Example code for mixture_KDE about pysustain

[noxtoby]

I don't know how you modify your code to produce a control sample from the same data. Putting that aside...

A singular matrix error often implies that the mixture modelling is labelling everyone (cases and controls) to be in one component (pre-event/post-event, a.k.a., normal/abnormal).

This can happen when your cases and controls histograms overlap too much for any feature. Such a feature doesn't have useful "disease signal" and should probably be excluded from your feature set (and shouldn't be called a biomarker).

Another possibility is that you have input an incorrect "disease direction" while also "fixing" controls to not swap labels, i.e., to stay as pre-event/normal.

[noxtoby]

Sorry, but you do need controls to fit a KDE mixture model. This then generates the event likelihoods that are input to the clustering part of SuStaIn.

If you want to run SuStaIn in the absence of controls, you’ll need to create a bespoke model for these event likelihoods.

Good luck.

[aratzan]

Thanks so much for your helpful response, this makes sense. My team has modified our code to now have a control sample and patient sample. We have been able to run the code up until generating an instance of the SuStaIn model and have actually been able to create an instance with mixture_GMM. However, we are still receiving the below error for the mixture_KDE version, which is more suited to our data.

LinAlgError                               Traceback (most recent call last)
~\AppData\Local\Temp\ipykernel_21144\1720235003.py in <module>
----> 1 main(hc_data, patient_data, sustainType)

~\AppData\Local\Temp\ipykernel_21144\1919658236.py in main(hc_data, patient_data, sustain_Type)
    116             mixtures = fit_all_gmm_models(full_data, full_data_labels)
    117         elif sustainType == "mixture_KDE":
--> 118             mixtures = fit_all_kde_models(full_data, full_data_labels)
    119 
    120         print(mixtures)
...
...
LinAlgError: Singular matrix

I'd be happy to provide the full error if that would be helpful. Please advise on how to progress.

Thanks