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I just confused about how can I use two plural words in one sentence.

For example,

1- The multivariate dependencies structures between two variables are complex.

2- The multivariate dependency structures between two variables are complex.

Dependence means the relationship between variables (say, age and blood pressure).

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It is better if you look at this as a single noun phrase rather than "two words in plural."

The main word in this noun phrase is "structure". It can then be put into plural irrespective of what its modifier (dependency/dependencies) is.

A structure is a relationship between multiple components. Thus, the singular form of your noun phrase is "dependencies structure" (in the computer science sense of "dependency" of "can't install A until you install/update X, Y, and Z"—each of which is a single dependency (just making this caveat in case anyone confuses a software dependency with uncountable "dependence")).

I'm finding this phrase, e.g., here, here, and here (this last example has it as "dependencies' structure", but there is really no need for an apostrophe, as the word "dependencies" easily becomes a noun adjunct (an adjective-fied noun).

Thus, the plural of this will be "dependencies structures."

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