Added source Matlab code for reference
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Waldir Leoncio
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186 changed files with 61405 additions and 1 deletions
235
matlab/linkage/transform4.m
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235
matlab/linkage/transform4.m
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function [data_clique, data_separator, noalle_clique, noalle_separator] = transform4(data, component_mat, linkage_model)
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% Filename: transform4.m
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% [data_clique,data_clique,noalle_clique, noalle_separator] = tranform4(data, component_mat, linkage_model)
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% DATA SHRINKAGE STEP IN THE END TO SAVE MEMORY USE
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% Further shrink the data using uint8 format.
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% Make sure that allele numbers smaller than 256.
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if strcmp(linkage_model,'linear')
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nindividuals = size(data,1);
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nloci = size(data,2)-1;
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% if ~all(diag(adj_mat)), adj_mat = adj_mat + diag(ones(nloci,1));, end;
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% [p,p,r]=dmperm(adj_mat);
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% UNSOLVED --- Need to find a better algorithm to count the numbers of
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% separators ,cliques and singletons.
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ncomponents = size(component_mat,1);
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cardinality = sum(component_mat>0,2)';
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ncliques = sum(cardinality-1);
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nsingletons = sum(cardinality==1);
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nseparators = sum(cardinality(find(cardinality>1))-2);
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data_clique = zeros(nindividuals, ncliques+nsingletons,'uint16');
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noalle_clique = zeros(ncliques+nsingletons,1,'uint16');
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data_separator = zeros(nindividuals, nseparators,'uint16');
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noalle_separator = zeros(nseparators,1,'uint16');
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% data_separator = []; % used for vectorization
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k = 1;
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for i = 1:ncomponents
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if (cardinality(i)==1) % singleton
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data_clique(:,k) = data(:,component_mat(i,1));
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temp = unique(data(:,component_mat(i,1)));
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if temp(1) == 0 % missing data found
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noalle_clique(k) = size(temp,1) -1;
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else
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noalle_clique(k) = size(temp,1);
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end
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k = k+1;
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else
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for j = 1:cardinality(i)-1
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% dealing with missing data
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% nonmissing = find(all(data(:,[component_mat(i,j) component_mat(i,j+1)]),2));
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% [b,m,n] = unique(data(nonmissing,[component_mat(i,j) component_mat(i,j+1)]),'rows');
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% data_clique(nonmissing,k) = n;
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% noalle_clique(k) = size(unique(data(nonmissing,component_mat(i,j))),1)*...
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% size(unique(data(nonmissing,component_mat(i,j+1))),1);
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[b,m,n] = unique(data(:,[component_mat(i,j) component_mat(i,j+1)]),'rows');
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data_clique(:,k) = n;
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noalle_clique(k) = size(unique(data(:,component_mat(i,j))),1)*...
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size(unique(data(:,component_mat(i,j+1))),1);
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k = k+1;
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end
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end
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end
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k = 1;
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for i = 1:ncomponents
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if (cardinality(i)>2)
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for j = 2:cardinality(i)-1
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data_separator(:,k) = data(:,component_mat(i,j));
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k = k+1;
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end
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end
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end
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if (k-1)~=nseparators
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error('ERROR in transform.m');
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return
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end
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for i = 1:nseparators
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% nonmissing = find(all(data_separator(:,i),2));
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% noalle_separator(i) = length(unique(data_separator(nonmissing,i)));
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noalle_separator(i) = length(unique(data_separator(:,i)));
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end
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elseif strcmp(linkage_model,'codon')
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nindividuals = size(data,1);
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nloci = size(data,2)-1;
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ncomponents = size(component_mat,1);
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cardinality = sum(component_mat>0,2)';
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ncliques = sum(cardinality(find(cardinality>2))-2);
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nsingletons = sum(cardinality==1 | cardinality ==2);
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nseparators = sum(cardinality(find(cardinality>2))-3);
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data_clique = zeros(nindividuals,ncliques+nsingletons,'uint16');
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noalle_clique = zeros(ncliques+nsingletons,1,'uint16');
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data_separator = zeros(nindividuals,nseparators,'uint16');
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noalle_separator = zeros(nseparators,1,'uint16');
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k = 1;
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for i = 1:ncomponents
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if (cardinality(i)==1) % singleton
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data_clique(:,k) = data(:,component_mat(i,1));
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temp = unique(data(:,component_mat(i,1)));
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if temp(1) == 0 % missing data found
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noalle_clique(k) = size(temp,1) -1;
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else
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noalle_clique(k) = size(temp,1);
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end
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k = k+1;
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elseif (cardinality(i)==2) % transform to linear linkage
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% dealing with missing data
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% nonmissing = find(all(data(:,[component_mat(i,1) component_mat(i,2)]),2));
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% [b,m,n] = unique(data(nonmissing,[component_mat(i,1) component_mat(i,2)]),'rows');
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[b,m,n] = unique(data(:,[component_mat(i,1) component_mat(i,2)]),'rows');
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data_clique(:,k) = uint16(n);
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% data_clique(nonmissing,k) = n;
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% noalle_clique(k) = size(unique(data(nonmissing,component_mat(i,1))),1)*...
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% size(unique(data(nonmissing,component_mat(i,2))),1);
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noalle_clique(k) = size(unique(data(:,component_mat(i,1))),1)*...
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size(unique(data(:,component_mat(i,2))),1);
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k = k+1;
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else
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for j = 1:cardinality(i)-2
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% dealing with missing data
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% nonmissing = find(all(data(:,[component_mat(i,j) component_mat(i,j+1) component_mat(i,j+2)]),2));
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% [b,m,n] = unique(data(nonmissing,[component_mat(i,j) component_mat(i,j+1) component_mat(i,j+2)]),'rows');
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% data_clique(nonmissing,k) = n;
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[b,m,n] = unique(data(:,[component_mat(i,j) component_mat(i,j+1) component_mat(i,j+2)]),'rows');
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data_clique(:,k) = uint16(n);
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% noalle_clique(k) = size(unique(data(nonmissing,component_mat(i,j))),1)*...
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% size(unique(data(nonmissing,component_mat(i,j+1))),1)*size(unique(data(nonmissing,component_mat(i,j+2))),1);
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noalle_clique(k) = size(unique(data(:,component_mat(i,j))),1)*...
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size(unique(data(:,component_mat(i,j+1))),1)*size(unique(data(:,component_mat(i,j+2))),1);
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k = k+1;
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end
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end
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end
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k = 1;
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for i = 1:ncomponents
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if (cardinality(i)>2)
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for j = 2:cardinality(i)-2
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% dealing with missing data
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% nonmissing = find(all(data(:,[component_mat(i,j) component_mat(i,j+1)]),2));
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% [b,m,n] = unique(data(nonmissing,[component_mat(i,j) component_mat(i,j+1)]),'rows');
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[b,m,n] = unique(data(:,[component_mat(i,j) component_mat(i,j+1)]),'rows');
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% data_separator(nonmissing,k) = n;
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data_separator(:,k) = uint16(n);
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% noalle_separator(k) = size(unique(data(nonmissing,component_mat(i,j))),1)*...
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% size(unique(data(nonmissing,component_mat(i,j+1))),1);
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noalle_separator(k) = size(unique(data(:,component_mat(i,j))),1)*...
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size(unique(data(:,component_mat(i,j+1))),1);
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k = k+1;
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end
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end
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end
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elseif strcmpi(linkage_model,'Independent')
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data_clique = data(:,[1:end-1]);
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data_separator = [];
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noalle_clique = max(data_clique); % Be sure the data is normalized.
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noalle_separator = [];
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elseif strcmp(linkage_model,'random')
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adj_mat = mk_adjmat(component_mat);
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nloci = size(adj_mat,1);
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ns = 4*ones(1,nloci);
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porder = [];
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stages = {[1:nloci]};
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clusters = {};
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[jtree,root2,cliques,B,w]=graph_to_jtree(adj_mat,ns,porder,stages,clusters);
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C = length(cliques);
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[is,js] = find(jtree > 0);
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separator = cell(C,C);
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for k=1:length(is)
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i = is(k); j = js(k);
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separator{i,j} = find(B(i,:) & B(j,:)); % intersect(cliques{i}, cliques{j});
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end
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nindividuals = size(data,1);
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if nloci ~= size(data,2)-1 error('*** ERROR: in transform3.m');
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return
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end
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ncliques = length(cliques);
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[i,j] = find(~cellfun('isempty',triu(separator)));
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ij = [i j];
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nseparators = length(i);
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data_clique = zeros(nindividuals, ncliques);
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noalle_clique = zeros(ncliques,1);
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data_separator = zeros(nindividuals, nseparators);
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noalle_separator = zeros(nseparators,1);
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k = 1;
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for i = 1:ncliques
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[b,m,n] = unique(data(:,cliques{i}),'rows');
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data_clique(:,k) = n;
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% for j = 1:length(cliques{i})
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% sz(j) = size(unique(data(:,cliques{i}(j))),1);
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% end
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% noalle_clique(k) = prod(sz);
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noalle_clique(k) = 4^length(cliques{i});
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k = k+1;
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% clear sz;
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end
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k = 1;
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for i = 1:nseparators
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[b,m,n] = unique(data(:,separator{ij(i,1),ij(i,2)}),'rows');
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data_separator(:,k) = n;
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% for j = 1:length(separator{ij(i,1),ij(i,2)})
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% sz(j) = size(unique(data(:,separator{ij(i,1),ij(i,2)}(j))),1);
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% end
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% noalle_separator(k) = prod(sz);
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noalle_separator(k) = 4^length(separator{ij(i,1),ij(i,2)});
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k = k+1;
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% clear sz;
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end
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end
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% Data shrinkage step
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informative_clique = find(noalle_clique~=1);
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informative_separator = find(noalle_separator~=1);
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data_clique = data_clique(:,informative_clique);
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data_separator = data_separator(:,informative_separator);
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noalle_clique = noalle_clique(informative_clique);
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noalle_separator = noalle_separator(informative_separator);
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clear data;
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