/// Refines this model based on a recently performed action and change in beliefs
void TransitionModel::trainIncremental(const GVec& beliefs, const GVec& actions, const GVec& nextBeliefs)
{
// Buffer the pattern
GVec& destIn = trainInput.row(trainPos);
GVec& destOut = trainOutput.row(trainPos);
trainPos++;
trainSize = std::max(trainSize, trainPos);
if(trainPos >= trainInput.rows())
trainPos = 0;
if(beliefs.size() + actions.size() != destIn.size() || beliefs.size() != destOut.size())
throw Ex("size mismatch");
destIn.put(0, beliefs);
destIn.put(beliefs.size(), actions);
for(size_t i = 0; i < destOut.size(); i++)
destOut[i] = 0.5 * (nextBeliefs[i] - beliefs[i]);
/*
destIn.print();
std::cout << "->";
destOut.print();
std::cout << "\n";
std::cout << to_str(0.5 * cos(destIn[2])) << ", " << to_str(0.5 * sin(destIn[2])) << "\n";
*/
// Refine the model
size_t iters = std::min(trainIters, 1000 * trainSize);
for(size_t i = 0; i < iters; i++)
doSomeTraining();
}
/// Decodes beliefs to predict observations
void ObservationModel::beliefsToObservations(const GVec& beliefs, GVec& observations)
{
observations.resize(decoder.outputLayer().outputs());
if(tutor)
tutor->state_to_observations(beliefs, observations);
else
{
decoder.forwardProp(beliefs);
observations.copy(decoder.outputLayer().activation());
}
}
/// Encodes observations to predict beliefs
void ObservationModel::observationsToBeliefs(const GVec& observations, GVec& beliefs)
{
beliefs.resize(encoder.outputLayer().outputs());
if(tutor)
tutor->observations_to_state(observations, beliefs);
else
{
beliefs.put(0, observations, 0, beliefs.size());
encoder.forwardProp(observations);
beliefs.copy(encoder.outputLayer().activation());
}
}
/// Refines the beliefs to correspond with actual observations
void ObservationModel::calibrateBeliefs(GVec& beliefs, const GVec& observations)
{
if(tutor)
tutor->observations_to_state(observations, beliefs);
else
{
GNeuralNetLayer& layIn = encoder.outputLayer();
for(size_t i = 0; i < calibrationIters; i++) {
decoder.forwardProp(beliefs);
decoder.backpropagate(observations);
decoder.layer(0).backPropError(&layIn);
beliefs.addScaled(decoder.learningRate(), layIn.error());
beliefs.clip(-1.0, 1.0);
}
}
}
void GNaiveBayes::predict(const GVec& in, GVec& out)
{
if(m_nSampleCount <= 0)
throw Ex("You must call train before you call eval");
for(size_t n = 0; n < m_pRelLabels->size(); n++)
out[n] = m_pOutputs[n]->predict(in.data(), m_equivalentSampleSize, &m_rand);
}
void GNaiveBayes::predictDistribution(const GVec& in, GPrediction* out)
{
if(m_nSampleCount <= 0)
throw Ex("You must call train before you call eval");
for(size_t n = 0; n < m_pRelLabels->size(); n++)
m_pOutputs[n]->eval(in.data(), &out[n], m_equivalentSampleSize);
}
/// Finds the best plan and copies its first step
void PlanningSystem::chooseNextActions(const GVec& beliefs, GVec& actions)
{
if(tutor)
tutor->choose_actions(beliefs, actions);
else
{
// Find the best plan (according to the contentment model) and ask the mentor to evaluate it
size_t planBestIndex = 0;
double bestContentment = -1e300;
for(size_t i = 0; i < plans.size(); i++)
{
double d = evaluatePlan(beliefs, *plans[i]);
if(d > bestContentment)
{
bestContentment = d;
planBestIndex = i;
}
}
//std::cout << "Best contentment: " << to_str(bestContentment) << "\n";
GMatrix& bestPlan = *plans[planBestIndex];
askMentorToEvaluatePlan(beliefs, bestPlan);
// Pick a random plan from the population and ask the mentor to evaluate it (for contrast)
size_t planBindex = rand.next(plans.size() - 1);
if(planBindex >= planBestIndex)
planBindex++;
askMentorToEvaluatePlan(beliefs, *plans[planBindex]);
// Make a random one-step plan, and ask the mentor to evaluate it (for contrast)
GVec& action = randomPlan[0];
action.fillUniform(rand);
askMentorToEvaluatePlan(beliefs, randomPlan);
// Copy the first action vector of the best plan for our chosen action
GVec* bestActions = &bestPlan[0];
if(burnIn > 0 || rand.uniform() < explorationRate)
bestActions = &randomPlan[0];
if(burnIn > 0)
burnIn--;
GAssert(bestActions->size() == actionDims);
actions.copy(*bestActions);
}
}
// virtual
void GNaiveInstance::trainIncremental(const GVec& pIn, const GVec& pOut)
{
if(!m_pHeap)
m_pHeap = new GHeap(1024);
double* pOutputs = (double*)m_pHeap->allocAligned(sizeof(double) * m_pRelLabels->size());
GVec::copy(pOutputs, pOut.data(), m_pRelLabels->size());
for(size_t i = 0; i < m_pRelFeatures->size(); i++)
{
if(pIn[i] != UNKNOWN_REAL_VALUE)
m_pAttrs[i]->addInstance(pIn[i], pOutputs);
}
}
// virtual
void GLinearDistribution::predictDistribution(const GVec& in, GPrediction* out)
{
m_pAInv->multiply(in, m_buf);
double v = in.dotProduct(m_buf);
for(size_t i = 0; i < m_pWBar->rows(); i++)
{
GNormalDistribution* pNorm = (*out).makeNormal();
double m = m_pWBar->row(i).dotProduct(in);
pNorm->setMeanAndVariance(m, v);
out++;
}
}
/// Refines the encoder and decoder based on the new observation.
void ObservationModel::trainIncremental(const GVec& observation)
{
// Buffer the pattern
GVec* dest;
if(validationPos < trainPos) {
dest = &validation.row(validationPos);
if(++validationPos >= validation.rows())
validationPos = 0;
validationSize = std::max(validationSize, validationPos);
} else {
dest = &train.row(trainPos);
trainPos++;
trainSize = std::max(trainSize, trainPos);
if(trainPos >= train.rows())
trainPos = 0;
}
dest->copy(observation);
// Train
size_t iters = std::min(trainIters, trainSize);
for(size_t i = 0; i < iters; i++)
doSomeTraining();
}
/// Predict the belief vector that will result if the specified action is performed
void TransitionModel::anticipateNextBeliefs(const GVec& beliefs, const GVec& actions, GVec& anticipatedBeliefs)
{
if(tutor)
tutor->transition(beliefs, actions, anticipatedBeliefs);
else
{
GAssert(beliefs.size() + actions.size() == model.layer(0).inputs());
buf.resize(beliefs.size() + actions.size());
buf.put(0, beliefs);
buf.put(beliefs.size(), actions);
model.forwardProp(buf);
anticipatedBeliefs.copy(beliefs);
anticipatedBeliefs.addScaled(2.0, model.outputLayer().activation());
anticipatedBeliefs.clip(-1.0, 1.0);
}
}
/// Perturbs a random plan
void PlanningSystem::mutate()
{
double d = rand.uniform();
GMatrix& p = *plans[rand.next(plans.size())];
if(d < 0.1) { // lengthen the plan
if(p.rows() < maxPlanLength) {
GVec* newActions = new GVec(actionDims);
newActions->fillUniform(rand);
p.takeRow(newActions, rand.next(p.rows() + 1));
}
}
else if(d < 0.2) { // shorten the plan
if(p.rows() > 1) {
p.deleteRow(rand.next(p.rows()));
}
}
else if(d < 0.7) { // perturb a single element of an action vector
GVec& actions = p[rand.next(p.rows())];
size_t i = rand.next(actions.size());
actions[i] = std::max(0.0, std::min(1.0, actions[i] + 0.03 * rand.normal()));
}
else if(d < 0.9) { // perturb a whole action vector
GVec& actions = p[rand.next(p.rows())];
for(size_t i = 0; i < actions.size(); i++) {
actions[i] = std::max(0.0, std::min(1.0, actions[i] + 0.02 * rand.normal()));
}
}
else { // perturb the whole plan
for(size_t j = 0; j < p.rows(); j++) {
GVec& actions = p[j];
for(size_t i = 0; i < actions.size(); i++) {
actions[i] = std::max(0.0, std::min(1.0, actions[i] + 0.01 * rand.normal()));
}
}
}
}
// virtual
void GWag::trainInner(const GMatrix& features, const GMatrix& labels)
{
GNeuralNetLearner* pTemp = NULL;
std::unique_ptr<GNeuralNetLearner> hTemp;
size_t weights = 0;
GVec pWeightBuf;
GVec pWeightBuf2;
for(size_t i = 0; i < m_models; i++)
{
m_pNN->train(features, labels);
if(pTemp)
{
// Average m_pNN with pTemp
if(!m_noAlign)
m_pNN->nn().align(pTemp->nn());
pTemp->nn().weightsToVector(pWeightBuf.data());
m_pNN->nn().weightsToVector(pWeightBuf2.data());
pWeightBuf *= (double(i) / (i + 1));
pWeightBuf.addScaled(1.0 / (i + 1), pWeightBuf2);
pTemp->nn().vectorToWeights(pWeightBuf.data());
}
else
{
// Copy the m_pNN
GDom doc;
GDomNode* pNode = m_pNN->serialize(&doc);
GLearnerLoader ll;
pTemp = new GNeuralNetLearner(pNode);
hTemp.reset(pTemp);
weights = pTemp->nn().weightCount();
pWeightBuf.resize(weights);
pWeightBuf2.resize(weights);
}
}
pTemp->nn().weightsToVector(pWeightBuf.data());
m_pNN->nn().vectorToWeights(pWeightBuf.data());
}
GEnsemblePredictWorker(GMasterThread& master, GEnsemble* pEnsemble, size_t outDims)
: GWorkerThread(master), m_pEnsemble(pEnsemble)
{
m_prediction.resize(outDims);
}
void GffLoader::load(GList<GenomicSeqData>& seqdata, GFValidateFunc* gf_validate,
bool doCluster, bool doCollapseRedundant,
bool matchAllIntrons, bool fuzzSpan, bool forceExons) {
GffReader* gffr=new GffReader(f, this->transcriptsOnly, false); //not only mRNA features, not sorted
gffr->showWarnings(this->showWarnings);
// keepAttrs mergeCloseExons noExonAttr
gffr->readAll(this->fullAttributes, this->mergeCloseExons, this->noExonAttrs);
GVec<int> pseudoAttrIds;
GVec<int> pseudoFeatureIds;
if (this->noPseudo) {
GffNameList& fnames = gffr->names->feats;
for (int i=0;i<fnames.Count();i++) {
char* n=fnames[i]->name;
if (startsWith(n, "pseudo")) {
pseudoFeatureIds.Add(fnames[i]->idx);
}
}
GffNameList& attrnames = gffr->names->attrs;
for (int i=0;i<attrnames.Count();i++) {
char* n=attrnames[i]->name;
char* p=strifind(n, "pseudo");
if (p==n || (p==n+2 && tolower(n[0])=='i' && tolower(n[1])=='s')) {
pseudoAttrIds.Add(attrnames[i]->idx);
}
}
}
//int redundant=0; //redundant annotation discarded
if (verbose) GMessage(" .. loaded %d genomic features from %s\n", gffr->gflst.Count(), fname.chars());
//int rna_deleted=0;
//add to GenomicSeqData, adding to existing loci and identifying intron-chain duplicates
for (int k=0;k<gffr->gflst.Count();k++) {
GffObj* m=gffr->gflst[k];
if (strcmp(m->getFeatureName(), "locus")==0 &&
m->getAttr("transcripts")!=NULL) {
continue; //discard locus meta-features
}
if (this->noPseudo) {
bool is_pseudo=false;
for (int i=0;i<pseudoFeatureIds.Count();++i) {
if (pseudoFeatureIds[i]==m->ftype_id) {
is_pseudo=true;
break;
}
}
if (is_pseudo) continue;
for (int i=0;i<pseudoAttrIds.Count();++i) {
char* attrv=NULL;
if (m->attrs!=NULL) attrv=m->attrs->getAttr(pseudoAttrIds[i]);
if (attrv!=NULL) {
char fc=tolower(attrv[0]);
if (fc=='t' || fc=='y' || fc=='1') {
is_pseudo=true;
break;
}
}
}
if (is_pseudo) continue;
//last resort:
// scan all the attribute values for "pseudogene" keyword (NCBI does that for "product" attr)
/*
if (m->attrs!=NULL) {
for (int i=0;i<m->attrs->Count();++i) {
GffAttr& a=*(m->attrs->Get(i));
if (strifind(a.attr_val, "pseudogene")) {
is_pseudo=true;
break;
}
}
}
if (is_pseudo) continue;
*/
} //pseudogene detection requested
char* rloc=m->getAttr("locus");
if (rloc!=NULL && startsWith(rloc, "RLOC_")) {
m->removeAttr("locus", rloc);
}
/*
if (m->exons.Count()==0 && m->children.Count()==0) {
//a non-mRNA feature with no subfeatures
//add a dummy exon just to have the generic exon checking work
m->addExon(m->start,m->end);
}
*/
if (forceExons) { // && m->children.Count()==0) {
m->exon_ftype_id=gff_fid_exon;
}
//GList<GffObj> gfadd(false,false); -- for gf_validate()?
if (gf_validate!=NULL && !(*gf_validate)(m, NULL)) {
continue;
}
m->isUsed(true); //so the gffreader won't destroy it
int i=-1;
GenomicSeqData f(m->gseq_id);
GenomicSeqData* gdata=NULL;
if (seqdata.Found(&f,i)) gdata=seqdata[i];
else { //entry not created yet for this genomic seq
gdata=new GenomicSeqData(m->gseq_id);
seqdata.Add(gdata);
}
/*
for (int k=0;k<gfadd.Count();k++) {
bool keep=placeGf(gfadd[k], gdata, doCluster, doCollapseRedundant, matchAllIntrons, fuzzSpan);
if (!keep) {
gfadd[k]->isUsed(false);
//DEBUG
GMessage("Feature %s(%d-%d) is going to be discarded..\n",gfadd[k]->getID(), gfadd[k]->start, gfadd[k]->end);
}
}
*/
bool keep=placeGf(m, gdata, doCluster, doCollapseRedundant, matchAllIntrons, fuzzSpan);
if (!keep) {
m->isUsed(false);
//DEBUG
//GMessage("Feature %s(%d-%d) is going to be discarded..\n",m->getID(), m->start, m->end);
}
} //for each read gffObj
//if (verbose) GMessage(" .. %d records from %s clustered into loci.\n", gffr->gflst.Count(), fname.chars());
if (f!=stdin) { fclose(f); f=NULL; }
delete gffr;
}
// virtual
void GNaiveBayes::trainIncremental(const GVec& in, const GVec& out)
{
for(size_t n = 0; n < m_pRelLabels->size(); n++)
m_pOutputs[n]->AddTrainingSample(in.data(), (int)out[n]);
m_nSampleCount++;
}
GEvolutionaryOptimizerNode(size_t dims)
{
m_pVector.resize(dims);
}