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Rapid improvement in quantum hardware has opened the door to complex problems, but the precise characterization of quantum systems itself remains a challenge. To address this obstacle, novel tomography schemes have been developed that employ generative machine learning models, enabling quantum state reconstruction from limited classical data. In particular, quantum-inspired Born machines provide a natural way to encode measured data into a model of a quantum state. Born machines have shown great success in learning from classical data; however, the full potential of a Born machine in learning from quantum measurement has thus far been unrealized. To this end, we devise a complex-valued basis-enhanced Born machine and show that it can reconstruct pure quantum states using projective measurements from only two Pauli measurement bases. We implement the basis-enhanced Born machine to learn the ground states across the phase diagram of a 1D chain of Rydberg atoms, reconstructing quantum states deep in ordered phases and even at critical points with quantum fidelities surpassing 99%. The model accurately predicts quantum correlations and different observables, and system sizes as large as 37 qubits are considered. Quantum states across the phase diagram of a 1D XY spin chain are also successfully reconstructed using this scheme. Our method only requires simple Pauli measurements with a sample complexity that scales quadratically with system size, making it amenable to experimental implementation.