In scientific writing, it is correct to write something like
The filter-based method is good.
But what if I have two nouns before
-based? Something like
The lowpass filter-based method is good.
Is it still correct?
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If lowpass modifies method --if it's the lowpass method --then leave it as it is. If lowpass modifies filter, then all three words should be hyphenated together, as in "The lowpass-filter-based method is good." You could also probably get away with "The lowpass-filter based method is good."
Basically the rule is you want to reduce the ambiguity by showing which words modify which other words. You can theoretically have a whole bunch of hyphens in a row, although you'd want to avoid that if you can, since there's no further way to indicate within the string which words modify which others.