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olderAO.m
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function [X,F,Cp,PP,Hist,params] = olderAO(funopts)
% A (Bayesian) gradient (curvature) descent optimisation routine, designed primarily
% for parameter estimation in nonlinear models.
%
% Getting started with default options:
%
% op = AO('options')
%
% op.fun = func; % function/model f(x0)
% op.x0 = x0(:); % start values: x0
% op.y = Y(:); % data we're fitting (for computation of objective fun, e.g. e = Y - f(x)
% op.V = V(:); % variance / step for each parameter, e.g. ones(length(x0),1)/8
%
% op.objective='gauss'; % select smooth Gaussian error function
%
% Run the routine:
% [X,F,CV,~,Hi] = AO(op);
%
%
% change objective to 'gaussmap' for MAP estimation%
%
% The algorithm combines a Newton-like gradient routine (& optionally
% MAP and ML) with line search and an optimisation on the composition of update
% parameters from a combination of the gradient flow and memories of previous updates.
% It further implements an exponential cost function hyperparameter which
% is tuned independently, and an iteratively updating precision operator.
%
% General idea: I have some data Y0 and a model (f) with some parameters x.
% Y0 = f(x) + e
%
% For a multivariate function f(x) where x = [p1 .. pn]' a gradient descent scheme
% is:
%
% x[p,t+1] = x[p,t] + a[p] *-dFdx[p]
%
% Note the use of different step sizes, a[p], for each parameter.
% Optionally, low dimensional hyperparameter tuning can be used to find
% the best step size a[p], by setting step_method = 6;
%
% x[p,t+1] = x[p,t] + (b*V) *-dFdx[p] ... where b is optimised independently
%
% See jaco.m for options, although by default these are computed using a
% finite difference approximation of the curvature, which retains the sign of the gradient:
%
% f0 = F(x[p]+h)
% fx = F(x[p] )
% f1 = F(x[p]-h)
%
% j(p,:) = (f0 - f1) / 2h
% ----------------------------
% (f0 - 2 * fx + f1) / h^2
%
% The algorithm computes the objective function itself based on user
% option; to retreive an empty options structure, do:
%
% opts = AO('options')
%
% Compulsory arguments are: (full list of optionals below)
%
% opts.y = data to fit
% opts.fun = model or function f(x)
% opts.x0 = parameter vector (initial guesses) for x in f(x)
% opts.V = Var vector, with initial variance for each elemtn of x
% opts.objective = the objective function selected from:
% {'sse' 'mse' 'rmse' 'mvgkl' 'gauss' 'gaussmap' 'gaussq' 'jsd' 'euclidean' 'gkld'}
%
% then to run the optmisation, pass the opts structure back into AO with
% these outputs:
%
% [X,F,Cp,PP,Hist,params] = AO(opts)
%
% Optional "step" methods (def 9: normal fixed step GD):
% -- step_method = 1 invokes steepest descent
% -- step_method = 3 or 4 invokes a vanilla dx = x + a*-J descent
% -- step_method = 6 invokes hyperparameter tuning of the step size.
% -- step_method = 7 invokes an eigen decomp of the Jacobian matrix
% -- step_method = 8 converts the routine to a mirror descent with
% Bregman proximity term.
%
% By default momentum is included (opts.im=1). The idea is that we can
% have more confidence in parameters that are repeatedly updated in the
% same direction, so we can take bigger steps for those parameters as the
% optimisation progresses.
%
% NOTE - the default option [2022] is now to use a regularised Newton routine:
%---------------------------------------------------------------------------
%
% dx = x + inv(H*L*H)*-J
%
% whewre H is the Hessian and J the jacobian (dFdx). L is a regularisation
% term that is optimised independently.
%
% The (best and default) objective function is you are unsure, is 'gauss'
% which is simply a smooth (approx Gaussian) error function, or 'gaussq'
% which is similar to gauss but implements a sort of pca.
%
% If you want true MAP estimates (or just to be Bayesian), use 'gaussmap'
% which implements a MAP routine:
%
% log(f(X|p)) + log(g(p))
%
%
% Other important stuff to know:
% -------------------------------
% if your function f(x) generates a vector output (not a single value),
% then you can compute the partial gradients along each oputput, which is
% necessary for proper implementation of some functions e.g. GaussNewton;
% flag:
%
% opts.ismimo = 1;
%
% The gradient computation can be done in parallel if you have a cluster or
% multicore computer, set:
%
% opts.doparallel = 1;
%
% Set opts.hypertune = 1 to append an exponential cost function to the chosen
% objective function. This is defined as:
%
% c = t * exp(1/t * data - pred)
%
% where t is a (temperature) hyperparameter controlled through a separate gradient
% descent routine.
%
% ALSO SET:
%
% opts.memory_optimise = 1; to optimise the weighting of dx on the gradient flow and recent memories
% opts.opts.rungekutta = 1; to invoke a runge-kutta optimisation locally around the gradient predicted dx
% opts.updateQ = 1; to update the error weighting on the precision matrix
%
% The {fe / free energy} objective function minimised is
%==========================================================================
% L(1) = spm_logdet(iS)*nq/2 - real(e'*iS*e)/2 - ny*log(8*atan(1))/2; % complexity minus accuracy of states
% L(2) = spm_logdet(ipC*Cp)/2 - p'*ipC*p/2; % complexity minus accuracy of parameters
% L(3) = spm_logdet(ihC*Ch)/2 - d'*ihC*d/2; % complexity minus accuracy of precision (hyperparameter)
% F = -sum(L);
%
%
% INPUTS:
%-------------------------------------------------------------------------
% To call this function using an options structure:
%-------------------------------------------------------------------------
% opts = AO('options'); % get the options struct
% opts.fun = @myfun % fill in what you want...
% opts.x0 = [0 1]; % start param value
% opts.V = [1 1]/8; % variances for each param
% opts.y = [...]; % data to fit - .e.g y = f(p) + e
% opts.maxit = 125; % max num iterations
% opts.step_method = 1; % step method - 1 (big), 3 (small) and 4 (vanilla)**.
% opts.im = 1; % flag to include momentum of parameters
% opts.order = 2; % partial derivate fun option (see jaco.m): 1 or 2
% opts.hyperparameters = 0; % flag to do a grad ascent on the precision (3rd term in FE)
% opts.criterion = -300 % convergence threshold
% opts.mleselect = 0; % maximum likelihood param selection
% opts.objective = 'fe'; % objective fun: 'free energy', 'logevidence','sse', ...
% opts.writelog = 0; % flag to write logbook instead of to console
% opts.Q = []; % square matrix precision operator ( size=length(y) )
% opts.inner_loop = 10; % limit on number of repeats on same decent (between grad comp)
% opts.DoMLE = 0; % flag to perform a sort of MLE via WLS
% opts.force_ls = 0; % flag to force a line search every time
% opts.ismimo = 0; % compute dFdx of a multi-output function, not just objective value
% opts.gradmemory = 0; % remember previous gradients
% opts.doparallel = 0; % compute gradients using parfor
% opts.fsd = 1; % use fixed step for derivative computation
% opts.allow_worsen = 0; % allow objective to get worse sometimes
% opts.doimagesc = 0; % if data/model outputs are matrix (not vector), plot as such
% opts.EnforcePriorProb = 0;% force the parameter updates to strictly adhere to prior distribution
% opts.FS = [] % feat selection function: FS(y)
% opts.userplotfun = []; % inject a user plot function into the main display
% opts.corrweight = 1; % weight error term by correlation
% opts.WeightByProbability = 0; % weight parameter step update by prob
% opts.faster = 0; % make faster by limiting loops
% opts.factorise_gradients = 1; % factorise gradients
% opts.sample_mvn = 0; % when stuck sample from a multivariate gauss
% opts.do_gpr = 0; % try to refine estimates using a Gauss process
% opts.normalise_gradients=0;% normalise gradients to a pdf
% opts.isGaussNewton = 0; % explicitly make the update a Gauss-Newton
% opts.do_poly=0; % same as do_gpr but using polynomials
% opts.steps_choice = []; % use multiple step methods and pick best on-line
% opts.hypertune = 1; % tune a hyperparameter using exponential cost
% opts.memory_optimise = 1; % switch on memory (recommend)
% opts.rungekutta = 1; % RK line search (recommend)
% opts.updateQ = 1; % update precision on each iteration(recommend)
% opts.DoMAP = 0; % maximum a posteriori
% opts.DoMAP_Bayes = 0; % Bayesian MAP (recommend, make sure mimo=1)
% opts.crit = [0 0 0 0 0 0 0 0];
% opts.save_constant = 0; % save .mat on each iteration
% opts.nocheck = 0; % skip some checks to make faster
% opts.isQR = 0; % use QR decomp to solve for dx
% opts.NatGrad = 0; % work in natural gradients
% opts.variance_estimation = 0; % try to estimate variances
% opts.gradtol = 1e-4; % minimum tol on dFdx
% opts.isGaussNewtonReg=1; % try to use DampedGaussNewton steps
% opts.orthogradient=1; % orthogonalise jacobian/partial gradients
%
% [X,F,Cp,PP,Hist] = AO(opts); % call the optimser, passing the options struct
%
% OUTPUTS:
%-------------------------------------------------------------------------
% X = posterior parameters
% F = fit value (depending on objective function specified)
% CP = parameter covariance
% Pp = posterior probabilites
% H = history
%
% *If the optimiser isn't working well, try making V smaller!
%
% Dependencies
%-------------------------------------------------------------------------
% atcm -> https://github.com/alexandershaw4/atcm
% spm -> https://github.com/spm/
%
% References
%-------------------------------------------------------------------------
%
% "Computing the objective function in DCM" Stephan, Friston & Penny
% https://www.fil.ion.ucl.ac.uk/spm/doc/papers/stephan_DCM_ObjFcn_tr05.pdf
%
% "The free energy principal: a rough guide to the brain?" Friston
% https://www.fil.ion.ucl.ac.uk/~karl/The%20free-energy%20principle%20-%20a%20rough%20guide%20to%20the%20brain.pdf
%
% "Likelihood and Bayesian Inference And Computation" Gelman & Hill
% http://www.stat.columbia.edu/~gelman/arm/chap18.pdf
%
% For the nonlinear least squares MLE / Gauss Newton:
% https://en.wikipedia.org/wiki/Gauss%E2%80%93Newton_algorithm
%
% For an explanation of momentum in gradient methods:
% https://distill.pub/2017/momentum/
%
% Approximation of derivaives by finite difference methods:
% https://www.ljll.math.upmc.fr/frey/cours/UdC/ma691/ma691_ch6.pdf
%
% For an explanation of normalised gradients in gradient descent
% https://jermwatt.github.io/machine_learning_refined/notes/3_First_order_methods/3_9_Normalized.html
%
% AS2019/2020/2021
% alexandershaw4@gmail.com
% Print the description of steps and exit
%--------------------------------------------------------------------------
if nargin == 1 && strcmp(lower(funopts),'help')
PrintHelp(); return;
end
if nargin == 1 && strcmp(lower(funopts),'options');
X = DefOpts; return;
end
% Inputs & Defaults...
%--------------------------------------------------------------------------
if isstruct(funopts)
parseinputstruct(funopts);
else
fprintf('You have to supply a funopts input struct now...\nTry AO(''options'')\n');
return;
end
% Set up log if requested
persistent loc ;
if writelog
name = datestr(now); name(name==' ') = '_';
name = [char(fun) '_' name '.txt'];
loc = fopen(name,'w');
else
loc = 1;
end
% If a feature selection function was passed, append it to the user fun
if ~isempty(FS) && isa(FS,'function_handle')
params.FS = FS;
end
% check functions, inputs, options... note: many of these are set/returned
% by the subfunctions parseinputstruct and DefOpts()
%--------------------------------------------------------------------------
%aopt = []; % reset
aopt.x0x0 = x0;
aopt.order = order; % first or second order derivatives [-1,0,1,2]
aopt.fun = fun; % (objective?) function handle
aopt.yshape = y;
aopt.y = y(:); % truth / data to fit
aopt.pp = x0(:); % starting parameters
aopt.Q = Q; % precision matrix
aopt.history = []; % error history when y=e & arg min y = f(x)
aopt.memory = gradmemory;% incorporate previous gradients when recomputing
aopt.fixedstepderiv = fsd;% fixed or adjusted step for derivative calculation
aopt.ObjectiveMethod = objective; % 'sse' 'fe' 'mse' 'rmse' (def sse)
aopt.hyperparameters = hyperparams;
aopt.forcels = force_ls; % force line search
aopt.mimo = ismimo; % derivatives w.r.t multiple output fun
aopt.parallel = doparallel; % compute dpdy in parfor
aopt.doimagesc = doimagesc; % change plot to a surface
aopt.rankappropriate = rankappropriate; % ensure facorised rank aprop cov
aopt.do_ssa = ssa;
aopt.corrweight = corrweight;
aopt.factorise_gradients = factorise_gradients;
aopt.hypertune = hypertune;
aopt.verbose = verbose;
BayesAdjust = mleselect; % Select params to update based in probability
IncMomentum = im; % Observe and use momentum data
givetol = allow_worsen; % Allow bad updates within a tolerance
EnforcePriorProb = EnforcePriorProb; % Force updates to comply with prior distribution
WeightByProbability = WeightByProbability; % weight parameter updates by probability
ExLineSearch = ext_linesearch;
params.aopt = aopt; % Need to move form global aopt to a structure
params.userplotfun = userplotfun;
if save_constant
name = ['optim_' date];
end
% parameter and step / distribution vectors
x0 = full(x0(:));
XX0 = x0;
V = full(V(:));
v = V;
pC = diag(V);
%crit = [0 0 0 0 0 0 0 0];
% variance (in reduced space)
%--------------------------------------------------------------------------
V = eye(length(x0)); %turn off svd
pC = V'*(pC)*V;
ipC = spm_inv(spm_cat(spm_diag({pC})));
red = (diag(pC));
aopt.updateh = true; % update hyperpriors
aopt.pC = red; % store for derivative & objective function access
aopt.ipC = ipC; % store ^
red_x0 = red;
% initial probs
aopt.pt = zeros(length(x0),1) + (1/length(x0));
params.aopt = aopt;
% initial objective value (approx at this point as missing covariance data)
[e0] = obj(x0,params);
n = 0;
iterate = true;
Vb = V;
% initial error plot(s)
%--------------------------------------------------------------------------
if doplot
f = setfig(); params = makeplot(x0,x0,params); aopt.oerror = params.aopt.oerror;
pl_init(x0,params)
end
% initialise counters
%--------------------------------------------------------------------------
n_reject_consec = 0;
search = 0;
% Initial probability threshold for inclusion (i.e. update) of a parameter
Initial_JPDtol = 1e-10;
JPDtol = Initial_JPDtol;
etol = 0;
% parameters (in reduced space)
%--------------------------------------------------------------------------
np = size(V,2);
p = [V'*x0];
ip = (1:np)';
Ep = V*p(ip);
dff = []; % tracks changes in error over iterations
localminflag = 0; % triggers when stuck in local minima
% print options before we start printing updates
if DoMLE; fprintf('Using GaussNewton/MLE option\n'); end
if BayesAdjust; fprintf('Using Probability-Based Parameter Selection option\n'); end
if IncMomentum; fprintf('Using Momentum option\n'); end
fprintf('Using step-method: %d\n',step_method);
fprintf('Using Jaco (gradient) option: %d\n',order);
fprintf('User fun has %d varying parameters\n',length(find(red)));
% print start point - to console or logbook (loc)
refdate(loc);pupdate(loc,n,0,e0,e0,'start: ');
if step_method == 0
% step method can switch between 1 (big) and 3 (small) automatcically
autostep = 1;
else autostep = 0;
end
all_dx = [];
all_ex = [];
Hist.e = [];
%etol = 0;
% start optimisation loop
%==========================================================================
while iterate
% counter
%----------------------------------------------------------------------
n = n + 1; tic;
% Save each step if requested
if save_constant
save(name,'x0','Hist');
end
if WeightByProbability
aopt.pp = x0(:);
end
% update Gaussian precision hyperparameters matrix
% integrate error-weighted Q over iterations: Q(t+1) = dt * Q(t) + dQ/de
%----------------------------------------------------------------------
if ~isempty(Q) && updateQ
if verbose; fprintf('| Updating Q...\n'); end
[~,~,erx,g0] = obj( V*x0(ip),params );
% extract residuals & convert to Gaussian mixture [gp]
RSE = erx(1:length(Q));%rescale(real(erx(1:length(Q))));
gerr = AGenQ(RSE);
% fit gauss residuals to data using lsq
b=AGenQ(RSE)\RSE-g0(1:length(Q));
aopt.Q = Q + diag(b'*gerr);
%aopt.Q = (Q + AGenQ(RSE) );
Hist.QQ(n,:) = rescale(real(erx(1:length(Q))));
%s=subplot(5,3,13);plot(real(diag(aopt.Q)),'color',[1 .7 .7],'linewidth',3);
s=subplot(5,3,12);imagesc(real(Q));
title('Gaussian Hyperparameter','color','w','fontsize',18);
ax = gca;
ax.XGrid = 'off';ax.YGrid = 'on';
s.YColor = [1 1 1];s.XColor = [1 1 1];s.Color = [.3 .3 .3];
drawnow;
end
% compute gradients & search directions
%----------------------------------------------------------------------
aopt.updatej = true; aopt.updateh = true; params.aopt = aopt;
if verbose; pupdate(loc,n,0,e0,e0,'gradnts',toc); end
% Second order partial derivates of F w.r.t x0 using Jaco.m
[e0,df0,~,~,~,~,params] = obj( V*x0(ip),params );
[e0,~,er] = obj( V*x0(ip),params );
df0 = real(df0);
if normalise_gradients
df0 = df0./sum(df0);
end
% catch instabilities in the gradient - ie explosive parameters
df0(isinf(df0)) = 0;
% Update aopt structure and place in params
aopt = params.aopt;
aopt.er = er;
aopt.updateh = false;
params.aopt = aopt;
% print end of gradient computation (just so we know it's finished)
if verbose; pupdate(loc,n,0,e0,e0,'grd-fin',toc); end
% update hyperparameter tuning plot
if hypertune; plot_hyper(params.hyper_tau,[Hist.e e0]); end
% update h_opt plot
if hyperparams; plot_h_opt(params.h_opt); drawnow; end
% Switching for different methods for calculating 'a' / step size
if autostep; search_method = autostepswitch(n,e0,Hist);
else; search_method = step_method;
end
% initial search direction (steepest) and slope
%----------------------------------------------------------------------
% Compute step, a, in scheme: dx = x0 + a*-J
if n == 1
a = red*0;
end
% Setting step size to 6 invokes low-dimensional hyperparameter tuning
if verbose
if search_method ~= 6
pupdate(loc,n,0,e0,e0,'stepsiz',toc);
else
pupdate(loc,n,0,e0,e0,'hyprprm',toc);
end
end
% Feature Scoring for MIMOs
%----------------------------------------------------------------------
if orthogradient && ismimo
if verbose; fprintf('Orthogonalising Jacobian\n'); end
params.aopt.J = symmetric_orthogonalise(params.aopt.J);
end
% i.e. where J(np,nf) & nf > 1
if ismimo
if verbose; pupdate(loc,n,0,e0,e0,'scoring',toc); end
JJ = params.aopt.J;
Q0 = aopt.Q;
if isempty(Q0)
Q0 = eye(length(y(:)));
end
padQ = size(JJ,2) - length(Q0);
Q0(end+1:end+padQ,end+1:end+padQ)=mean(Q0(:))/10;
Q0 = atcm.fun.gausvdpca(Q0,np);
for i = 1:np
for j = 1:np
% information score / approximate (precision weighted) Hessian
score(i,j) = trace(JJ(i,:).*Q0.*JJ(j,:)');
end
end
% integrate: da(t) = (expm(da/dx*t) - I)*inv(da/dx)*f
red = spm_dx(score,diag(pC),1);
% optimise by re-regularising step size if needed
if any(isnan(red)) || any(isinf(red)) || norm(red) > 1e2
Reg = 1/8;
while true
red = spm_dx(score,diag(pC),Reg);
if any(isnan(red)) || any(isinf(red)) || norm(red) > 1e2
Reg = Reg*Reg;
else
break;
end
end
end
end
% Select step size method
%----------------------------------------------------------------------
if ~ismimo
[a,J,nJ,L,D] = compute_step(df0,red,e0,search_method,params,x0,a,df0);
else
[a,J,nJ,L,D] = compute_step(params.aopt.J,red,e0,search_method,params,x0,a,df0);
J = -df0(:);
end
% if simplelinesearch
% if verbose; pupdate(loc,n,0,e0,e0,'linesrc',toc); end
% fls = @(r) obj(x0 - (red.*r).*df0,params);
% a = hypertuner(fls,ones(size(red))/2);
% end
if verbose;
if search_method ~= 6
pupdate(loc,n,0,e0,e0,'stp-fin',toc);
else
pupdate(loc,n,0,e0,e0,'hyp-fin',toc);
end
end
% Log start of iteration (these are returned)
Hist.e(n) = e0;
Hist.p{n} = x0;
Hist.J{n} = df0;
Hist.a{n} = a;
if ismimo
Hist.Jfull{n} = aopt.J;
end
% Make copies of error and param set for inner while loops
x1 = x0;
e1 = e0;
% Start counters
improve = true;
nfun = 0;
% check norm of gradients (def gradtol = 1e-4)
if norm(J) < gradtol
fprintf('Gradient step below tolerance (%d)\n',norm(J));
[X,F,Cp,PP] = finishup(V,x0,ip,e0,doparallel,params,J,Ep,red,writelog,loc,aopt);
return;
end
% Update expectation on variance (2nd moments) using Jacobian
%----------------------------------------------------------------------
Hist.red(n,:) = red;
% if variance_estimation
% if n > 1
% % this is also a prediction of the step size for the next iter
% ored = red;
%
% for l = 1:np
% PR(l) = normcdf(mean(Hist.Jfull{end}(l,:)),mean(Hist.Jfull{end-1}(l,:)),std(Hist.Jfull{end-1}(l,:)));
% end
%
% red = red_x0 + (red_x0(:) .* PR(:));
%
% % update saved inverse
% %params.aopt.ipC = spm_inv(diag(red));
% % aopt.red = red;
%
% % update plot
% s = subplot(5,3,14);
% b = bar([red-ored]);
%
% %b(1).FaceColor = [1 1 1];
% b(1).FaceColor = [1 .7 .7];
%
% title('Step Change','color','w','fontsize',18);
% ax = gca;
% ax.XGrid = 'off';
% ax.YGrid = 'on';
% s.YColor = [1 1 1];
% s.XColor = [1 1 1];
% s.Color = [.3 .3 .3];
% drawnow;
%
% end
% end
% iterative descent on this (-gradient) trajectory
%======================================================================
while improve
% Log number of function calls on this iteration
nfun = nfun + 1;
% Compute The Parameter Step (from gradients and step sizes):
% % x[p,t+1] = x[p,t] + a[p]*-dfdx[p]
%------------------------------------------------------------------
% dx ~ x1 + ( a * J );
dx = compute_dx(x1,a,J,red,search_method,params);
if (isGaussNewton && ismimo) || (isQuasiNewton && ismimo)
% [note this is now just a newton method, not gn!]
%
% note for this full Newton method you need both Hess and Grad
% from the jaco_par.m function because the step size is
% determined by the inverse of the inner prouect of the hessian
if verbose; pupdate(loc,n,nfun,e1,e1,'Newton ',toc); end
% by using the variance (red) as a lambda on the inverse
% Hessian, this becomes a relaxed or 'damped' Newton scheme
for i = 1:size(J,1);
for j = 1:size(J,1);
H(i,j) = spm_trace(aopt.J(i,:),aopt.J(j,:));
end
end
%H = [aopt.J];
H = (red.*H./norm(H));%./norm(H);
if isQuasiNewton
[u,s0,v0] = svd(H);
H = pinv(u);
end
% the non-parallel finite different functions return gradients
% in reduced space - embed in full vector space
Jo = cat(1,aopt.Jo{:,1});
JJ = x0*0;
JJ(find(diag(pC))) = Jo;
Hstep = spm_dx(H,JJ,{-4});
Gdx = x1 - Hstep;
dx = Gdx;
if verbose; fprintf('Selected Newton Step\n'); end
%if obj(Gdx,params) < obj(dx,params) && ~docompare
% dx = Gdx;
% fprintf('Selected Newton Step\n');
%end
end
if isGaussNewtonReg && ismimo
% [note this is now just a newton method, not gn!]
%
% note for this full Newton method you need both Hess and Grad
% from the jaco_par.m function because the step size is
% determined by the inverse of the inner prouect of the hessian
if verbose; pupdate(loc,n,nfun,e1,e1,'Newton ',toc);end
% by using the variance (red) as a lambda on the inverse
% Hessian, this becomes a relaxed or 'damped' Newton scheme
for i = 1:size(J,1);
for j = 1:size(J,1);
H(i,j) = spm_trace(aopt.J(i,:),aopt.J(j,:));
end
end
%H = [aopt.J];
H = (red.*H./norm(H));%./norm(H);
% the non-parallel finite different functions return gradients
% in reduced space - embed in full vector space
Jo = cat(1,aopt.Jo{:,1});
if length(Jo) ~= length(x1)
JJ = x0*0;
JJ(find(diag(pC))) = Jo;
else
JJ = Jo;
end
% essentially here we are tiuning this part of the Newton
% scheme:
% ______
% xhat = x - inv(H*L*H')*J
% tunable regularisation function
Gf = @(L) pinv(H*(L*eye(length(H)))*H');
Gff = @(x) obj(x1 - Gf(x)*JJ,params);
[XX] = fminsearch(Gff,1);
Hstep = pinv(H*(XX*eye(length(H)))*H')*JJ;
GRdx = x1 - Hstep;
%dx = GRdx;
% only take a Newton step if its better than the vanilla
% gradient step
if obj(GRdx,params) < obj(dx,params) && ~docompare
dx = GRdx;
if verbose; fprintf('Selected Regularised Newton Step\n'); end
end
if forcenewton
dx = GRdx;
if verbose; fprintf('Forced Newton Step\n');end
end
end
% if NatGrad
% % retrieve derivatives
% if ~ismimo; j = J(:)*er';
% else; j = aopt.J;
% end
%
% lambda = 1/8;
% D = size(j,1);
% % compute natural gradient
% fim = inv(lambda*eye(D)+j*j');
% dx = x1 - sum(fim*j,2);
% end
%
% if isQR && ismimo
% if verbose; pupdate(loc,n,nfun,e1,e1,'QRmodel',toc); end
% % Use QR factorisation to estimate dx from jacobian and
% % residual - i.e. under assumption local-linearity
% % (ensure ismimo = 1)
%
% % note this is the QR equivalent of the normal equations for a
% % linear least squares problem
% [q,r] = qr(params.aopt.J);
% dx = q\((r./norm(r))*er);
% end
if lsqjacobian
jx = aopt.J'\y;
dx = x1 - jx;
end
% The following options are like 'E-steps' or line search options
% - i.e. they estimate the missing variables (parameter indices &
% values) that should be optimised in this iteration
%==================================================================
% Compute the probabilities of each (predicted) new parameter
% coming from the same distribution defined by the prior (last best)
dx = real(dx);
x1 = real(x1);
red = real(red);
% [Prior] distributions
pt = zeros(1,length(x1));
for i = 1:length(x1)
%vv = real(sqrt( red(i) ));
vv = real(sqrt( red(i) ))*2;
if vv <= 0 || isnan(vv) || isinf(vv); vv = 1/64; end
pd(i) = makedist('normal','mu', real(aopt.pp(i)),'sigma', vv);
end
% Curb parameter estimates trying to exceed their distirbution bounds
if EnforcePriorProb
odx = dx;
nst = 1;
for i = 1:length(x1)
if red(i)
if dx(i) < ( pd(i).mu - (nst*pd(i).sigma) )
dx(i) = pd(i).mu - (nst*pd(i).sigma);
elseif dx(i) > ( pd(i).mu + (nst*pd(i).sigma) )
dx(i) = pd(i).mu + (nst*pd(i).sigma);
end
end
end
end
% Compute relative change
pdx = pt*0;
for i = 1:length(x1)
if red(i)
%vv = real(sqrt( red(i) ));
vv = real(sqrt( red(i) ))*2;
if vv <= 0 || isnan(vv) || isinf(vv); vv = 1/64; end
pd(i) = makedist('normal','mu', real(aopt.pp(i)),'sigma', vv);
pdx(i) = normcdf(dx(i),pd(i).mu,pd(i).sigma);
%pdx(i) = (1./(1+exp(-pdf(pd(i),dx(i))))) ./ (1./(1+exp(-pdf(pd(i),aopt.pp(i)))));
else
end
end
pt = pdx;
prplot(pt);
aopt.pt = [aopt.pt pt(:)];
% If WeightByProbability is set, use p(dx) as a weight on dx
% iteratively until n% of p(dx[i]) are > threshold
% -------------------------------------------------------------
if WeightByProbability
dx = x1 + ( pt(:).*(dx-x1) );
if verbose; pupdate(loc,n,1,e1,e1,'OptP(p)',toc); end
optimise = true;
num_optloop = 0;
while optimise
pdx = pt*0;
num_optloop = num_optloop + 1;
for i = 1:length(x1)
if red(i)
vv = real(sqrt( red(i) ))*2;
if vv <= 0 || isnan(vv) || isinf(vv); vv = 1/64; end
pd(i) = makedist('normal','mu', real(aopt.pp(i)),'sigma', vv);
pdx(i) = normcdf(dx(i),pd(i).mu,pd(i).sigma);
%pdx(i) = (1./(1+exp(-pdf(pd(i),dx(i))))) ./ (1./(1+exp(-pdf(pd(i),aopt.pp(i)))));
else
end
end
% integrate (update) dx
dx = x1 + ( pt(:).*(dx-x1) );
% convergence
if length(find(pdx(~~red) > 0.8))./length(pdx(~~red)) > 0.7 || num_optloop > 2000
optimise = false;
end
end
end
% Save for computing gradient ascent on probabilities
p_hist(n,:) = pt;
Hist.pt(:,n) = pt;
% Update plot: probabilities
[~,oo] = sort(pt(:),'descend');
%probplot(cumprod(pt(oo)),0.95,oo);
% This is a variation on the Gauss-Newton algorithm - compute
% MLE via WLS - where the weights are the probabilities
%------------------------------------------------------------------
% if DoMLE
% iter_mle = true;
% nmfun = 0;
% clear b
%
% while iter_mle
% if verbose; pupdate(loc,n,nmfun,e1,e1,'MLE/WLS',toc);end
% nmfun = nmfun + 1;
% nfun = nfun + 1;
%
% % parameter derivatives
% if ~ismimo; j = J(:)*er';
% else; j = aopt.J;
% end
%
% % weights and residuals
% w = pt;
% r0 = spm_vec(y) - spm_vec(params.aopt.fun(spm_unvec(x1,aopt.x0x0)));
%
% if ~isempty(FS)
% r0 = FS(r0);
% end
%
% db = ( pinv(j'*diag(w)*j)*j'*diag(w) )'*r0;
%
% % b(s+1) = b(s) - (J'*J)^-1*J'*r(s)
% try b = b - db;
% catch; b = db;
% end
%
% % inclusion of a weight essentially makes this a Marquardt regularisation parameter
% if isvector(a)
% dxd = x1 - a.*b;
% else
% dxd = x1 - a*b; % recompose dx including step matrix (a)
% end
%
% % update x
% if obj(dxd,params) < obj(x1,params) && (nmfun < 3)
% x1 = dxd;
% x0 = x1;
% e1 = obj(x1,params);
% e0 = e1;
% else
% iter_mle = false;
% dx = dxd;
% end
% end
% end
%
% if DoMAP
% % Do MAP estimation of parameter values with lambda as a
% % hyperparameter
%
% if verbose; pupdate(loc,n,n,e1,e1,'MAP est',toc); end
%
% % retrieve derivatives
% if ~ismimo; j = J(:)*er';
% else; j = aopt.J;
% end
%
% % remove extra stuff in Jacobian added by feature selection
% j = j(:,1:size(y,1));
%
% lambda = 1/8;
% D = size(j,1);
%
% % try to force a wanring suppression within anonym func call
% warning('off','MATLAB:singularMatrix')
% wn = @() warning('off','MATLAB:nearlysingularMatrix');
% wwn = @() suppress(wn);
% warning('off','MATLAB:curvefit:fit:noStartPoint');
%
% map = @(lambda) [feval(wwn) (lambda*eye(D)+j*j')\(j*y)];
% gmap = @(lambda) obj(x1 - red.*map(lambda),params);
%
% % optimise - find lambda
% ddx = fminsearch(gmap,1/8);
%
% % recover dx
% dx = x1 - red.*map(ddx);
%
% end
%
% if DoMAP_Bayes
% % Fully Bayesian MAP estimation of parameter values with
% % lambda as an optimisable hyperparameter
% % -- also provides an updated expectation for the variance
%
% if verbose; pupdate(loc,n,nfun,e1,e1,'bMAPest',toc); end
%
% % retrieve derivatives
% if ~ismimo; j = J(:)*er';
% else; j = aopt.J;
% end
%
% % remove extra stuff in Jacobian added by feature selection
% j = j(:,1:size(y,1));
%
% % largest eigenvalue normalisation
% [ev,ei] = eig(j*j');
% j = j ./ max(diag(ei));
%
% lambda = 1/8;
%
% D = size(j,1);
%
% % inject warning silence to anon function 'map'
% warning('off','MATLAB:singularMatrix')
% wn = @() warning('off','MATLAB:nearlysingularMatrix');
% wwn = @() suppress(wn);
% warning('off','MATLAB:curvefit:fit:noStartPoint');
%
% % compute residual and weight
% r0 = spm_vec(y) - spm_vec(params.aopt.fun(spm_unvec(x1,aopt.x0x0)));
% if length(aopt.iS) == length(r0)
% r0 = r0.*aopt.iS.*r0';
% r0 = r0(1:size(j,2),1:size(j,2));
% else
% r0 = r0.*aopt.iS(1:length(r0),1:length(r0)).*r0';
% end
% r0 = diag(r0);
%
% % MAP projection using Gauss-Newton / Regularised Levenberg-marquardt
% map = @(lambda) [feval(wwn) (lambda*eye(D)+j*j')\(j*r0)];
% gmap = @(lambda) obj(x1 - red.*map(lambda),params);
%