In the framework of Economic Complexity, the concept of capabilities represents a fundamental theoretical construct for modeling economic systems. These capabilities, while extensively theorized as the hidden endowments driving countries' productive structures, have remained empirically elusive, never subjected to direct inference attempts. The present work addresses this critical gap by developing an approach to infer and extract information about this theoretical capabilities layer directly from empirical data. Our methodology employs Italian municipal-level economic data, specifically utilizing ATECO codes (the Italian classification system for economic activities harmonized with the European NACE nomenclature) organized in a binary matrix format, representing the presence or absence of economic activities in municipalities.