The discovery of scientific formulae that parsimoniously explain natural phenomena and align with existing background theory is a key goal in science. Historically, scientists have derived natural laws by manipulating equations based on existing knowledge, forming new equations, and verifying them experimentally. In recent years, data-driven scientific discovery has emerged as a viable competitor in settings with large amounts of experimental data. Unfortunately, data-driven methods often fail to discover valid laws when data is noisy or scarce. Accordingly, recent works combine regression and reasoning to eliminate formulae inconsistent with background theory. However, the problem of searching over the space of formulae consistent with background theory to find one that fits the data best is not well-solved. We propose a solution to this problem when all axioms and scientific laws are expressible via polynomial equalities and inequalities and argue that our approach is widely applicable. We further model notions of minimal complexity using binary variables and logical constraints, solve polynomial optimization problems via mixed-integer linear or semidefinite optimization, and prove the validity of our scientific discoveries in a principled manner using Positivestellensatz certificates. Remarkably, the optimization techniques leveraged in this paper allow our approach to run in polynomial time with fully correct background theory, or non-deterministic polynomial (NP) time with partially correct background theory. We demonstrate that some famous scientific laws, including Kepler’s Third Law of Planetary Motion, the Hagen-Poiseuille Equation, and the Radiated Gravitational Wave Power equation, can be derived in a principled manner from background axioms and experimental data.