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Is the idea that you want to embed each sample? In that case, you can convert your dataframe into a NumPy array of shape (50, 1000), and use pymde.preserve_neighbors or pymde.preserve_distances to obtain an embedding for each sample.
The documentation explains how to do things like this. Let me know if you have follow-up questions, or if something in the documentation is not clear.
for example if I have a dataframe shape of (50,1000), 50 samples with time series length of 1000 each
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