotLevel(C, PA[j], -1) <= pseudoknotLevel*/)
{
#ifdef _DEBUG
std::cout << "\t\t--> dominate(weights, delta) == 1 and (tabu[PA[j]] == 0 or dom != -1)" << std::endl;
#endif
delta = weights;
m = 1;
id = int(j);
}
}
#ifdef _DEBUG
std::cout << "\tM2 ?" << std::endl;
#endif
// m2
for ( j = 0, size = OM.size(); j != size; j++) {
weights = {std::get<2>(OM[j])[0]+fc[0],
std::get<2>(OM[j])[1]+fc[1],
std::get<2>(OM[j])[2]+fc[2]};
dom = 0;
for(l = 0, size3 = fbest.size(); l < size3 and dom != -1; l++) {
dom = dominate(weights, fbest[l]);
}
weights = std::get<2>(OM[j]);
#ifdef _DEBUG
std::cout << "\t\tdominate(weigths, delta) = " << dominate(weights, delta) << " ; dom = " << dom << " ; tabu[std::get<0>(OM[j])] = " << tabu[std::get<0>(OM[j])] << std::endl;
#endif
if(dominate(weights, delta) == 1
and (tabu[std::get<0>(OM[j])] == 0 or dom == 1)
/*and findPseudoknotLevel(C, std::get<0>(OM[j]), std::get<1>(OM[j])) <= pseudoknotLevel*/)
{
#ifdef _DEBUG
std::cout << "\t\t--> dominate(weights, delta) == 1 and (tabu[std::get<0>(OM[j])] == 0 or dom != -1)" << std::endl;
#endif
delta = std::get<2>(OM[j]);
m = 2;
id = int(j);
}
}
#ifdef _DEBUG
std::cout << "\tM3 ?" << std::endl;
#endif
// m3
for ( j = 0, size = C.size(); j != size; j++) {
weights = {-verticesWCt[C[j]],
-verticesWE[C[j]],
-verticesWP[C[j]]};
#ifdef _DEBUG
std::cout << "\t\tdominate(weigths, delta) = " << dominate(weights, delta) << std::endl;
#endif
if( dominate(weights, delta) == 1) {
#ifdef _DEBUG
std::cout << "\t\t--> dominate(weights, delta) == 1" << std::endl;
#endif
delta = weights;
m = 3;
id = int(j);
}
}
#ifdef _DEBUG
std::cout << "\tMOVE : m = " << m;
if (m == 1) {
std::cout << " ; vertex = " << PA[id] << std::endl;
}
else if (m == 2) {
std::cout << " ; vertex = " << std::get<0>(OM[id]) << std::endl;
}
else if (m == 3) {
std::cout << " ; vertex = " << C[id] << std::endl;
}
else {
std::cout << std::endl;
}
#endif
// Perform the best move
if(m == 1) {
add = PA[ulong(id)];
C.push_back(add);
std::sort(C.begin(), C.end());
// Update fc
fc[0] += delta[0];
fc[1] += delta[1];
fc[2] += delta[2];
// Update PA, OM and OC
PA1 = PA;
// OM
for(j = 0, size = OM.size(); j != size; j++) {
if (std::find(Nv[add].begin(), Nv[add].end(), std::get<0>(OM[j])) == Nv[add].end()) {
OM.erase(OM.begin() + j);
j--;
size--;
}
}
verticesToPairs.clear();
std::set_intersection(NvB[add].begin(), NvB[add].end(), PA.begin(), PA.end(), std::back_inserter(verticesToPairs));
for(j = 0, size = verticesToPairs.size(); j != size; j++) {
weights = {verticesWCt[verticesToPairs[j]] - verticesWCt[add],
verticesWE[verticesToPairs[j]] - verticesWE[add],
verticesWP[verticesToPairs[j]] - verticesWP[add]};
OM.push_back(std::make_tuple(verticesToPairs[j], add, weights));
}
// PA
PA.clear();
std::set_intersection(Nv[add].begin(), Nv[add].end(), PA1.begin(), PA1.end(), std::back_inserter(PA));
// Update tabu list
for( j = 0, size = tabu.size(); j != size; j++) {
tabu[j] >= 1 ? tabu[j]-- : tabu[j] = 0;
}
} else if (m == 2) {
add = std::get<0>(OM[ulong(id)]);
del = std::get<1>(OM[ulong(id)]);
C.erase(std::find(C.begin(), C.end(), del));
C.push_back(add);
std::sort(C.begin(), C.end());
// Update fc
fc[0] += delta[0];
fc[1] += delta[1];
fc[2] += delta[2];
// Update PA OM
PA.clear();
OM.clear();
omUpdate.clear(); // omUpdate is a hash table where the key is a vertex and the associated element is
// either nothing : the vertex is linked to all the vertices of the clique
// or another vertex : the key vertex is linked to all the vertices of the clique except to the associated vertex
if (C.size() > 1) {
// Initial first hash
for(j = 0, size = Nv[C[0]].size(); j != size; j++) {
omUpdate[Nv[C[0]][j]] = std::nullopt;
}
j = 1;
NvIt = Nv[C[j]].begin();
NvEnd = Nv[C[j]].end();
omUpdateIt = omUpdate.begin();
while (omUpdateIt != omUpdate.end()) {
if (NvIt == NvEnd) {
break;
}
if (*NvIt < omUpdateIt->first) {
omUpdate[*NvIt] = C[0];
++NvIt;
} else if (*NvIt > omUpdateIt->first){
omUpdateIt->second = C[j];
++omUpdateIt;
} else {
++omUpdateIt;
++NvIt;
}
}
while (NvIt != NvEnd) {
omUpdate[*NvIt] = C[0];
NvIt++;
}
while (omUpdateIt != omUpdate.end()) {
omUpdateIt->second = C[j];
++omUpdateIt;
}
if (C.size() > 2) {
for(j = 2, size = C.size(); j != size; j++) {
NvIt = Nv[C[j]].begin();
NvEnd = Nv[C[j]].end();
omUpdateIt = omUpdate.begin();
while (NvIt != NvEnd) {
if (omUpdateIt == omUpdate.end()) {
break;
}
if (*NvIt < omUpdateIt->first) {
++NvIt;
} else if (*NvIt > omUpdateIt->first){
if(omUpdateIt->second.has_value()) {
omUpdateIt = omUpdate.erase(omUpdateIt);
} else {
omUpdateIt->second = C[j];
++omUpdateIt;
}
} else {
++omUpdateIt;
++NvIt;
}
}
while (omUpdateIt != omUpdate.end()) {
if(omUpdateIt->second.has_value()) {
omUpdateIt = omUpdate.erase(omUpdateIt);
} else {
omUpdateIt->second = C[j];
++omUpdateIt;
}
}
}
}
omUpdateIt = omUpdate.begin();
for(;omUpdateIt != omUpdate.end(); omUpdateIt++) {
if (omUpdateIt->second.has_value()){
if(omUpdateIt->first != omUpdateIt->second.value()) {
weights = {verticesWCt[omUpdateIt->first] - verticesWCt[omUpdateIt->second.value()],
verticesWE[omUpdateIt->first] - verticesWE[omUpdateIt->second.value()],
verticesWP[omUpdateIt->first] - verticesWP[omUpdateIt->second.value()]};
OM.push_back(std::make_tuple(omUpdateIt->first, omUpdateIt->second.value(),
weights));
}
} else {
PA.push_back(omUpdateIt->first);
}
}
} else if (int(C.size()) == 1) {
for(j = 0; vertices[j] != C[0]; j++) {
weights = { verticesWCt[vertices[j]] - verticesWCt[C[0]],
verticesWE[vertices[j]] - verticesWE[C[0]],
verticesWP[vertices[j]] - verticesWP[C[0]] };
OM.push_back(std::make_tuple(vertices[j], C[0],weights));
}
j++;
for(size = vertices.size(); j != size; j++) {
weights = { verticesWCt[vertices[j]] - verticesWCt[C[0]],
verticesWE[vertices[j]] - verticesWE[C[0]],
verticesWP[vertices[j]] - verticesWP[C[0]] };
OM.push_back(std::make_tuple(vertices[j], C[0],weights));
}
PA = Nv[C[0]];
}
// Update tabu list
for( j = 0, size = tabu.size(); j != size; j++) {
tabu[j] >= 1 ? tabu[j]-- : tabu[j] = 0;
}
if( OM.empty())
tabu[del] = phi;
else
tabu[del] = phi + rand() % uint(OM.size()) + 1;
} else if (m == 3) {
del = C[ulong(id)];
C.erase(C.begin() + id);
// Update fc
fc[0] += delta[0];
fc[1] += delta[1];
fc[2] += delta[2];
// Update PA OM
PA.clear();
OM.clear();
omUpdate.clear(); // omUpdate is a hash table where the key is a vertex and the associated element is
// either nothing : the vertex is linked to all the vertices of the clique
// or another vertex : the key vertex is linked to all the vertices of the clique except to the associated vertex
if (C.size() > 1) {
// Initial first hash
for(j = 0, size = Nv[C[0]].size(); j != size; j++) {
omUpdate[Nv[C[0]][j]] = std::nullopt;
}
j = 1;
NvIt = Nv[C[j]].begin();
NvEnd = Nv[C[j]].end();
omUpdateIt = omUpdate.begin();
while (omUpdateIt != omUpdate.end()) {
if (NvIt == NvEnd) {
break;
}
if (*NvIt < omUpdateIt->first) {
omUpdate[*NvIt] = C[0];
++NvIt;
} else if (*NvIt > omUpdateIt->first){
omUpdateIt->second = C[j];
++omUpdateIt;
} else {
++omUpdateIt;
++NvIt;
}
}
while (NvIt != NvEnd) {
omUpdate[*NvIt] = C[0];
NvIt++;
}
while (omUpdateIt != omUpdate.end()) {
omUpdateIt->second = C[j];
++omUpdateIt;
}
if (C.size() > 2) {
for(j = 2, size = C.size(); j != size; j++) {
NvIt = Nv[C[j]].begin();
NvEnd = Nv[C[j]].end();
omUpdateIt = omUpdate.begin();
while (NvIt != NvEnd) {
if (omUpdateIt == omUpdate.end()) {
break;
}
if (*NvIt < omUpdateIt->first) {
++NvIt;
} else if (*NvIt > omUpdateIt->first){
if(omUpdateIt->second.has_value()) {
omUpdateIt = omUpdate.erase(omUpdateIt);
} else {
omUpdateIt->second = C[j];
++omUpdateIt;
}
} else {
++omUpdateIt;
++NvIt;
}
}
while (omUpdateIt != omUpdate.end()) {
if(omUpdateIt->second.has_value()) {
omUpdateIt = omUpdate.erase(omUpdateIt);
} else {
omUpdateIt->second = C[j];
++omUpdateIt;
}
}
}
}
omUpdateIt = omUpdate.begin();
for(;omUpdateIt != omUpdate.end(); omUpdateIt++) {
if (omUpdateIt->second.has_value()){
if(omUpdateIt->first != omUpdateIt->second.value()) {
weights = {verticesWCt[omUpdateIt->first] - verticesWCt[omUpdateIt->second.value()],
verticesWE[omUpdateIt->first] - verticesWE[omUpdateIt->second.value()],
verticesWP[omUpdateIt->first] - verticesWP[omUpdateIt->second.value()]};
OM.push_back(std::make_tuple(omUpdateIt->first, omUpdateIt->second.value(),
weights));
}
} else {
PA.push_back(omUpdateIt->first);
}
}
} else if (int(C.size()) == 1) {
for(j = 0; vertices[j] != C[0]; j++) {
weights = { verticesWCt[vertices[j]] - verticesWCt[C[0]],
verticesWE[vertices[j]] - verticesWE[C[0]],
verticesWP[vertices[j]] - verticesWP[C[0]] };
OM.push_back(std::make_tuple(vertices[j], C[0],weights));
}
j++;
for(size = vertices.size(); j != size; j++) {
weights = { verticesWCt[vertices[j]] - verticesWCt[C[0]],
verticesWE[vertices[j]] - verticesWE[C[0]],
verticesWP[vertices[j]] - verticesWP[C[0]] };
OM.push_back(std::make_tuple(vertices[j], C[0],weights));
}
PA = Nv[C[0]];
}
// Update tabu list
for( j = 0, size = tabu.size(); j != size; j++) {
tabu[j] >= 1 ? tabu[j]-- : tabu[j] = 0;
}
if( OM.empty())
tabu[del] = phi;
else
tabu[del] = phi + rand() % uint(OM.size()) + 1;
}
#ifdef _DEBUG
std::cout << "\tBEST MOVE PERFORMED : ";
std::cout << "C : ";
printVector(1);
printVector(4);
printVector(5);
#endif
iter++;
} // End of for loop (search for best move, perform the best move)
} // End of perturbation with set A
#ifdef _DEBUG
std::cout << "END OF PERTURBATION" << std::endl;
std::cout << std::endl;
#endif
iter++;
} // End of the big while loop
iter_ = iter;
#ifdef _DEBUG
std::cout << std::endl;
std::cout << "####################################################################################################\n" << std::endl;
std::cout << std::endl;
std::cout << "TOTAL NUMBER OF ITERATIONS = " << iter_ << std::endl;
std::cout << std::endl;
std::cout << std::endl;
#endif
}
unsigned int Predictor::get_iter_()
{
return iter_;
}
std::vector < std::tuple < std::vector < unsigned int >, std::vector < float > > > Predictor::get_best_cliques_()
{
std::vector < std::tuple < std::vector < unsigned int >, std::vector < float > > > res;
for(size_t i = 0, size = Cbest.size(); i != size; i++) {
std::tuple < std::vector < unsigned int >, std::vector < float > > clique = std::make_pair(Cbest[i], fbest[i]);
res.push_back(clique);
}
return res;
}
/* Return 1 if c1 dominates c2,
* Return 0 if c1 is not comparable to c2
* Return -1 if c1 is dominated by c2 */
int Predictor::dominate(std::vector < float > c1, std::vector < float > c2) {
/* First objective : max constraint
* Second objective : min energy
* Third objective : max probing */
int dominate = 0;
int c1dominatesc2 = 0, c2dominatesc1 = 0;
float absEpsilon = 1e-2;
float relEpsilon = 1e-4;
for(size_t i = 0, size = c1.size(); i < size; i++) {
if (i == 1) { // min energy
if (!approximatelyEqualAbsRel(c1[i], c2[i], absEpsilon, relEpsilon)) {
if (c1[i] < c2[i]) {
c1dominatesc2++;
} else if (c1[i] > c2[i]) {
c2dominatesc1++;
}
}
} else { // max
if (!approximatelyEqualAbsRel(c1[i], c2[i], absEpsilon, relEpsilon)) {
if (c1[i] > c2[i]) {
c1dominatesc2++;
} else if (c1[i] < c2[i]) {
c2dominatesc1++;
}
}
}
}
if (c1dominatesc2 == int(c1.size()) or (c1dominatesc2 > 0 and c2dominatesc1 == 0)){
dominate = 1;
} else if (c2dominatesc1 == int(c1.size()) or (c2dominatesc1 > 0 and c1dominatesc2 == 0)){
dominate = -1;
}
return dominate;
}
bool Predictor::approximatelyEqualAbsRel(float a, float b, float absEpsilon, float relEpsilon)
{
// Function retrieved from :https://www.learncpp.com/cpp-tutorial/relational-operators-and-floating-point-comparisons/
// Check if the numbers are really close -- needed when comparing numbers near zero.
float diff{ std::fabs(a - b) };
if (diff <= absEpsilon)
return true;
// Otherwise fall back to Knuth's algorithm
return (diff <= (std::max(std::fabs(a), std::fabs(b)) * relEpsilon));
}
// Check if hard constraint are respected
bool Predictor::paretoRespectHardCT(uint nbHardCT) {
bool hardCT=false;
for(uint i =0, size = fbest.size(); i != size; i++) {
if (fbest[i][0] >= 100*nbHardCT)
hardCT=true;
}
return hardCT;
}
// Check for the pseudoknot level
int Predictor::findPseudoknotLevel (std::vector< uint > clique, int add, int del) {
int level = 0;
size_t i,j,l, size, size2, size3;
if (del != -1 and add != -1) {
clique.erase(std::find(clique.begin(), clique.end(), del));
clique.push_back(add);
std::sort(clique.begin(), clique.end());
} else if (del != -1) {
clique.erase(std::find(clique.begin(), clique.end(), del));
} else if (add != -1) {
clique.push_back(add);
std::sort(clique.begin(), clique.end());
}
std::vector < unsigned int > G2, colors, givenColors, neighborColors, intersec;
for(i = 0, size = G2vertices.size(); i != size; i++) {
// Recover corresponding pseudoknot graph, vertex sorted by the beginning of the intervals
G2.clear();
for(j = 0, size2 = clique.size(); j != size2; j++) {
for(l = 0, size3 = G2G1correspondance[i].size(); l != size3; l++) {
if(clique[j] == G2G1correspondance[i][l]){
G2.push_back(G2vertices[i][l]);
}
}
}
// Compute chromatic number
// Initialize colors
colors.clear();
for(j = 0, size2 = G2.size(); j != size2; j++)
colors.push_back(uint(j));
givenColors.clear();
intersec.clear();
// While the graph is not entirely colored
for(j = 0, size2 = G2.size(); j != size2; j++) {
neighborColors.clear();
//std::cout << "Voisinage de G2[j] " << G2[j] << ": ";
for(l = 0, size3 = G2Nv[i][j].size(); l != size3; l++) {
// Recover the colors given in the neighborhood of G2[j]
//std::cout << G2Nv[i][j][l] << " ";
if(G2Nv[i][j][l] < givenColors.size()) {
neighborColors.push_back(givenColors[G2Nv[i][j][l]]);
//std::cout << "(" << givenColors[G2Nv[i][j][l]] << ") ";
}
}
//std::cout << std::endl;
intersec.clear();
/* find the colors not already attributed yet */
std::set_difference(colors.begin(), colors.end(),
neighborColors.begin(), neighborColors.end(),
std::back_inserter(intersec));
/*std::cout << "Couleurs non déjà attribuées dans le voisinage : ";
for(l = 0, size3 = intersec.size(); l != size3; l++) {
std::cout << intersec[l] << " ";
}
std::cout << std::endl;*/
// If the color is not already in givenColors then put it */
if (std::find(givenColors.begin(), givenColors.end(), intersec[0]) == givenColors.end())
givenColors.push_back(intersec[0]);
}
//std::cout << "givenColors.Size() " << givenColors.size() << std::endl;
if (int(givenColors.size()) > level)
level = int(givenColors.size());
}
return level;
}
// Used when _DEBUG is defined
void Predictor::printVector (int opt) {
size_t i, size, j, size2;
if (opt == 1) {
std::cout << "{";
for (i = 0, size = C.size(); i != size; i++) {
if (i != size-1){
std::cout << C[i] << ", ";
} else{
std::cout << C[i] << "}";
}
}
std::cout << " ; fc (Constraints, Energy, Probing) : (";
for (i = 0, size = fc.size(); i != size; i++) {
if (i != size-1) {
std::cout << fc[i] << ", ";
}
else {
std::cout << fc[i] << ")";
}
}
std::cout << std::endl;
} else if (opt == 3) {
for (i = 0, size = Cbest.size(); i != size; i++) {
std::cout << "\t\tClique " << i << " : {";
for(j = 0, size2 = Cbest[i].size(); j != size2; j++){
if ( j != size2-1 ){
std::cout << Cbest[i][j] << ", ";
}
else {
std::cout << Cbest[i][j] << "}";
}
}
std::cout << " ; fc (Constraints, Energy, Probing) : (";
for (j = 0, size2 = fbest[i].size(); j != size2; j++) {
if (j != size2-1) {
std::cout << fbest[i][j] << ", ";
}
else {
std::cout << fbest[i][j] << ")";
}
}
std::cout << std::endl;
}
} else if (opt == 4) {
std::cout << "\tPA :" << std::endl;
std::cout << "\t\t[" ;
if (PA.size() == 0) {
std::cout << "]";
} else {
for (i = 0, size = PA.size(); i != size; i++) {
if (i != size-1){
std::cout << PA[i] << ", ";
} else{
std::cout << PA[i] << "]";
}
}
}
std::cout << std::endl;
} else if (opt == 5) {
std::cout << "\tOM :" << std::endl;
std::cout << "\t\t[" ;
for (i = 0, size = OM.size(); i != size; i++) {
if (i != size-1){
std::cout << "[" << std::get<0>(OM[i]) << ", " << std::get<1>(OM[i]) << ", " << std::get<2>(OM[i])[1] << "], ";
} else{
std::cout << "[" << std::get<0>(OM[i]) << ", " << std::get<1>(OM[i]) << ", " << std::get<2>(OM[i])[1] << "]]";
}
}
std::cout << std::endl;
}
}