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Effective representation of brain anatomical architecture is fundamental in understanding brain regularity and variability. Despite numerous efforts, it is still difficult to infer reliable anatomical correspondence at finer scale, given the tremendous individual variability in cortical folding patterns. It is even more challenging to disentangle common and individual patterns when comparing brains at different neuro-developmental stages. In this work, we developed a novel learning-based few-shot embedding framework to encode the cortical folding patterns into a latent space represented by a group of anatomically meaningful embedding vectors. Specifically, we adopted 3-hinge (3HG) network as the substrate and designed an autoencoder-based embedding framework to learn a common embedding vector for each 3HG's multi-hop feature: each 3HG can be represented as a combination of these feature embeddings via a set of individual specific coefficients to characterize individualized anatomical information. That is, the regularity of folding patterns is encoded into the embeddings, while the individual variations are preserved by the multi=hop combination coefficients. To effectively learn the embeddings for the population with very limited samples, few-shot learning was adopted. We applied our method on adult HCP and pediatric datasets with 1,000+ brains (from 34 gestational weeks to young adult). Our experimental results show that: 1) the learned embedding vectors can quantitatively encode the commonality and individuality of cortical folding patterns; 2) with the embeddings we can robustly infer the complicated many-to-many anatomical correspondences among different brains and 3) our model can be successfully transferred to new populations with very limited training samples.