feature volatility analysis in q2-longitudinal

Hi all,

We would like to repeat feature volatility analysis with q2-longitudinal code multiple times to obtain more accurate machine learning models, using paired samples. To check the overall accuracy of the final accumulated model, I would like to have the sample information used for training and the coordinate data used for the calculation of accuracy-results for each feature volatility analysis with q2-longitudinal, but I cannot output them.

Could you tell me how to output the following data in feature volatility analysis in q2-longitudinal?
1) Sample information used for training and test
2) The coordinate data used for the calculation of accuracy-results

Thank you for your help!

Hi @Shimpei ,
feature-volatility is a pipeline that runs multiple different actions under the hood — and it only outputs some of the results, it throws out the intermediate data (e.g., specifics on which samples were used for training/testing). You should instead:

  1. use q2-sample-classifier directly. The regress-samples pipeline will give you what you need.
  2. you can then pass the outputs to q2-longitudinal's plot-feature-volatility action to obtain the plots of feature volatility and importance.

regress-samples will output this information.

You can also use q2-sample-classifier's split-table action directly if you want a little more control over this step.

This is in your sample metadata file, whatever the target variable is (e.g., time). But regress-samples will also output this information... the true target values and predicted target values for each test sample.

good luck!

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Hi @Nicholas_Bokulich ,

Thank you so much for the quick response!
I would like to try the analysis using the method you gave me.

Two more questions,

  1. Are feature abundances used as variables for machine learning in the feature-volatility pipeline in q2-longitudinal?
  2. Are the variables used for machine learning different in between q2-sample-classifier pipeline and feature-volatility pipeline in q2-longitudinal?

Thanks a lot!

yes

q2-longitudinal wraps q2-sample-classifier to perform machine learning. So what I outlined above was basically to perform the underlying steps directly in q2-sample-classifier so that you can access the intermediate files that you need. The outputs can be passed to q2-longitudinal to generate the same visualization.