結果:
Automating Parameter Identifiability Analysis in SimBiology
Is it possible to develop a MATLAB Live Script that automates a series of SimBiology model fits to obtain likelihood profiles? The goal is to fit a kinetic model to experimental data while systematically fixing the value of one kinetic constant (e.g., k1) and leaving the others unrestricted.
The script would perform the following:
Use a pre-configured SimBiology project where the best fit to the experimental data has already been established (including dependent/independent variables, covariates, the error model, and optimization settings).
Iterate over a defined sequence of fixed values for a chosen parameter.
For each fixed value, run the estimation to optimize the remaining parameters.
Record the resulting Sum of Squared Errors (SSE) for each run.
The final output would be a likelihood profile—a plot of SSE versus the fixed parameter value (e.g., k1)—to assess the practical identifiability of each model parameter.
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For some time now, this has been bugging me - so I thought to gather some more feedback/information/opinions on this.
What would you classify Recursion? As a loop or as a vectorized section of code?
For context, this query occured to me while creating Cody problems involving strict (so to speak) vectorization - (Everyone is more than welcome to check my recent Cody questions).
To make problems interesting and/or difficult, I (and other posters) ban functions and functionalities - such as for loops, while loops, if-else statements, arrayfun() and the rest of the fun() family functions. However, some of the solutions including the reference solution I came up with for my latest problem, contained recursion.
I am rather divided on how to categorize it. What do you think?
Hey cody fellows :-) !
I recently created two problem groups, but as you can see I struggle to set their cover images :
What is weird given :
- I already did it successfully twice in the past for my previous groups ;
- If you take one problem specifically, Problem 60984. Mesh the icosahedron for instance, you can normally see the icon of the cover image in the top right hand corner, can't you ?
- I always manage to set cover images to my contributions (mostly in the filexchange).
I already tried several image formats, included .png 4/3 ratio, but still the cover images don't set.
Could you please help me to correctly set my cover images ?
Thank you.
Nicolas
I want to observe the time (Tmax) to reach maximum drug concentration (Cmax) in my model. I have set up the OBSERVABLES as follows (figure1): Cmax = max(Blood.lL15); Tmax_LT = time(Conc_lL15_LT_nm == max(Conc_lL15_LT_nm)); Tmax_Tm = time(Conc_lL15_Tumor_nm == max(Conc_lL15_Tumor_nm)); After running the Sobol indices program for global sensitivity analysis, with inputs being some parameters and their ranges, the output for Cmax works, but there are some prompts, as shown in figure2. Additionally, when outputting Tmax, the program does not run successfully and reports some errors, as shown in figure2. How can I resolve the errors when outputting Tmax?
I like this problem by James and have solved it in several ways. A solution by Natalie impressed me and introduced me to a new function conv2. However, it occured to me that the numerous test for the problem only cover cases of square matrices. My original solutions, and Natalie's, did niot work on rectangular matrices. I have now produced a solution which works on rectangular matrices. Thanks for this thought provoking problem James.
I have written, tested, and prepared a function with four subsunctions on my computer for solving one of the problems in the list of Cody problems in MathWorks in three days. Today, when I wanted to upload or copy paste the codes of the function and its subfunctions to the specified place of the problem of Cody page, I do not see a place to upload it, and the ability to copy past the codes. The total of the entire codes and their documentations is about 600 lines, which means that I cannot and it is not worth it to retype all of them in the relevent Cody environment after spending a few days. I would appreciate your guidance on how to enter the prepared codes to the desired environment in Cody.
I've been trying this problem a lot of time and i don't understand why my solution doesnt't work.
In 4 tests i get the error Assertion failed but when i run the code myself i get the diag and antidiag correctly.
function [diag_elements, antidg_elements] = your_fcn_name(x)
[m, n] = size(x);
% Inicializar los vectores de la diagonal y la anti-diagonal
diag_elements = zeros(1, min(m, n));
antidg_elements = zeros(1, min(m, n));
% Extraer los elementos de la diagonal
for i = 1:min(m, n)
diag_elements(i) = x(i, i);
end
% Extraer los elementos de la anti-diagonal
for i = 1:min(m, n)
antidg_elements(i) = x(m-i+1, i);
end
end
My following code works running Matlab 2024b for all test cases. However, 3 of 7 tests fail (#1, #4, & #5) the QWERTY Shift Encoder problem. Any ideas what I am missing?
Thanks in advance.
keyboardMap1 = {'qwertyuiop[;'; 'asdfghjkl;'; 'zxcvbnm,'};
keyboardMap2 = {'QWERTYUIOP{'; 'ASDFGHJKL:'; 'ZXCVBNM<'};
if length(s) == 0
se = s;
end
for i = 1:length(s)
if double(s(i)) >= 65 && s(i) <= 90
row = 1;
col = 1;
while ~strcmp(s(i), keyboardMap2{row}(col))
if col < length(keyboardMap2{row})
col = col + 1;
else
row = row + 1;
col = 1;
end
end
se(i) = keyboardMap2{row}(col + 1);
elseif double(s(i)) >= 97 && s(i) <= 122
row = 1;
col = 1;
while ~strcmp(s(i), keyboardMap1{row}(col))
if col < length(keyboardMap1{row})
col = col + 1;
else
row = row + 1;
col = 1;
end
end
se(i) = keyboardMap1{row}(col + 1);
else
se(i) = s(i);
end
% if ~(s(i) = 65 && s(i) <= 90) && ~(s(i) >= 97 && s(i) <= 122)
% se(i) = s(i);
% end
end
I was browsing the MathWorks website and decided to check the Cody leaderboard. To my surprise, William has now solved 5,000 problems. At the moment, there are 5,227 problems on Cody, so William has solved over 95%. The next competitor is over 500 problems behind. His score is also clearly the highest, approaching 60,000.
I've been working on some matrix problems recently(Problem 55225)
and this is my code
It turns out that "Undefined function 'corr' for input arguments of type 'double'." However, should't the input argument of "corr" be column vectors with single/double values? What's even going on there?
Hi All,
I'm currently verifying a global sensitivity analysis done in SimBiology and I'm a touch confused. This analysis was run with every parameter and compartment volume in the model. To my understanding the fraction of unexplained variance is 1 - the sum of the first order variances, therefore if the model dynamics are dominated by interparameter effects you might see a higher fraction of unexplained variance. In this analysis however, as the attached figure shows (with input at t=20 minutes), the most sensitive four parameters seem to sum, in first order sensitivities to roughly one at each time point and the total order sensitivies appear nearly identical. So how is the fraction of unexplained variance near one?
Thank you for your help!
function ans = your_fcn_name(n)
n;
j=sum(1:n);
a=zeros(1,j);
for i=1:n
a(1,((sum(1:(i-1))+1)):(sum(1:(i-1))+i))=i.*ones(1,i);
end
disp
