How to estimate coefficients for a system of ODE's?
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Danny Helwegen
le 24 Jan 2019
Commenté : Nisrina Pargustan
le 21 Nov 2020
Hi guys, I need some help with how to process the code in matlab. I have set up a system of ODE's, got the initial values and have values for A at specific times and now I need to estimate the values of k1, k2 and k3. I tried several things, but I still don't have a clue on how to process this into matlab, this is what i got:
ODE's
dAdt = -k1*A*B-k2*A*C-k3*A*D
dBdt = -k1*A*B
dCdt = k1*A*B-k2*A*C
dDdt = k1*A*B+k2*A*C-k3*A*D
dEdt = k3*A*D
dFdt = k2*A*C+k3*A*D
Inital values
A = 20.09; B = 6.96; C = 0; D = 0; E = 0; F = 0
Specific values for A at different times:
numdata = xlsread('dataset.xlsx')
t = numdata(:,1);
A = numdata(:,2);
eg. numdata =
4.5000 15.4000
8.6700 14.2200
12.6700 13.3500
Is there someone that can help me?
1 commentaire
Nisrina Pargustan
le 21 Nov 2020
hai danny, i got the exact same problem as you. so i tried to run your code but i got the error message. can you please send me your matlab code for this problem?
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Star Strider
le 24 Jan 2019
If you are doing parameter estimation of a system of ordinary differential equations, these will likely provide some guidance:
This is usually a fairly straightforward problem.
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Star Strider
le 25 Jan 2019
Here it is (a version of previous code, this time using ga), attached.
Since all the parameters are positive (by definition of the model), I constrained them to be greater than or equal to zero. Change that if your parameters are allowed to be negative.
Note that you will have to re-state your objective function in terms of the fitness function (in this code, ‘ftns’):
ftns = @(B) norm(A_data - Kinetics(B, time));
You mentioned that your parameters are on the order of 100, so change the options structure to:
opts = optimoptions('ga', 'PopulationSize',PopSz, 'InitialPopulationMatrix',randi(1E+2,PopSz,Parms), 'MaxGenerations',2E3, 'PlotFcn','gaplotbestf');
That should make it converge faster, however it will likely still take a few minutes. Also, ‘theta’ in my code is ‘B’ in yours.
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