# Talk:Chromosome structure via Euclidean Distance Matrices

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(New page: <pre> %%% Ronan Fleming, E.coli molecule data %%% -Jon Dattorro, August 2008 clear all load ecoli frame = 12; % 1 through 12 G = her49imfs12movful...) |
(New section: E.coli realization) |
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plot3(Xs(1,:), Xs(2,:), Xs(3,:), '.') | plot3(Xs(1,:), Xs(2,:), Xs(3,:), '.') | ||

</pre> | </pre> | ||

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+ | == E.coli realization == | ||

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+ | I regard the autocorrelation data you provided as a Gram matrix. | ||

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+ | Then the conversion to an EDM is straightforward - Chapter 5.4.2 of Convex Optimization & Distance Geometry. | ||

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+ | The program calculates the first 20 eigenvalues of the projection of the EDM on the positive semidefinite (PSD) cone. | ||

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+ | You can see that there are many significant eigenvalues; which means, the Euclidean body lives in a space higher than dimension 3, assuming I have interpreted the E.coli data correctly. | ||

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+ | To get a picture corresponding to physical reality, you have to project on the PSD cone, rank 3 subset. |

## Revision as of 22:56, 6 August 2008

%%% Ronan Fleming, E.coli molecule data %%% -Jon Dattorro, August 2008 clear all load ecoli frame = 12; % 1 through 12 G = her49imfs12movfull(frame).cdata; % uint8 G = (double(G)-128)/128; % Gram matrix N = size(G,1); D = diag(G)*ones(N,1)' + ones(N,1)*diag(G)' - 2*G; % EDM D clear her49imfs12movfull G; Vn = [-ones(1,N-1); speye(N-1)]; VDV = (-Vn'*D*Vn)/2; clear D Vn [evec evals flag] = eigs(VDV, [], 20, 'LR'); if flag, disp('convergence problem'), return, end; close all Xs = sqrt(real(evals(1:3,1:3)))*real(evec(:,1:3))'; % Projection of -VDV on PSD cone rank 3 plot3(Xs(1,:), Xs(2,:), Xs(3,:), '.')

## E.coli realization

I regard the autocorrelation data you provided as a Gram matrix.

Then the conversion to an EDM is straightforward - Chapter 5.4.2 of Convex Optimization & Distance Geometry.

The program calculates the first 20 eigenvalues of the projection of the EDM on the positive semidefinite (PSD) cone.

You can see that there are many significant eigenvalues; which means, the Euclidean body lives in a space higher than dimension 3, assuming I have interpreted the E.coli data correctly.

To get a picture corresponding to physical reality, you have to project on the PSD cone, rank 3 subset.