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The lecturer is saying

It includes how to collect your data, how to label your data, how to choose an architecture, but also how to design a proper loss function to optimize.

there is no "not only", is it idiomatic to say "but also"?

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I think it could be argued either way. On one hand, it sounds like he is just listing a series of features, which would normally be a comma-separated list and then the final feature linked with "and":

It includes how to collect your data, how to label your data, how to choose an architecture, and how to design a proper loss function to optimize.

As you state, if his intention was to contrast the first three features with the final one it would have made more sense to lead with "not only". However, in spoken, extemperaneous speech, we don't always know how a sentence is going to end when we begin it. It may be that the lecturer felt the last feature in his list was something contrasting to the others but didn't think to set that up from the beginning?

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