Certifying nonnegativity of polynomials is a well-known NP-hard problem with direct applications spanning non-convex optimization, control, robotics, and beyond. A sufficient condition for nonnegativity is the Sum of Squares (SOS) property, i.e., it can be written as a sum of squares of other polynomials. In practice, however, certifying the SOS criterion remains computationally expensive and often involves solving a Semidefinite Program (SDP), whose dimensionality grows quadratically in the size of the monomial basis of the SOS expression; hence, various methods to reduce the size of the monomial basis have been proposed. In this work, we introduce the first learning-augmented algorithm to certify the SOS criterion. To this end, we train a Transformer model that predicts an almost-minimal monomial basis for a given polynomial, thereby drastically reducing the size of the corresponding SDP. Our overall methodology comprises three key components: efficient training dataset generation of over 100 million SOS polynomials, design and training of the corresponding Transformer architecture, and a systematic fallback mechanism to ensure correct termination, which we analyze theoretically. We validate our approach on over 200 benchmark datasets, achieving speedups of over $100\times$ compared to state-of-the-art solvers and enabling the solution of instances where competing approaches fail. Our findings provide novel insights towards transforming the practical scalability of SOS programming.