Talk:Chromosome structure via Euclidean Distance Matrices

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(E.coli realization)
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I regard the autocorrelation data you provided as a Gram matrix.
I regard the autocorrelation data you provided as a Gram matrix.
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Then conversion to an EDM is straightforward - Chapter 5.4.2 of [http://meboo.convexoptimization.com/BOOK/EuclideanDistanceMatrix.pdf Convex Optimization & Distance Geometry].
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Then conversion to a Euclidean distance matrix (EDM) is straightforward - <br>Chapter 5.4.2 of [http://meboo.convexoptimization.com/BOOK/EuclideanDistanceMatrix.pdf Convex Optimization & Euclidean Distance Geometry].
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The program calculates only the first 20 eigenvalues of the projection of the EDM on a positive semidefinite (PSD) cone.
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The program calculates only the first 20 eigenvalues of a projection of the EDM on a positive semidefinite (PSD) cone.
You can see at runtime that there are many significant eigenvalues; which means, the Euclidean body (the molecule) lives in a space higher than dimension 3, assuming I have interpreted the E.coli data correctly.
You can see at runtime that there are many significant eigenvalues; which means, the Euclidean body (the molecule) 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, we project the EDM on that PSD cone, rank 3 subset; this means, precisely, we truncate eigenvalues.
To get a picture corresponding to physical reality, we project the EDM on that PSD cone, rank 3 subset; this means, precisely, we truncate eigenvalues.
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It is unlikely that this picture is an accurate representation unless the number of eigenvalues of the EDM projection approaches 3 to begin with.
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It is unlikely that this picture is an accurate representation unless the number of eigenvalues of that EDM projection approaches 3 to begin with.
Matlab Figures allow 3D rotation in real time, so you can get a good idea of the body's shape.
Matlab Figures allow 3D rotation in real time, so you can get a good idea of the body's shape.
I include a low-resolution figure here (frame 4) for reference.
I include a low-resolution figure here (frame 4) for reference.

Revision as of 20:35, 7 August 2008

%%% Ronan Fleming, E.coli molecule data 
%%% -Jon Dattorro, August 2008
clear all
load ecoli

frame = 4;                                          % 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, 'LA');
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

Test image E.coli
Test image E.coli

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

Then conversion to a Euclidean distance matrix (EDM) is straightforward -
Chapter 5.4.2 of Convex Optimization & Euclidean Distance Geometry.

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

You can see at runtime that there are many significant eigenvalues; which means, the Euclidean body (the molecule) 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, we project the EDM on that PSD cone, rank 3 subset; this means, precisely, we truncate eigenvalues.

It is unlikely that this picture is an accurate representation unless the number of eigenvalues of that EDM projection approaches 3 to begin with.

Matlab Figures allow 3D rotation in real time, so you can get a good idea of the body's shape.

I include a low-resolution figure here (frame 4) for reference.

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