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spm_ALAP.m
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spm_ALAP.m
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function [DEM] = spm_ALAP(DEM)
% Laplacian model inversion (see also spm_LAP) with action
% FORMAT DEM = spm_ALAP(DEM)
%
% DEM.G - generative process
% DEM.M - recognition model
% DEM.C - causes (n x t)
% DEM.U - prior expectation of causes
%__________________________________________________________________________
%
% generative model
%--------------------------------------------------------------------------
% M(i).g = v = g(x,v,P) {inline function, string or m-file}
% M(i).f = dx/dt = f(x,v,P) {inline function, string or m-file}
%
% M(i).ph = pi(v) = ph(x,v,h,M) {inline function, string or m-file}
% M(i).pg = pi(x) = pg(x,v,g,M) {inline function, string or m-file}
%
% pi(v,x) = vectors of log-precisions; (h,g) = precision parameters
%
% M(i).pE = prior expectation of p model-parameters
% M(i).pC = prior covariances of p model-parameters
% M(i).hE = prior expectation of h log-precision (cause noise)
% M(i).hC = prior covariances of h log-precision (cause noise)
% M(i).gE = prior expectation of g log-precision (state noise)
% M(i).gC = prior covariances of g log-precision (state noise)
%
% M(i).Q = precision components (input noise)
% M(i).R = precision components (state noise)
% M(i).V = fixed precision (input noise)
% M(i).W = fixed precision (state noise)
% M(i).xP = precision (states)
%
% M(i).m = number of hidden inputs v(i + 1);
% M(i).n = number of hidden states x(i);
% M(i).l = number of outputs v(i);
%
% or (inital values)
%
% M(i).x = hidden states
% M(i).v = hidden causes
%
% hierarchical process G(i)
%--------------------------------------------------------------------------
% G(i).g = y(t) = g(x,v,[a],P) {inline function, string or m-file}
% G(i).f = dx/dt = f(x,v,[a],P) {inline function, string or m-file}
%
% G(i).pE = model-parameters
% G(i).U = precision (on sensory prediction errors - for action)
% G(i).V = precision (input noise)
% G(i).W = precision (state noise)
%
% G(i).m = number of inputs v(i + 1);
% G(i).n = number of states x(i)
% G(i).l = number of output v(i)
% G(i).k = number of action a(i)
%
% or (inital values)
%
% G(i).x = states
% G(i).v = causes
% G(i).a = action
%
% Returns the following fields of DEM
%--------------------------------------------------------------------------
%
% true model-states - u
%--------------------------------------------------------------------------
% pU.x = hidden states
% pU.v = causal states v{1} = response (Y)
%
% model-parameters - p
%--------------------------------------------------------------------------
% pP.P = parameters for each level
%
% hyper-parameters (log-transformed) - h,g
%--------------------------------------------------------------------------
% pH.h = cause noise
% pH.g = state noise
%
% conditional moments of model-states - q(u)
%--------------------------------------------------------------------------
% qU.a = Action
% qU.x = Conditional expectation of hidden states
% qU.v = Conditional expectation of causal states
% qU.w = Conditional prediction error (states)
% qU.z = Conditional prediction error (causes)
% qU.C = Conditional covariance: cov(v)
% qU.S = Conditional covariance: cov(x)
%
% conditional moments of model-parameters - q(p)
%--------------------------------------------------------------------------
% qP.P = Conditional expectation
% qP.C = Conditional covariance
%
% conditional moments of hyper-parameters (log-transformed) - q(h)
%--------------------------------------------------------------------------
% qH.h = Conditional expectation (cause noise)
% qH.g = Conditional expectation (state noise)
% qH.C = Conditional covariance
%
% F = log-evidence = log-marginal likelihood = negative free-energy
%
%__________________________________________________________________________
% Accelerated methods: To accelerate computations one can specify the
% nature of the model equations using:
%
% M(1).E.linear = 0: full - evaluates 1st and 2nd derivatives
% M(1).E.linear = 1: linear - equations are linear in x and v
% M(1).E.linear = 2: bilinear - equations are linear in x, v & x*v
% M(1).E.linear = 3: nonlinear - equations are linear in x, v, x*v, & x*x
% M(1).E.linear = 4: full linear - evaluates 1st derivatives (for GF)
%
% similarly, for evaluating precisions:
%
% M(1).E.method.h = 0,1 switch for precision parameters (hidden causes)
% M(1).E.method.g = 0,1 switch for precision parameters (hidden states)
% M(1).E.method.x = 0,1 switch for precision (hidden causes)
% M(1).E.method.v = 0,1 switch for precision (hidden states)
%__________________________________________________________________________
%
%__________________________________________________________________________
%
% spm_ALAP implements a variational scheme under the Laplace
% approximation to the conditional joint density q on states u, parameters
% p and hyperparameters (h,g) of an analytic nonlinear hierarchical dynamic
% model, with additive Gaussian innovations.
%
% q(u,p,h,g) = max E[L(t)] - H(q(u,p,h,g))
%
% L is the ln p(y,u,p,h,g|M) under the model M. The conditional covariances
% obtain analytically from the curvature of L with respect to the unknowns.
%
% This implementation is the same as spm_LAP but integrates both the
% generative process and model inversion in parallel. Its functionality is
% exactly the same apart from the fact that confounds are not accommodated
% explicitly. The generative model is specified by DEM.G and the veridical
% causes by DEM.C; these may or may not be used as priors on the causes for
% the inversion model DEM.M (i.e., DEM.U = DEM.C). Clearly, DEM.G does not
% require any priors or precision components; it will use the values of the
% parameters specified in its prior expectation fields.
%
% This routine is not used for model inversion per se but to simulate the
% dynamical inversion of models. Critically, it includes action
% variables a - that couple the model back to the generative process
% This enables active inference (c.f., action-perception) or embodied
% inference.
%__________________________________________________________________________
% Copyright (C) 2012 Wellcome Trust Centre for Neuroimaging
% Karl Friston
% $Id: spm_ALAP.m 6290 2014-12-20 22:11:50Z karl $
% check model, data and priors
%==========================================================================
DEM = spm_ADEM_set(DEM);
M = DEM.M;
G = DEM.G;
C = DEM.C;
U = DEM.U;
% ensure embedding dimensions are compatible
%--------------------------------------------------------------------------
G(1).E.n = M(1).E.n;
G(1).E.d = M(1).E.n;
% set regularisation
%--------------------------------------------------------------------------
try
dt = DEM.M(1).E.v;
catch
dt = 0;
DEM.M(1).E.v = dt;
end
% number of iterations of active inference
%--------------------------------------------------------------------------
try, nN = M(1).E.nN; catch, nN = 16; end
% ensure integration scheme evaluates gradients at each time-step
%--------------------------------------------------------------------------
M(1).E.linear = 4;
% assume precisions have a Gaussian autocorrelation function
%--------------------------------------------------------------------------
try
form = M(1).E.form;
catch
form = 'Gaussian';
end
% checks for state-dependent precision (precision functions; ph and pg)
%--------------------------------------------------------------------------
for i = 1:length(M)
try
feval(M(i).ph,M(i).x,M(i + 1).v,M(i).hE,M(i));
catch
M(i).ph = inline('spm_LAP_ph(x,v,h,M)','x','v','h','M');
end
try
feval(M(i).pg,M(i).x,M(i + 1).v,M(i).gE,M(i));
catch
M(i).pg = inline('spm_LAP_pg(x,v,h,M)','x','v','h','M');
end
end
% order parameters (d = n = 1 for static models) and checks
%==========================================================================
d = M(1).E.d + 1; % embedding order of q(v)
n = M(1).E.n + 1; % embedding order of q(x)
s = M(1).E.s; % smoothness - s.d. (bins)
% number of states and parameters - generative model
%--------------------------------------------------------------------------
ns = size(C,2); % number of samples
nl = size(M,2); % number of levels
nv = sum(spm_vec(M.m)); % number of v (casual states)
nx = sum(spm_vec(M.n)); % number of x (hidden states)
ny = M(1).l; % number of y (inputs)
nc = M(end).l; % number of c (prior causes)
nu = nv*d + nx*n; % number of generalised states
ne = nv*n + nx*n + ny*n; % number of generalised errors
% number of states and parameters - generative process
%--------------------------------------------------------------------------
gv = sum(spm_vec(G.l)); % number of v (outputs)
ga = sum(spm_vec(G.k)); % number of a (active states)
gx = sum(spm_vec(G.n)); % number of x (hidden states)
gy = ny; % number of y (inputs)
na = ga; % number of a (action)
% precision (R) of generalised errors and null matrices for concatenation
%==========================================================================
Rh = spm_DEM_R(n,s,form);
Rg = spm_DEM_R(n,s,form);
QW = sparse(nx*n,nx*n);
QV = sparse((ny + nv)*n,(ny + nv)*n);
% restriction matrix, mapping prediction errors to action
%--------------------------------------------------------------------------
for i = 1:nl
Qh{i,i} = sparse(M(i).l,M(i).l);
Qg{i,i} = sparse(M(i).n,M(i).n);
end
Qh{1} = G(1).U;
iG = blkdiag(kron(Rh,spm_cat(Qh)),kron(Rg,spm_cat(Qg)));
% fixed priors on states (u)
%--------------------------------------------------------------------------
Px = kron(spm_DEM_R(n,2),spm_cat(spm_diag({M(1:end).xP})));
Pv = kron(spm_DEM_R(d,2),spm_cat(spm_diag({M(2:end).vP})));
Pu = spm_cat(spm_diag({Px Pv}));
Pa = spm_speye(na,na)*exp(-2);
% hyperpriors
%--------------------------------------------------------------------------
ph.h = spm_vec({M.hE M.gE}); % prior expectation of h,g
ph.c = spm_cat(spm_diag({M.hC M.gC})); % prior covariances of h,g
Ph = spm_inv(ph.c); % prior precision of h,g
qh.h = {M.hE}; % conditional expectation h
qh.g = {M.gE}; % conditional expectation g
nh = length(spm_vec(qh.h)); % number of hyperparameters h
ng = length(spm_vec(qh.g)); % number of hyperparameters g
nb = nh + ng; % number of hyperparameters
% priors on parameters (in reduced parameter space)
%==========================================================================
pp.c = cell(nl,nl);
qp.p = cell(nl,1);
for i = 1:(nl - 1)
% eigenvector reduction: p <- pE + qp.u*qp.p
%----------------------------------------------------------------------
qp.u{i} = spm_svd(M(i).pC,0); % basis for parameters
M(i).p = size(qp.u{i},2); % number of qp.p
qp.p{i} = sparse(M(i).p,1); % initial deviates
pp.c{i,i} = qp.u{i}'*M(i).pC*qp.u{i}; % prior covariance
end
Up = spm_cat(spm_diag(qp.u));
% priors on parameters
%--------------------------------------------------------------------------
pp.p = spm_vec(M.pE);
pp.c = spm_cat(pp.c);
Pp = spm_inv(pp.c);
% initialise conditional density q(p)
%--------------------------------------------------------------------------
for i = 1:(nl - 1)
try
qp.p{i} = qp.p{i} + qp.u{i}'*(spm_vec(M(i).P) - spm_vec(M(i).pE));
end
end
np = size(Up,2);
% initialise cell arrays for D-Step; e{i + 1} = (d/dt)^i[e] = e[i]
%==========================================================================
qu.x = cell(n,1);
qu.v = cell(n,1);
qu.a = cell(1,1);
qu.y = cell(n,1);
qu.u = cell(n,1);
pu.v = cell(n,1);
pu.x = cell(n,1);
pu.z = cell(n,1);
pu.w = cell(n,1);
[qu.x{:}] = deal(sparse(nx,1));
[qu.v{:}] = deal(sparse(nv,1));
[qu.a{:}] = deal(sparse(na,1));
[qu.y{:}] = deal(sparse(ny,1));
[qu.u{:}] = deal(sparse(nc,1));
[pu.v{:}] = deal(sparse(gv,1));
[pu.x{:}] = deal(sparse(gx,1));
[pu.z{:}] = deal(sparse(gv,1));
[pu.w{:}] = deal(sparse(gx,1));
% initialise cell arrays for hierarchical structure of x[0] and v[0]
%--------------------------------------------------------------------------
qu.x{1} = spm_vec({M(1:end - 1).x});
qu.v{1} = spm_vec({M(1 + 1:end).v});
qu.a{1} = spm_vec({G.a});
pu.x{1} = spm_vec({G.x});
pu.v{1} = spm_vec({G.v});
% derivatives for Jacobian of D-step
%--------------------------------------------------------------------------
Dx = kron(spm_speye(n,n,1),spm_speye(nx,nx,0));
Dv = kron(spm_speye(d,d,1),spm_speye(nv,nv,0));
Dc = kron(spm_speye(d,d,1),spm_speye(nc,nc,0));
Dw = kron(spm_speye(n,n,1),spm_speye(gx,gx,0));
Dz = kron(spm_speye(n,n,1),spm_speye(gv,gv,0));
Iw = kron(spm_speye(n,n,0),spm_speye(gx,gx,0));
Du = spm_cat(spm_diag({Dx,Dv}));
Ib = spm_speye(np + nb,np + nb);
dbdt = sparse(np + nb,1);
dydv = kron(speye(n,n),speye(gy,gv));
% gradients of generalised weighted errors
%--------------------------------------------------------------------------
dedh = sparse(nh,ne);
dedg = sparse(ng,ne);
dedv = sparse(nv,ne);
dedx = sparse(nx,ne);
dedhh = sparse(nh,nh);
dedgg = sparse(ng,ng);
% curvatures of Gibb's energy w.r.t. hyperparameters
%--------------------------------------------------------------------------
dHdh = sparse(nh,1);
dHdg = sparse(ng,1);
dHdp = sparse(np,1);
dHdu = sparse(nu,1);
% test for dependency of precisions on hyperparameters and states
%--------------------------------------------------------------------------
[p,dp] = spm_LAP_eval(M,qu,qh);
try method.h = M(1).E.method.h; catch, method.h = any(dp.h.dh(:)); end
try method.g = M(1).E.method.g; catch, method.g = any(dp.g.dg(:)); end
try method.x = M(1).E.method.x; catch, method.x = any([dp.g.dx(:);dp.h.dx(:)]); end
try method.v = M(1).E.method.v; catch, method.v = any([dp.g.dv(:);dp.h.dv(:)]); end
M(1).E.method = method;
% preclude unnecessary iterations and set switches
%--------------------------------------------------------------------------
mnh = nh*method.h;
mng = ng*method.g;
mnx = nx*method.x;
mnv = nv*method.v;
if ~np && ~logical(mnh) && ~logical(mng), nN = 1; end
% preclude very precise states from entering free-energy/action
%--------------------------------------------------------------------------
ih = p.h < 8;
ig = p.g < 8;
ie = kron(ones(n,1),ih);
ix = kron(ones(n,1),ig);
iv = kron(ones(d,1),ih((1:nv) + ny));
je = find([ie; ix]); ix(1:nx) = 1;
ju = find([ix; iv]);
% and other useful indices
%--------------------------------------------------------------------------
ix = (1:nx);
ih = (1:nb);
iv = (1:nv) + nx*n;
ip = (1:np) + nu;
% create innovations (and add causes)
%--------------------------------------------------------------------------
[z w] = spm_DEM_z(G,ns);
z{end} = C + z{end};
a = {G.a};
Z = spm_cat(z(:));
W = spm_cat(w(:));
A = spm_cat(a(:));
% number of iterations for convergence
%--------------------------------------------------------------------------
convergence = -4;
% Iterate Laplace scheme
%==========================================================================
F = -Inf;
for iN = 1:nN
% get time and clear persistent variables in evaluation routines
%----------------------------------------------------------------------
tic; clear spm_DEM_eval qa
% [re-]set states & their derivatives
%----------------------------------------------------------------------
try
pu = Q(1).r;
qu = Q(1).u;
end
% D-Step: (over time)
%======================================================================
for is = 1:ns
% pass action to pu.a (external states)
%==================================================================
if exist('qa','var'), A = spm_cat({qa,qu.a}); end
% derivatives of responses and random fluctuations
%------------------------------------------------------------------
pu.z = spm_DEM_embed(Z,n,is);
pu.w = spm_DEM_embed(W,n,is);
pu.a = spm_DEM_embed(A,n,is);
qu.u = spm_DEM_embed(U,n,is);
% evaluate generative process
%------------------------------------------------------------------
[pu dg df] = spm_ADEM_diff(G,pu);
% and pass response to qu.y
%==================================================================
for i = 1:n
y = spm_unvec(pu.v{i},{G.v});
qu.y{i} = y{1};
end
% evaluate recognition model functions and derivatives
%==================================================================
% prediction errors (E) and precision vectors (p)
%------------------------------------------------------------------
[E dE] = spm_DEM_eval(M,qu,qp);
[p dp] = spm_LAP_eval(M,qu,qh);
% gradients of log(det(iS)) dDd...
%==================================================================
% get precision matrices
%------------------------------------------------------------------
iSh = diag(exp(p.h));
iSg = diag(exp(p.g));
iS = blkdiag(kron(Rh,iSh),kron(Rg,iSg));
% gradients of trace(diag(p)) = sum(p); p = precision vector
%------------------------------------------------------------------
dpdx = n*sum(spm_cat({dp.h.dx; dp.g.dx}));
dpdv = n*sum(spm_cat({dp.h.dv; dp.g.dv}));
dpdh = n*sum(dp.h.dh);
dpdg = n*sum(dp.g.dg);
dpdx = kron(sparse(1,1,1,1,n),dpdx);
dpdv = kron(sparse(1,1,1,1,d),dpdv);
dDdu = [dpdx dpdv]';
dDdh = [dpdh dpdg]';
% gradients precision-weighted generalised error dSd..
%==================================================================
% gradients w.r.t. hyperparameters
%------------------------------------------------------------------
for i = 1:nh
diS = diag(dp.h.dh(:,i).*exp(p.h));
diSdh{i} = blkdiag(kron(Rh,diS),QW);
dedh(i,:) = E'*diSdh{i};
end
for i = 1:ng
diS = diag(dp.g.dg(:,i).*exp(p.g));
diSdg{i} = blkdiag(QV,kron(Rg,diS));
dedg(i,:) = E'*diSdg{i};
end
% gradients w.r.t. hidden states
%------------------------------------------------------------------
for i = 1:mnx
diV = diag(dp.h.dx(:,i).*exp(p.h));
diW = diag(dp.g.dx(:,i).*exp(p.g));
diSdx{i} = blkdiag(kron(Rh,diV),kron(Rg,diW));
dedx(i,:) = E'*diSdx{i};
end
% gradients w.r.t. causal states
%------------------------------------------------------------------
for i = 1:mnv
diV = diag(dp.h.dv(:,i).*exp(p.h));
diW = diag(dp.g.dv(:,i).*exp(p.g));
diSdv{i} = blkdiag(kron(Rh,diV),kron(Rg,diW));
dedv(i,:) = E'*diSdv{i};
end
dSdx = kron(sparse(1,1,1,n,1),dedx);
dSdv = kron(sparse(1,1,1,d,1),dedv);
dSdu = [dSdx; dSdv];
dEdh = [dedh; dedg];
dEdp = dE.dp'*iS;
dEdu = dE.du'*iS;
% curvatures w.r.t. hyperparameters
%------------------------------------------------------------------
for i = 1:nh
for j = i:nh
diS = diag(dp.h.dh(:,i).*dp.h.dh(:,j).*exp(p.h));
diS = blkdiag(kron(Rh,diS),QW);
dedhh(i,j) = E'*diS*E;
dedhh(j,i) = dedhh(i,j);
end
end
for i = 1:ng
for j = i:ng
diS = diag(dp.g.dg(:,i).*dp.g.dg(:,j).*exp(p.g));
diS = blkdiag(QV,kron(Rg,diS));
dedgg(i,j) = E'*diS*E;
dedgg(j,i) = dedgg(i,j);
end
end
% combined curvature
%------------------------------------------------------------------
dSdhh = spm_cat({dedhh [] ;
[] dedgg});
% errors (from prior expectations) (NB pp.p = 0)
%------------------------------------------------------------------
Eu = spm_vec(qu.x(1:n),qu.v(1:d));
Ep = spm_vec(qp.p);
Eh = spm_vec(qh.h,qh.g) - ph.h;
% first-order derivatives of Gibb's Energy
%==================================================================
dLdu = dEdu*E + dSdu*E/2 - dDdu/2 + Pu*Eu;
dLdh = dEdh*E/2 - dDdh/2 + Ph*Eh;
dLdp = dEdp*E + Pp*Ep;
% and second-order derivatives of Gibb's Energy
%------------------------------------------------------------------
dLduu = dEdu*dE.du + Pu;
dLdpp = dEdp*dE.dp + Pp;
dLdhh = dSdhh/2 + Ph;
dLdup = dEdu*dE.dp;
dLdhp = dEdh*dE.dp;
dLdpu = dLdup';
dLdph = dLdhp';
% precision and covariances for entropy
%------------------------------------------------------------------
dLdaa = spm_cat({dLduu dLdup ;
dLdpu dLdpp});
dLdbb = spm_cat({dLdpp dLdph ;
dLdhp dLdhh});
Cup = spm_inv(dLdaa);
Chh = spm_inv(dLdhh);
% first-order derivatives of Entropy term
%==================================================================
% log-precision
%------------------------------------------------------------------
for i = 1:nh
Luub = dE.du'*diSdh{i}*dE.du;
Lpub = dE.dp'*diSdh{i}*dE.du;
Lppb = dE.dp'*diSdh{i}*dE.dp;
diCdh = spm_cat({Luub Lpub';
Lpub Lppb});
dHdh(i) = spm_trace(diCdh,Cup)/2;
end
for i = 1:ng
Luub = dE.du'*diSdg{i}*dE.du;
Lpub = dE.dp'*diSdg{i}*dE.du;
Lppb = dE.dp'*diSdg{i}*dE.dp;
diCdg = spm_cat({Luub Lpub';
Lpub Lppb});
dHdg(i) = spm_trace(diCdg,Cup)/2;
end
% parameters
%------------------------------------------------------------------
for i = 1:np
Luup = dE.dup{i}'*dEdu';
Lpup = dEdp*dE.dup{i};
Luup = Luup + Luup';
diCdp = spm_cat({Luup Lpup';
Lpup [] });
dHdp(i) = spm_trace(diCdp,Cup)/2;
end
% and concatenate
%------------------------------------------------------------------
dHdb = [dHdh; dHdg];
dHdb = [dHdp; dHdb];
dLdb = [dLdp; dLdh];
% whiten generalised ascent on parameters and hyperparameters
%==================================================================
% accumulate curvatures of [hyper] parameters
%------------------------------------------------------------------
try
dLdB = dLdB*(1 - 1/ns) + dLdb/ns;
dLdBB = dLdBB*(1 - 1/ns) + dLdbb/ns;
catch
dLdB = dLdb - dLdb;
dLdBB = Ib*32;
end
% whiten gradient (and curvatures) with regularised precision
%------------------------------------------------------------------
Cb = spm_inv(dLdBB + Ib*exp(dt));
dLdb = Cb*dLdB;
dHdb = Cb*dHdb;
% prior precision of fluctuations on [hyper] parameters
%------------------------------------------------------------------
Kb = ns*Ib;
% derivatives and curvature generative process (and action)
%==================================================================
% tensor products for Jacobian
%------------------------------------------------------------------
Dgda = kron(spm_speye(n,1,1),dg.da);
Dgdv = kron(spm_speye(n,n,1),dg.dv);
Dgdx = kron(spm_speye(n,n,1),dg.dx);
dfda = kron(spm_speye(n,1,0),df.da);
dfdv = kron(spm_speye(n,n,0),df.dv);
dfdx = kron(spm_speye(n,n,0),df.dx);
dgda = kron(spm_speye(n,1,0),dg.da);
dgdx = kron(spm_speye(n,n,0),dg.dx);
% change in error w.r.t. action
%------------------------------------------------------------------
Dfdx = 0;
for i = 1:n
Dfdx = Dfdx + kron(spm_speye(n,n,-i),df.dx^(i - 1));
end
% dE/da with restriction
%------------------------------------------------------------------
dE.dv = dE.dy*dydv;
dE.da = dE.dv*(dgda + dgdx*Dfdx*dfda);
% first-order derivatives
%------------------------------------------------------------------
dVda = -dE.da'*iG*E - Pa*spm_vec(qu.a{1:1});
% and second-order derivatives
%------------------------------------------------------------------
dVdaa = -dE.da'*iG*dE.da - Pa;
dVduv = -dE.du'*iS*dE.dv;
dVduc = -dE.du'*iS*dE.dc;
dVdua = -dE.du'*iS*dE.da;
dVdav = -dE.da'*iG*dE.dv;
dVdau = -dE.da'*iG*dE.du;
dVdac = -dE.da'*iG*dE.dc;
% save conditional moments (and prediction error) at Q{t}
%==================================================================
% save means
%------------------------------------------------------------------
Q(is).E = diag(diag(iS))*E;
Q(is).e = E;
Q(is).u = qu;
Q(is).p = qp;
Q(is).h = qh;
Q(is).r = pu;
% and action
%------------------------------------------------------------------
if na, qa(:,is) = qu.a{1}; end
% and conditional covariances
%------------------------------------------------------------------
Q(is).u.s = Cup(ix,ix);
Q(is).u.c = Cup(iv,iv);
Q(is).p.c = Cup(ip,ip);
Q(is).h.c = Chh(ih,ih);
% Free-energy (components)
%------------------------------------------------------------------
Fc(is,1) = - E(je)'*iS(je,je)*E(je)/2;
Fc(is,2) = - Eu(ju)'*Pu(ju,ju)*Eu(ju)/2;
Fc(is,3) = - n*ny*log(2*pi)/2;
Fc(is,4) = spm_logdet(iS(je,je))/2;
Fc(is,5) = spm_logdet(Pu(ju,ju)*Cup(ju,ju))/2;
% update conditional moments
%==================================================================
% assemble true states and conditional means
%------------------------------------------------------------------
r.v = pu.v(1:n);
r.x = pu.x(1:n);
r.z = pu.z(1:n);
r.w = pu.w(1:n);
q.x = qu.x(1:n);
q.v = qu.v(1:d);
q.c = qu.u(1:d);
q.a = qu.a(1:1);
q.p = qp.p;
q.h = qh.h;
q.g = qh.g;
q.d = dbdt;
% flow
%------------------------------------------------------------------
g.v = Dz*spm_vec(r.v) ;
g.x = Dw*spm_vec(r.x) ;
g.z = Dz*spm_vec(r.z) ;
g.w = Dw*spm_vec(r.w) ;
f.u = Du*spm_vec(q.x,q.v) - dLdu - dHdu;
f.c = Dc*spm_vec(q.c) ;
f.a = dVda ;
f.b = spm_vec(q.d) ;
f.d = -Kb*spm_vec(q.d) - dLdb - dHdb;
% Jacobian (variational flow)
%------------------------------------------------------------------
dfdq = {...
Dgdv Dgdx Dz [] [] [] Dgda [] [];
dfdv dfdx [] Iw [] [] dfda [] [];
[] [] Dz [] [] [] [] [] [];
[] [] [] Dw [] [] [] [] [];
dVduv [] [] [] Du-dLduu dVduc dVdua [] [];
[] [] [] [] [] Dc [] [] [];
dVdav [] [] [] dVdau dVdac dVdaa [] [];
[] [] [] [] [] [] [] [] Ib;
[] [] [] [] [] [] [] -Ib -Kb};
% update conditional modes of states
%==================================================================
dq = spm_dx(spm_cat(dfdq),spm_vec(g,f),1);
[r,q] = spm_unvec(spm_vec(r,q) + dq,r,q);
% unpack conditional means
%------------------------------------------------------------------
pu.v(1:n) = r.v;
pu.x(1:n) = r.x;
qu.x(1:n) = q.x;
qu.v(1:d) = q.v;
qu.a(1:1) = q.a;
qp.p = q.p;
qh.h = q.h;
qh.g = q.g;
dbdt = q.d;
end % sequence (ns)
% Bayesian parameter averaging
%======================================================================
% Conditional moments of time-averaged parameters
%----------------------------------------------------------------------
Ep = 0;
Qp = 0;
for i = 1:ns
P = spm_inv(Q(i).p.c);
Ep = Ep + P*spm_vec(Q(i).p.p);
Qp = Qp + P;
end
Ep = spm_inv(Qp)*Ep;
Cp = spm_inv(Qp + (1 - ns)*Pp);
% conditional moments of hyper-parameters
%----------------------------------------------------------------------
Eh = 0;
Qh = 0;
for i = 1:ns
P = spm_inv(Q(i).h.c);
Eh = Eh + P*spm_vec({Q(i).h.h Q(i).h.g});
Qh = Qh + P;
end
Eh = spm_inv(Qh)*Eh - ph.h;
Ch = spm_inv(Qh + (1 - ns)*Ph);
% Free-action of states plus free-energy of parameters
%======================================================================
FC(1) = sum(Fc(:,1)); % - E'*iS*E/2;
FC(2) = sum(Fc(:,2)); % - Eu'*Pu*Eu/2;
FC(3) = sum(Fc(:,3)); % - n*ny*log(2*pi)/2;
FC(4) = sum(Fc(:,4)); % spm_logdet(iS)/2;
FC(5) = sum(Fc(:,5)); % spm_logdet(Pu*Cu)/2;
FC(6) = -Ep'*Pp*Ep/2;
FC(7) = -Eh'*Ph*Eh/2;
FC(8) = spm_logdet(Pp*Cp)/2;
FC(9) = spm_logdet(Ph*Ch)/2;
Fe = sum(FC);
% if F is decreasing, revert [hyper] parameters and slow down
%----------------------------------------------------------------------
if Fe < F(iN) && iN > 4
% save free-energy
%------------------------------------------------------------------
F(iN + 1) = F(iN);
% load current MAP estimates
%------------------------------------------------------------------
qp = PQ.qp;
qh = PQ.qh;
% decrease update time
%------------------------------------------------------------------
dt = max(dt + 2,2);
% convergence
%------------------------------------------------------------------
if dt > 6; convergence = 1; end
else
% convergence
%------------------------------------------------------------------
if Fe - F(iN) < 1, convergence = convergence + 1; end
% save free-energy
%------------------------------------------------------------------
F(iN) = Fe;
F(iN + 1) = Fe;
% save current MAP estimates
%------------------------------------------------------------------
PQ.qp = qp;
PQ.qh = qh;
% increase update time
%------------------------------------------------------------------
dt = max(dt - 1,-8);
end
% Convergence
%======================================================================
if convergence > 0; break, end
% otherwise save conditional moments (for each time point)
%======================================================================
for t = 1:length(Q)
% states
%------------------------------------------------------------------
a = spm_unvec(Q(t).u.a{1},{G.a});
v = spm_unvec(Q(t).r.v{1},{G.v});
x = spm_unvec(Q(t).r.x{1},{G.x});
z = spm_unvec(Q(t).r.z{1},{G.v});
w = spm_unvec(Q(t).r.w{1},{G.x});
for i = 1:nl
try
pU.v{i}(:,t) = spm_vec(v{i});
pU.z{i}(:,t) = spm_vec(z{i});
end
try
pU.x{i}(:,t) = spm_vec(x{i});
pU.w{i}(:,t) = spm_vec(w{i});
end
try
qU.a{i}(:,t) = spm_vec(a{i});
end
end
% states and predictions
%------------------------------------------------------------------
v = spm_unvec(Q(t).u.v{1},{M(1 + 1:end).v});
x = spm_unvec(Q(t).u.x{1},{M(1:end - 1).x});
z = spm_unvec(Q(t).e(1:(ny + nv)),{M.v});
e = spm_unvec(Q(t).E(1:(ny + nv)),{M.v});
w = spm_unvec(Q(t).e((1:nx) + (ny + nv)*n),{M.x});
u = spm_unvec(Q(t).E((1:nx) + (ny + nv)*n),{M.x});
for i = 1:(nl - 1)
if M(i).m, qU.v{i + 1}(:,t) = spm_vec(v{i}); end
if M(i).n, qU.x{i}(:,t) = spm_vec(x{i}); end
if M(i).n, qU.w{i}(:,t) = spm_vec(w{i}); end
if M(i).l, qU.z{i}(:,t) = spm_vec(z{i}); end
if M(i).n, qU.W{i}(:,t) = spm_vec(u{i}); end
if M(i).l, qU.Z{i}(:,t) = spm_vec(e{i}); end
end
if M(nl).l, qU.z{nl}(:,t) = spm_vec(z{nl}); end
if M(nl).l, qU.Z{nl}(:,t) = spm_vec(e{nl}); end
qU.v{1}(:,t) = spm_vec(Q(t).u.y{1}) - spm_vec(z{1});
% and conditional covariances
%------------------------------------------------------------------
qU.S{t} = Q(t).u.s;
qU.C{t} = Q(t).u.c;
% parameters
%------------------------------------------------------------------
qP.p{t} = spm_vec(Q(t).p.p);
qP.c{t} = Q(t).p.c;
% hyperparameters
%------------------------------------------------------------------
qH.p{t} = spm_vec({Q(t).h.h Q(t).h.g});
qH.c{t} = Q(t).h.c;
end
% graphics (states)
%----------------------------------------------------------------------
spm_figure('GetWin','GF');
spm_DEM_qU(qU)
% graphics (parameters and log-precisions)
%----------------------------------------------------------------------
if np && nb
subplot(2*nl,2,4*nl - 2)
plot(1:ns,spm_cat(qP.p))
set(gca,'XLim',[1 ns])
title('parameters (modes)','FontSize',16)
subplot(2*nl,2,4*nl)
plot(1:ns,spm_cat(qH.p))
set(gca,'XLim',[1 ns])
title('log-precision','FontSize',16)
elseif nb
subplot(nl,2,2*nl)
plot(1:ns,spm_cat(qH.p))
set(gca,'XLim',[1 ns])
title('log-precision','FontSize',16)
elseif np
subplot(nl,2,2*nl)
plot(1:ns,spm_cat(qP.p))
set(gca,'XLim',[1 ns])
title('parameters (modes)','FontSize',16)
end
drawnow
% report (EM-Steps)
%----------------------------------------------------------------------
try
dF = F(iN) - F(iN - 1);