Interpretable machine learning is rapidly becoming a crucial tool for scientific discovery. Among existing approaches, variational autoencoders (VAEs) have shown promise in extracting the hidden physical features of some input data, with no supervision nor prior knowledge of the system at study. Yet the ability of VAEs to create meaningful, interpretable representations relies on their accurate approximation of the underlying probability distribution of their input. When dealing with quantum data, VAEs must hence account for its intrinsic randomness and complex correlations. While VAEs have been previously applied to quantum data, they have often neglected its probabilistic nature, hindering the extraction of meaningful physical descriptors. Here we demonstrate that two key modifications enable VAEs to learn physically meaningful latent representations: a decoder capable of faithfully reproducing the probability distributions of quantum states and a probabilistic loss tailored to this task. Using benchmark quantum spin models, we identify regimes where standard methods fail while the representations learned by our approach remain meaningful and interpretable. Applied to experimental data from Rydberg atom arrays, the model autonomously uncovers the phase structure without access to prior labels, Hamiltonian details, or knowledge of relevant order parameters, highlighting its potential as an unsupervised and interpretable tool for the study of quantum systems.

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• Phase diagrams
• Quantum phase transitions
• Quantum simulation
• 1-dimensional spin chains
• Rydberg atoms & molecules
• Machine learning