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I have encountered it countless times, but I have two clear examples in my mind at this time:

1. Grey Matter from Ben 10

From Ben 10 Wikia

Grey Matter's small size belies his great calculative and technical intellect. He can create complicated machines from spare parts, understand the function of any device at a glance, and make sophisticated repairs to complex machines, (such as a warp-drive engine). Grey Matter's intellect serves as a problem solver and analytical help in difficult situations. This allows Grey Matter to think more strategically when brute force is inefficient.

The Omnitrix was invented by a Grey Matter.

2. Rocket the Racoon from Guardians of the Galaxy

I'll tell you what I am! A genius of myself.
- Rocket

He can build smart weapons using garbage and can build bad-ass weapons which can annihilate starships and can create strategies to beat best-in-class security systems of best-in-class prison in the universe.

You got the best tactical mind I ever met.
- Starlord (to Rocket)


The core concept is old which you can see even in non sci-fi works. For example, Jerry is also able to screw Tom. Also, in a kid story in Panchatantra, a rabbit fooled a lion by telling him there was a lion in the well who wanted him (lion) dead and later that lion jumped on its own image in well (western versions can exist). But, here, Jerry's and that rabbit's intelligence can't be called hyper. Maybe, I can rephrase the question: Which work brought the concept of "size matters not" and "intelligence supreme" to science fiction and applied it to little aliens and technology?

Note: Little green martians won't qualify as a race. The story must show that an individual little alien is hyper intelligent than the other characters shown in the story.

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    The 1943 comic book supervillain Mr. Mind is a 2-inch worm from outer space and a scientific, technological, and criminal genius, but [SPOILER WARNING] in the end he gets caught, so maybe he isn't smart enough for the purposes of your question. – user14111 Apr 17 '17 at 10:25

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