sbiopredictionci return empty result

Question

Jesse Chao 2022-10-19

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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/1830703-sbiopredictionci-return-empty-result

评论： Jeremy Huard 2022-11-22

采纳的回答： Jeremy Huard

fitWeightFunction.mat

在 MATLAB Online 中打开

Hello team,

I was trying to comput the prediction confident interval for my parameter estimation results.

I first used sbioparameterci to check with my estimated parameters.

The estimattions are not perfect, but all of the status for my estimated parameters were either estimatable or constrained.

Thus, I further use sbiopredictionci to get the prediction confident interval.

By excuting the following code for defults setting, I was able to get prediction CI, but the results were not ideal.

ciPred = sbiopredictionci(fitWeightFunction);

Thus, I tried to use bootstrap method with following code to see if I could get better results.

ciPred = sbiopredictionci(fitWeightFunction, 'Alpha', 0.1, 'Type', 'bootstrap', 'NumSamples', 1000, 'UseParallel', true,'Display','final')

However, the ciPred I got is an empty output '0x0 PredictionConfidenceInterval'

Please find the OptimResults of my fitWeightFunction data in the attachment file.

Thank you very much.

Best,

Jesse

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Answer 1

Jeremy Huard 2022-10-19

2
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此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/1830703-sbiopredictionci-return-empty-result#answer_1078938

编辑：Jeremy Huard 2022-10-19

在 MATLAB Online 中打开

Hi Jesse,

it looks like your model uses an external function calculate_P_A2B_factor. You will need to pass this function to the parallel pool you are using.

So, if you already have an open parallel pool, you can enter the following command before calling sbiopredictionci:

addAttachedFiles(gcp,"calculate_P_A2B_factor.m")

If your parallel pool is not open yet, you can open it and attach the file with this command:

c = parcluster('local');
parpool('local',c.NumWorkers,AttachedFiles="calculate_P_A2B_factor.m");

Best regards,

Jérémy

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Jesse Chao 2022-10-19

在 MATLAB Online 中打开

Hello Jérémy,

I just tried to do the same thing with adding the line you provided

addAttachedFiles(gcp,"calculate_P_A2B_factor.m")

However, I got the following warning, and this code ran forever unstop even with only 3 smaples...

ciPred = sbiopredictionci(fitWeightFunction, 'Alpha', 0.1, 'Type', 'bootstrap', 'NumSamples', 3, 'UseParallel', true,'Display','final');
Warning: Observation data contains NaN. This may cause the computation of 'bootstrap' confidence intervals to error. 
> In SimBiology.fit/LeastSquaresResults/validateDataForBootstrapping (line 2685)
In SimBiology.fit/LeastSquaresResults/validatePredictionCIInput (line 2633)
In SimBiology.fit/LeastSquaresResults/predictionci (line 1052)
In sbiopredictionci (line 68) 
Computing 90% bootstrap prediction confidence intervals
-------------------------------------------------------
Warning: You have passed PARTICLESWARM options to LSQNONLIN. LSQNONLIN will use the common options and ignore the PARTICLESWARM options that do not apply.
To avoid this warning, convert the PARTICLESWARM options using OPTIMOPTIONS. 
> In optim.options/SolverOptions/convertForSolver (line 777)
In SimBiology.fit.internal.validateOptions>convertOptionsForMethod (line 167)
In SimBiology.fit.internal.validateOptions (line 15)
In SimBiology.fit.internal/FitObject/initializeReRun (line 376)
In SimBiology.fit.internal/FitObject/rerunFit (line 314)
In SimBiology.fit.LeastSquaresResults.createBootFun/getBootstrapSample (line 1806)
In SimBiology.fit.LeastSquaresResults>@(x)getBootstrapSample(x,numGroups,groupIdx,groupSize,resampleWeights,refIdx,obj.Data,obj.Weights,obj.ConfidenceIntervalData.EstimInfo,restartData,obj.Beta.Estimate,exitFlag,fcn) (line 1764)
In bootci (line 146)
In SimBiology.fit/LeastSquaresResults/predCIBootstrap (line 1576)
In SimBiology.fit.LeastSquaresResults>@(obj)predCIBootstrap(obj,alpha,numSamples,useParallel) (line 1060)
In SimBiology.fit/LeastSquaresResults/dispatchConfidenceIntervalComputation (line 1880)
In SimBiology.fit/LeastSquaresResults/predictionci (line 1068)
In sbiopredictionci (line 68) 
Warning: You have passed PARTICLESWARM options to LSQNONLIN. LSQNONLIN will use the common options and ignore the PARTICLESWARM options that do not apply.
To avoid this warning, convert the PARTICLESWARM options using OPTIMOPTIONS. 
> In optim.options/SolverOptions/convertForSolver (line 777)
In SimBiology.fit.internal.validateOptions>convertOptionsForMethod (line 167)
In SimBiology.fit.internal.validateOptions (line 15)
In SimBiology.fit.internal/FitObject/initializeReRun (line 376)
In SimBiology.fit.internal/FitObject/rerunFit (line 314)
In SimBiology.fit.LeastSquaresResults.createBootFun/getBootstrapSample (line 1806)
In SimBiology.fit.LeastSquaresResults>@(x)getBootstrapSample(x,numGroups,groupIdx,groupSize,resampleWeights,refIdx,obj.Data,obj.Weights,obj.ConfidenceIntervalData.EstimInfo,restartData,obj.Beta.Estimate,exitFlag,fcn) (line 1764)
In bootstrp (line 178)
In bootci>bootper (line 207)
In bootci (line 167)
In SimBiology.fit/LeastSquaresResults/predCIBootstrap (line 1576)
In SimBiology.fit.LeastSquaresResults>@(obj)predCIBootstrap(obj,alpha,numSamples,useParallel) (line 1060)
In SimBiology.fit/LeastSquaresResults/dispatchConfidenceIntervalComputation (line 1880)
In SimBiology.fit/LeastSquaresResults/predictionci (line 1068)
In sbiopredictionci (line 68) 

Is there anyway I could resolve it?

Please let me know. Thank you in advance.

Best,

Jesse

Jesse Chao 2022-11-21

fitComb.mat

Hello Jérémy,

Indeed, I did double chack on the optimoptions('particleswarm'). It is a bug in my script.

However, after I corrected this mistake with the correct lsqnonlin, the problem remained.

I have attached the corrected version of the fitWeightFunction considering the optimoption error with the name of fitComb in the attachment file in this post.

Hope you could provide me with some insights. Thank you very much.

Best,

Jesse

Jeremy Huard 2022-11-22

Hi Jesse,

could you please send the calculate_P_A2B_factor.m file as well as the script you use to call sbiopredictionci?

Thanks,

Jérémy

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