Complex behavior poses challenges in extracting models from experiment. An example is spin liquid formation in frustrated magnets like Dy$_2$Ti$_2$O$_7$. Understanding has been hindered by issues including disorder, glass formation, and interpretation of scattering data. Here, we use a novel automated capability to extract model Hamiltonians from data, and to identify different magnetic regimes. This involves training an autoencoder to learn a compressed representation of three-dimensional diffuse scattering, over a wide range of spin Hamiltonians. The autoencoder finds optimal matches according to scattering and heat capacity data and provides confidence intervals. Validation tests indicate that our optimal Hamiltonian accurately predicts temperature and field dependence of both magnetic structure and magnetization, as well as glass formation and irreversibility in Dy$_2$Ti$_2$O$_7$. The autoencoder can also categorize different magnetic behaviors and eliminate background noise and artifacts in raw data. Our methodology is readily applicable to other materials and types of scattering problems.
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