crf2ChainTrainDemo.m

%% Demonstrate training a chain-structured CRF
% Based on
% http://www.cs.ubc.ca/~schmidtm/Software/UGM/trainCRF.html

% This file is from pmtk3.googlecode.com


%% Get  data
setSeed(0);
load rain.mat % X is 1059*28
y = X+1; % Convert from {0,1} to {1,2} representation
[nInstances,nNodes] = size(y);

% test using a subset of the training set
Ntest = 100;
yTest = y(1:Ntest, :);
figure; imagesc(yTest); title('yTest truth'); colormap(gray);

%% Create chain model
nNodes = size(y,2);
adj = chainAdjMatrix(nNodes);
nStates = 2*ones(1,nNodes);
model = crf2Create(adj, nStates, 'method', 'Chain');
nEdges = model.nEdges;

%% No features
Xnode = ones(nInstances,1,nNodes);
Xedge = ones(nInstances,1,nEdges);

model = crf2Train(model, Xnode, Xedge, y);
yhat = crf2Map(model, Xnode(1:Ntest,:,:), Xedge(1:Ntest,:,:));
figure; imagesc(yhat);
title('MAP with no features'); colormap(gray);

%% month is added as node features
nFeatures = 12;
Xnode = zeros(nInstances,nFeatures,nNodes);
for m = 1:nFeatures
    Xnode(months==m,m,:) = 1;
end
Xnode = [ones(nInstances,1,nNodes) Xnode];

model = crf2Train(model, Xnode, Xedge, y);
yhat = crf2Map(model, Xnode(1:Ntest,:,:), Xedge(1:Ntest,:,:));
figure; imagesc(yhat);
title('MAP with month node feature'); colormap(gray);

%% Month is added as edge feature
sharedFeatures = 1:13;
Xedge = UGM_makeEdgeFeatures(Xnode, model.edgeStruct.edgeEnds, sharedFeatures);

model = crf2Train(model, Xnode, Xedge, y, 'lambdaEdge', 0, 'lambdaNode', 0);
yhat = crf2Map(model, Xnode(1:Ntest,:,:), Xedge(1:Ntest,:,:));
figure; imagesc(yhat);
title('MAP with month node and edge feature'); colormap(gray);

nodeBel = crf2InferNodesAndEdges(model, Xnode(1:Ntest,:,:), Xedge(1:Ntest,:,:));
figure; imagesc(nodeBel(:,:,1));
title('mariginals with month node and edge feature'); colormap(gray);

% Sample from a case for specific months
mths = [12, 8]; % December, August
for jj=1:length(mths)
  mth = mths(jj);
  ndx = find(months==mth);
  ndx = ndx(1);
  samples = crf2Sample(model, squeeze(Xnode(ndx,:,:)), squeeze(Xedge(ndx,:,:)), 100);
  figure; imagesc(samples);colormap(gray);
  title(sprintf('samples given month=%d, with month node and edge feature', mth));
end