Benzene rings might be an example.
The new understanding of benzene, and hence of all aromatic compounds, proved to be so important for both pure and applied chemistry that in 1890 the German Chemical Society organized an elaborate appreciation in Kekulé's honor, celebrating the twenty-fifth anniversary of his first benzene paper. Here Kekulé spoke of the creation of the theory. He said that he had discovered the ring shape of the benzene molecule after having a reverie or day-dream of a snake seizing its own tail (this is a common symbol in many ancient cultures known as the Ouroboros or Endless knot). This vision, he said, came to him after years of studying the nature of carbon-carbon bonds. This was 7 years after he had solved the problem of how carbon atoms could bond to up to four other atoms at the same time.
My own
intuition supposition: we do a lot of probablistic reasoning subconsciously while learning, and what we call intuitions are our way of linking ideas together. To that extent, we learn our intuitions.