def PMCMCstep(self, iteration):
        #progressbar(iteration / (self.nbiterations - 1))
        progressbar(iteration / (self.nbiterations - 1), text = " acceptance rate: %.3f" % \
                (sum(self.acceptations[0:iteration]) / iteration))
        #print "iteration %i, acceptance rate until now: %.3f" % (iteration, sum(self.acceptations[0:iteration]) / iteration)
        if (random.uniform(size = 1) < self.proposalmixtureweights[0]):
            transformedthetastar = self.modeltheta.proposal(self.transformedtheta[:, newaxis], self.fixedproposalcovmatrix)[:, 0]
        else:
            transformedthetastar = self.modeltheta.proposal(self.transformedtheta[:, newaxis], self.adaptiveproposalcovmatrix)[:, 0]
        thetastar = self.modeltheta.untransform(transformedthetastar[:,newaxis])[:,0]
        proposedSIRs = ParallelSIRs(self.Nx, thetastar[:, newaxis], self.observations, self.modelx)
        proposedSIRs.first_step()
        proposedSIRs.next_steps()
        proposedloglike = proposedSIRs.getTotalLogLike()[0]
        proposedlogomega = proposedloglike + self.modeltheta.priorlogdensity(transformedthetastar)
        currentlogomega = self.totalLogLike + self.modeltheta.priorlogdensity(self.transformedtheta)
        acceptation  = (log(random.uniform(size = 1)) < (proposedlogomega - currentlogomega))
#        if not(acceptation):
#            print "\nproposed loglikelihood:", proposedloglike
#            print "\ncurrent loglikelihood:", self.totalLogLike
#            print "\naccept:", acceptation
        if acceptation:
            self.theta = thetastar.copy()
            self.transformedtheta = transformedthetastar.copy()
            self.totalLogLike = proposedloglike.copy()
        self.chain[:, iteration] = self.theta.copy()
        self.transformedchain[:, iteration] = self.transformedtheta.copy()
        if iteration > 10:
            self.adaptiveproposalcovmatrix = (5.6644 / self.thetadim) * cov(self.transformedchain[:, 1:iteration])
            #print "\n", self.adaptiveproposalcovmatrix
        self.loglikechain[iteration] = self.totalLogLike
        self.acceptations[iteration] = acceptation
 def __init__(self, model, algorithmparameters, autoinit = True):
     # get the model:
     self.modelx = model["modelx"]
     self.modeltheta = model["modeltheta"]
     self.observations = model["observations"]
     self.Nx = algorithmparameters["N"]
     self.nbiterations = algorithmparameters["nbiterations"]
     #
     self.theta = self.modeltheta.priorgenerator(1)[:,0]
     self.thetadim = self.theta.shape[0]
     self.transformedtheta = self.modeltheta.transform(self.theta[:, newaxis])[:,0]
     self.chain = zeros((self.thetadim, self.nbiterations))
     self.transformedchain = zeros((self.thetadim, self.nbiterations))
     self.chain[:, 0] = self.theta.copy()
     self.transformedchain[:, 0] = self.transformedtheta.copy()
     #
     self.acceptations = zeros(self.nbiterations)
     self.fixedproposalcovmatrix = diag(repeat(0.01 / self.thetadim, self.thetadim))
     self.adaptiveproposalcovmatrix = diag(repeat(5.6644 / self.thetadim, self.thetadim))
     self.proposalmixtureweights = [0.5, 0.5]
     currentSIRs = ParallelSIRs(self.Nx, self.theta[:, newaxis], self.observations, self.modelx)
     currentSIRs.first_step()
     currentSIRs.next_steps()
     self.totalLogLike = currentSIRs.getTotalLogLike()[0]
     self.loglikechain = zeros(self.nbiterations)
     self.loglikechain[0] = self.totalLogLike
     print "------------------"
     print "launching adaptive PMCMC, with algorithm parameters:"
     for key, element in algorithmparameters.items():
         print key, ":", element
     print "------------------"
     if autoinit:
         self.allsteps()
Beispiel #3
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    def PMCMCstep(self, t):
        """
        Perform a PMMH move step on each theta-particle.
        """
        transformedthetastar = self.modeltheta.proposal(self.transformedthetaparticles, \
                self.proposalcovmatrix, hyperparameters = self.modeltheta.hyperparameters,\
                proposalmean = self.proposalmean, proposalkernel = self.AP["proposalkernel"])
        thetastar = self.modeltheta.untransform(transformedthetastar)
        proposedSIRs = ParallelSIRs(self.Nx, thetastar,
                                    self.observations[0:(t + 1)], self.modelx)
        proposedSIRs.first_step()
        proposedSIRs.next_steps()
        proposedTotalLogLike = proposedSIRs.getTotalLogLike()
        acceptations = zeros(self.Ntheta)
        proposedpriordensityeval = apply_along_axis(func1d = self.modeltheta.priorlogdensity,\
                arr = transformedthetastar, axis = 0)
        proposedlogomega = proposedTotalLogLike + proposedpriordensityeval
        currentlogomega = self.totalLogLike + self.priordensityeval
        # if proposal kernel == "randomwalk", then nothing else needs to be computed
        # since the RW is symmetric. If the proposal kernel is independent, then
        # the density of the multivariate gaussian used to generate the proposals
        # needs to be taken into account
        if self.AP["proposalkernel"] == "randomwalk":
            pass
        elif self.AP["proposalkernel"] == "independent":
            invSigma = linalg.inv(self.proposalcovmatrix)

            def multinorm_logpdf(x):
                centeredx = (x - self.proposalmean)
                return -0.5 * dot(dot(centeredx, invSigma), centeredx)
            proposaltermstar = apply_along_axis(func1d = multinorm_logpdf, \
                    arr = transformedthetastar, axis = 0)
            proposedlogomega -= proposaltermstar
            proposaltermcurr = apply_along_axis(func1d = multinorm_logpdf, \
                    arr = self.transformedthetaparticles, axis = 0)
            currentlogomega -= proposaltermcurr
        for i in range(self.Ntheta):
            acceptations[i] = (log(random.uniform(size=1)) <
                               (proposedlogomega[i] - currentlogomega[i]))
            if acceptations[i]:
                self.transformedthetaparticles[:,
                                               i] = transformedthetastar[:,
                                                                         i].copy(
                                                                         )
                self.thetaparticles[:, i] = thetastar[:, i].copy()
                self.totalLogLike[i] = proposedTotalLogLike[i].copy()
                self.priordensityeval[i] = proposedpriordensityeval[i].copy()
                self.xparticles[:, :, i] = proposedSIRs.xparticles[:, :,
                                                                   i].copy()
        acceptrate = sum(acceptations) / self.Ntheta
        self.acceptratios.append(acceptrate)
Beispiel #4
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    def PMCMCstep(self, t):
        """
        Perform a PMMH move step on each theta-particle.
        """
        
        #### INGMAR: This is where the proposal is computed
        transformedthetastar = self.modeltheta.proposal(self.transformedthetaparticles, \
                self.proposalcovmatrix, hyperparameters = self.modeltheta.hyperparameters,\
                proposalmean = self.proposalmean, proposalkernel = self.AP["proposalkernel"])
        thetastar = self.modeltheta.untransform(transformedthetastar)
        
        ###### INGMAR: This is where the likelihood is estimated
        proposedSIRs = ParallelSIRs(self.Nx, thetastar, self.observations[0:(t+1)], self.modelx)
        proposedSIRs.first_step()
        proposedSIRs.next_steps()
        proposedTotalLogLike = proposedSIRs.getTotalLogLike()
        
        
        acceptations = zeros(self.Ntheta)

        proposedpriordensityeval = apply_along_axis(func1d = self.modeltheta.priorlogdensity,\
                arr = transformedthetastar, axis = 0)
                
        proposedlogomega = proposedTotalLogLike + proposedpriordensityeval
        currentlogomega = self.totalLogLike + self.priordensityeval
        # if proposal kernel == "randomwalk", then nothing else needs to be computed
        # since the RW is symmetric. If the proposal kernel is independent, then
        # the density of the multivariate gaussian used to generate the proposals
        # needs to be taken into account
        if self.AP["proposalkernel"] == "randomwalk":
            pass
        elif self.AP["proposalkernel"] == "independent":
            invSigma = linalg.inv(self.proposalcovmatrix)
            def multinorm_logpdf(x):
                centeredx = (x - self.proposalmean)
                return -0.5 * dot(dot(centeredx, invSigma), centeredx)
            proposaltermstar = apply_along_axis(func1d = multinorm_logpdf, \
                    arr = transformedthetastar, axis = 0)
            proposedlogomega -= proposaltermstar
            proposaltermcurr = apply_along_axis(func1d = multinorm_logpdf, \
                    arr = self.transformedthetaparticles, axis = 0)
            currentlogomega  -= proposaltermcurr
        for i in range(self.Ntheta):
            acceptations[i]  = (log(random.uniform(size = 1)) < (proposedlogomega[i] - currentlogomega[i]))
            if acceptations[i]:
                self.transformedthetaparticles[:, i] = transformedthetastar[:, i].copy()
                self.thetaparticles[:, i] = thetastar[:, i].copy()
                self.totalLogLike[i] = proposedTotalLogLike[i].copy()
                self.priordensityeval[i] = proposedpriordensityeval[i].copy()
                self.xparticles[:, :, i] = proposedSIRs.xparticles[:, :, i].copy()
        acceptrate = sum(acceptations) / self.Ntheta
        self.acceptratios.append(acceptrate)
Beispiel #5
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 def increaseParticlesNb(self, t):
     """
     Double the number of x-particles.
     """
     print "increasing Nx: from %i to %i" % (self.Nx, 2 * self.Nx)
     self.Nx = 2 * self.Nx
     biggerSIRs = ParallelSIRs(self.Nx, self.thetaparticles, self.observations[0:(t+1),:], self.modelx)
     biggerSIRs.first_step()
     biggerSIRs.next_steps()
     biggerTotalLogLike = biggerSIRs.getTotalLogLike()
     self.thetalogweights[t, :] = self.thetalogweights[t, :] +  biggerTotalLogLike - self.totalLogLike
     self.totalLogLike = biggerTotalLogLike.copy()
     self.xparticles = biggerSIRs.xparticles.copy()
     self.xweights = zeros_like(biggerSIRs.xweights)
     self.logxweights = zeros_like(biggerSIRs.xweights)
     self.Nxlist.append(self.Nx)
     self.increaseindices.append(t)
Beispiel #6
0
 def increaseParticlesNb(self, t):
     """
     Double the number of x-particles.
     """
     print "increasing Nx: from %i to %i" % (self.Nx, 2 * self.Nx)
     self.Nx = 2 * self.Nx
     biggerSIRs = ParallelSIRs(self.Nx, self.thetaparticles, self.observations[0:(t+1),:], self.modelx)
     biggerSIRs.first_step()
     biggerSIRs.next_steps()
     biggerTotalLogLike = biggerSIRs.getTotalLogLike()
     self.thetalogweights[t, :] = self.thetalogweights[t, :] +  biggerTotalLogLike - self.totalLogLike
     self.totalLogLike = biggerTotalLogLike.copy()
     self.xparticles = biggerSIRs.xparticles.copy()
     self.xweights = zeros_like(biggerSIRs.xweights)
     self.logxweights = zeros_like(biggerSIRs.xweights)
     self.Nxlist.append(self.Nx)
     self.increaseindices.append(t)