The unavoidable presence of noise is a crucial roadblock for the development of large-scale quantum computers and the ability to characterize quantum noise reliably and efficiently with high precision is essential to scale quantum technologies further. Although estimating an arbitrary quantum channel requires exponential resources, it is expected that physically relevant noise has some underlying local structure, for instance that errors across different qubits have a conditional independence structure. Previous works showed how it is possible to estimate Pauli noise channels with an efficient number of samples in a way that is robust to state preparation and measurement errors, albeit departing from a known conditional independence structure. We present a novel approach for learning Pauli noise channels over n qubits that addresses this shortcoming. Unlike previous works that focused on learning coefficients with a known conditional independence structure, our method learns both the coefficients and the underlying structure. We achieve our results by leveraging a groundbreaking result by Bresler for efficiently learning Gibbs measures and obtain an optimal sample complexity of O(log(n)) to learn the unknown structure of the noise acting on n qubits. This information can then be leveraged to obtain a description of the channel that is close in diamond distance from O(poly(n)) samples. Furthermore, our method is efficient both in the number of samples and postprocessing without giving up on other desirable features such as SPAM-robustness, and only requires the implementation of single qubit Cliffords. In light of this, our novel approach enables the large-scale characterization of Pauli noise in quantum devices under minimal experimental requirements and assumptions.