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mean (something) by (something)
To have some hidden or ulterior meaning, judgment, or intention behind one's words or actions. Often used in questions and negative constructions. I didn't mean anything by what I said—I was just making an observation about your clothes, that's all! A: "It's not bad, for someone like you." B: "Hey, what do you mean by that?"
mean by something
to intend a certain meaning by words or deeds. What do you mean by that? I did not mean anything special by my remarks.