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I'm a bit confused on how to reference the datasets and outputs of my ML models in a Bokeh WebApp.

The documentation only demonstrates Bokeh plots with dummy data. Isn't the point to create interactive visualizations of the DSS workflow?
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I assume you are using python to write your Bokeh app.

You import the DSS datasets in the python code as you would in any other python recipe or notebook in DSS:

df  = dataiku.Dataset("YOUR_DATA").get_dataframe()
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