diff options
Diffstat (limited to 'sourcecodes/bnt-master/BNT/potentials/@cpot')
22 files changed, 220 insertions, 0 deletions
diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/CVS/Entries b/sourcecodes/bnt-master/BNT/potentials/@cpot/CVS/Entries new file mode 100644 index 00000000..7f4397ef --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/CVS/Entries @@ -0,0 +1,14 @@ +/cpot.m/1.1.1.1/Wed May 29 15:59:58 2002// +/cpot_to_mpot.m/1.1.1.1/Wed May 29 15:59:58 2002// +/display.m/1.1.1.1/Wed May 29 15:59:58 2002// +/divide_by_pot.m/1.1.1.1/Wed May 29 15:59:58 2002// +/domain_pot.m/1.1.1.1/Wed May 29 15:59:58 2002// +/enter_cts_evidence_pot.m/1.1.1.1/Wed May 29 15:59:58 2002// +/marginalize_pot.m/1.1.1.1/Wed May 29 15:59:58 2002// +/multiply_by_pot.m/1.1.1.1/Wed May 29 15:59:58 2002// +/multiply_pots.m/1.1.1.1/Wed May 29 15:59:58 2002// +/normalize_pot.m/1.1.1.1/Wed May 29 15:59:58 2002// +/pot_to_marginal.m/1.1.1.1/Wed May 29 15:59:58 2002// +/rescale_pot.m/1.1.1.1/Wed May 29 15:59:58 2002// +/set_domain_pot.m/1.1.1.1/Wed May 29 15:59:58 2002// +D diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/CVS/Entries.Log b/sourcecodes/bnt-master/BNT/potentials/@cpot/CVS/Entries.Log new file mode 100644 index 00000000..24f16336 --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/CVS/Entries.Log @@ -0,0 +1 @@ +A D/Old//// diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/CVS/Repository b/sourcecodes/bnt-master/BNT/potentials/@cpot/CVS/Repository new file mode 100644 index 00000000..12ecad25 --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/CVS/Repository @@ -0,0 +1 @@ +FullBNT/BNT/potentials/@cpot diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/CVS/Root b/sourcecodes/bnt-master/BNT/potentials/@cpot/CVS/Root new file mode 100644 index 00000000..f3bd14a6 --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/CVS/Root @@ -0,0 +1 @@ +:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/Old/CVS/Entries b/sourcecodes/bnt-master/BNT/potentials/@cpot/Old/CVS/Entries new file mode 100644 index 00000000..3345f808 --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/Old/CVS/Entries @@ -0,0 +1,3 @@ +/cpot_to_mpot.m/1.1.1.1/Wed May 29 15:59:58 2002// +/normalize_pot.convert.m/1.1.1.1/Wed May 29 15:59:58 2002// +D diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/Old/CVS/Repository b/sourcecodes/bnt-master/BNT/potentials/@cpot/Old/CVS/Repository new file mode 100644 index 00000000..bdb2b68d --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/Old/CVS/Repository @@ -0,0 +1 @@ +FullBNT/BNT/potentials/@cpot/Old diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/Old/CVS/Root b/sourcecodes/bnt-master/BNT/potentials/@cpot/Old/CVS/Root new file mode 100644 index 00000000..f3bd14a6 --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/Old/CVS/Root @@ -0,0 +1 @@ +:ext:nsaunier@bnt.cvs.sourceforge.net:/cvsroot/bnt diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/Old/cpot_to_mpot.m b/sourcecodes/bnt-master/BNT/potentials/@cpot/Old/cpot_to_mpot.m new file mode 100644 index 00000000..05899b99 --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/Old/cpot_to_mpot.m @@ -0,0 +1,25 @@ +function mom = cpot_to_mpot(can) +% CPOT_TO_MPOT Convert a canonical potential to moment form. +% mom = cpot_to_mpot(can) + +[logp, mu, Sigma] = canonical_to_moment(can.g, can.h, can.K); +mom = mpot(can.domain, can.sizes, logp, mu, Sigma); + +%%%%%%% + +function [logp, mu, Sigma] = canonical_to_moment(g, h, K) +% CANONICAL_TO_MOMENT Convert canonical characteristics to moment form. +% [logp, mu, Sigma] = canonical_to_moment(g, h, K) + +if det(K)==0 + Sigma = inf*size(K); +else + Sigma = inv(K); +end +mu = Sigma*h; +n = length(mu); +if isempty(mu) + logp = g - 0.5*(log(det(K)) - n*log(2*pi)); +else + logp = g - 0.5*(log(det(K)) - n*log(2*pi) - mu'*K*mu); +end diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/Old/normalize_pot.convert.m b/sourcecodes/bnt-master/BNT/potentials/@cpot/Old/normalize_pot.convert.m new file mode 100644 index 00000000..59c473cc --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/Old/normalize_pot.convert.m @@ -0,0 +1,9 @@ +function [mom2, loglik] = normalize_pot(can) +% NORMALIZE_POT Convert the canonical potential Pr(X,E) into moment potential Pr(X|E) and return log Pr(E). +% [mom, loglik] = normalize_pot(can) + +mom = cpot_to_mpot(can); +mom = struct(mom); % violate privacy of object +loglik = mom.logp; +%mom.logp = 0; % now represents Pr(X | E) instead of Pr(X, E). +mom2 = mpot(mom.domain, mom.sizes, 0, mom.mu, mom.Sigma); diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/cpot.m b/sourcecodes/bnt-master/BNT/potentials/@cpot/cpot.m new file mode 100644 index 00000000..b8dfbf03 --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/cpot.m @@ -0,0 +1,17 @@ +function pot = cpot(members, sizes, g, h, K) +% CPOT Make a canonical Gaussian potential. +% pot = cpot(members, sizes, g, h, K) +% +% All params default to 0 if omitted. + +n = sum(sizes); +if nargin < 3, g = 0; end +if nargin < 4, h = zeros(n,1); end +if nargin < 5, K = zeros(n,n); end + +pot.domain = members; +pot.sizes = sizes(:)'; +pot.g = g; +pot.h = h; +pot.K = K; +pot = class(pot, 'cpot'); diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/cpot_to_mpot.m b/sourcecodes/bnt-master/BNT/potentials/@cpot/cpot_to_mpot.m new file mode 100644 index 00000000..73739d7e --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/cpot_to_mpot.m @@ -0,0 +1,29 @@ +function mom = cpot_to_mpot(can) +% CPOT_TO_MPOT Convert a canonical potential to moment form. +% mom = cpot_to_mpot(can) + +[logp, mu, Sigma] = canonical_to_moment(can.g, can.h, can.K); +mom = mpot(can.domain, can.sizes, logp, mu, Sigma); + +%%%%%%% + +function [logp, mu, Sigma] = canonical_to_moment(g, h, K) +% CANONICAL_TO_MOMENT Convert canonical characteristics to moment form. +% [logp, mu, Sigma] = canonical_to_moment(g, h, K) + +n = length(K); +if isempty(K) + logp = g - 0.5*(log(det(K)) - n*log(2*pi)); + Sigma = []; + mu = []; +else + if det(K)==0 + Sigma = inf*ones(n,n); + mu = zeros(n,1); % if the precision is zero, the mean is arbitrary + logp = g; % the scaling factor for the uniform distribution is 1 + else + Sigma = inv(K); + mu = Sigma*h; + logp = g - 0.5*(log(det(K)) - n*log(2*pi) - mu'*K*mu); + end +end diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/display.m b/sourcecodes/bnt-master/BNT/potentials/@cpot/display.m new file mode 100644 index 00000000..35a4f0b3 --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/display.m @@ -0,0 +1,4 @@ +function display(pot) + +disp('canonical potential object'); +disp(struct(pot)); diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/divide_by_pot.m b/sourcecodes/bnt-master/BNT/potentials/@cpot/divide_by_pot.m new file mode 100644 index 00000000..1e2bb2b9 --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/divide_by_pot.m @@ -0,0 +1,13 @@ +function bigpot = divide_by_pot(bigpot, smallpot) +% DIVIDE_BY_POT bigpot /= smallpot for cpot +% bigpot = divide_by_pot(bigpot, smallpot) +% +% smallpot's domain must be a subset of bigpot's domain. + +bigpot.g = bigpot.g - smallpot.g; +if sum(smallpot.sizes) > 0 + mask = find_equiv_posns(smallpot.domain, bigpot.domain); + u = block(mask, bigpot.sizes); + bigpot.h(u) = bigpot.h(u) - smallpot.h; + bigpot.K(u, u) = bigpot.K(u, u) - smallpot.K; +end diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/domain_pot.m b/sourcecodes/bnt-master/BNT/potentials/@cpot/domain_pot.m new file mode 100644 index 00000000..aa5ce392 --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/domain_pot.m @@ -0,0 +1,5 @@ +function dom = domain_pot(pot) +% DOMAIN_POT Return the domain of this cpot. +% dom = domain_pot(pot) + +dom = pot.domain; diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/enter_cts_evidence_pot.m b/sourcecodes/bnt-master/BNT/potentials/@cpot/enter_cts_evidence_pot.m new file mode 100644 index 00000000..246729ae --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/enter_cts_evidence_pot.m @@ -0,0 +1,15 @@ +function pot = enter_cts_evidence_pot(pot, Y, y) +% function pot = enter_cts_evidence_pot(pot, Y, y) (cpot) + +ns = sparse(1, max(pot.domain)); +ns(pot.domain) = pot.sizes; + +X = mysetdiff(pot.domain, Y); +[hx, hy, KXX, KXY, KYX, KYY] = partition_matrix_vec(pot.h, pot.K, X, Y, ns); +pot.g = pot.g + hy'*y - 0.5*y'*KYY*y; +if ~isempty(X) + pot.h = hx - KXY*y; + pot.K = KXX; +end + +pot.sizes(find_equiv_posns(Y,pot.domain)) = 0; diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/marginalize_pot.m b/sourcecodes/bnt-master/BNT/potentials/@cpot/marginalize_pot.m new file mode 100644 index 00000000..ae9ee839 --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/marginalize_pot.m @@ -0,0 +1,31 @@ +function smallpot = marginalize_pot(bigpot, keep, maximize, useC) +% MARGINALIZE_POT Marginalize a cpot onto a smaller domain. +% smallpot = marginalize_pot(bigpot, keep, maximize, useC) +% +% The maximize argument is ignored - maxing out a Gaussian is the same as summing it out, +% since the mode and mean are equal. +% The useC argument is ignored. + +node_sizes = sparse(1, max(bigpot.domain)); +node_sizes(bigpot.domain) = bigpot.sizes; +sum_over = mysetdiff(bigpot.domain, keep); + +if sum(node_sizes(sum_over))==0 % isempty(sum_over) + %smallpot = bigpot; + smallpot = cpot(keep, node_sizes(keep), bigpot.g, bigpot.h, bigpot.K); +else + [h1, h2, K11, K12, K21, K22] = partition_matrix_vec(bigpot.h, bigpot.K, sum_over, keep, node_sizes); + n = length(h1); + K11inv = inv(K11); + g = bigpot.g + 0.5*(n*log(2*pi) - log(det(K11)) + h1'*K11inv*h1); + if length(h2) > 0 % ~isempty(keep) % we are are actually keeping something + A = K21*K11inv; + h = h2 - A*h1; + K = K22 - A*K12; + else + h = []; + K = []; + end + smallpot = cpot(keep, node_sizes(keep), g, h, K); +end + diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/multiply_by_pot.m b/sourcecodes/bnt-master/BNT/potentials/@cpot/multiply_by_pot.m new file mode 100644 index 00000000..1ab24f55 --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/multiply_by_pot.m @@ -0,0 +1,13 @@ +function bigpot = multiply_by_pot(bigpot, smallpot, varargin) +% MULTIPLY_BY_POT bigpot *= smallpot for cpot +% bigpot = multiply_by_pot(bigpot, smallpot) +% +% smallpot's domain must be a subset of bigpot's domain. + +bigpot.g = bigpot.g + smallpot.g; +if sum(smallpot.sizes) > 0 + mask = find_equiv_posns(smallpot.domain, bigpot.domain); + u = block(mask, bigpot.sizes); + bigpot.h(u) = bigpot.h(u) + smallpot.h; + bigpot.K(u, u) = bigpot.K(u, u) + smallpot.K; +end diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/multiply_pots.m b/sourcecodes/bnt-master/BNT/potentials/@cpot/multiply_pots.m new file mode 100644 index 00000000..3506e36e --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/multiply_pots.m @@ -0,0 +1,11 @@ +function T = multiply_pots(T1, T2) +% MULTIPLY_POTS Multiply a pair of dpots together pointwise (cpot) +% T = multiply_pots(pots) + +dom = myunion(T1.domain, T2.domain); +ns = sparse(1, max(dom)); +ns(T1.domain) = T1.sizes; +ns(T2.domain) = T2.sizes; +T = cpot(dom, ns(dom)); +T = multiply_by_pot(T, T1); +T = multiply_by_pot(T, T2); diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/normalize_pot.m b/sourcecodes/bnt-master/BNT/potentials/@cpot/normalize_pot.m new file mode 100644 index 00000000..c6f89dc3 --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/normalize_pot.m @@ -0,0 +1,10 @@ +function [pot, loglik] = normalize_pot(pot) +% NORMALIZE_POT Convert the canonical potential Pr(X,E) into Pr(X|E) and return log Pr(E). +% [pot, loglik] = normalize_pot(pot) + +mom = cpot_to_mpot(pot); % move the normalizing constant out of g, to reveal the coefficient +%loglik = scaling_factor_pot(mom); +%loglik = mom.logp; +[temp, loglik] = normalize_pot(mom); +pot.g = pot.g - loglik; + diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/pot_to_marginal.m b/sourcecodes/bnt-master/BNT/potentials/@cpot/pot_to_marginal.m new file mode 100644 index 00000000..4c3fb79f --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/pot_to_marginal.m @@ -0,0 +1,6 @@ +function m = pot_to_marginal(pot) +% POT_TO_MARGINAL Convert a cpot to a marginal structure. +% m = pot_to_marginal(pot) + +mom = cpot_to_mpot(pot); +m = pot_to_marginal(mom); diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/rescale_pot.m b/sourcecodes/bnt-master/BNT/potentials/@cpot/rescale_pot.m new file mode 100644 index 00000000..ad962455 --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/rescale_pot.m @@ -0,0 +1,5 @@ +function pot = rescale_pot(pot, s) +% RESCALE_POT Add a constant to the cpot scale factor. +% pot = rescale_pot(pot, s) + +pot.g = pot.g + s; diff --git a/sourcecodes/bnt-master/BNT/potentials/@cpot/set_domain_pot.m b/sourcecodes/bnt-master/BNT/potentials/@cpot/set_domain_pot.m new file mode 100644 index 00000000..2178c51d --- /dev/null +++ b/sourcecodes/bnt-master/BNT/potentials/@cpot/set_domain_pot.m @@ -0,0 +1,5 @@ +function pot = set_domain_pot(pot, domain) +% SET_DOMAIN_POT Change the domain of a potential (dpot) +% pot = set_domain_pot(pot, domain) + +pot.domain = domain; |