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Abstract The emergence of quantum sensor networks has presented opportunities for enhancing complex sensing tasks, while simultaneously introducing significant challenges in designing and analyzing quantum sensing protocols due to the intricate nature of entanglement and physical processes. Supervised learning assisted by an entangled sensor network (SLAEN) (Zhuang and Zhang 2019Phys. Rev.X9041023) represents a promising paradigm for automating sensor-network design through variational quantum machine learning. However, the original SLAEN, constrained by the Gaussian nature of quantum circuits, is limited to learning linearly separable data. Leveraging the universal quantum control available in cavity quantum electrodynamics experiments, we propose a generalized SLAEN capable of handling nonlinear data classification tasks. We establish a theoretical framework for physical-layer data classification to underpin our approach. Through training quantum probes and measurements, we uncover a threshold phenomenon in classification error across various tasks—when the energy of probes exceeds a certain threshold, the error drastically diminishes to zero, providing a significant improvement over the Gaussian SLAEN. Despite the non-Gaussian nature of the problem, we offer analytical insights into determining the threshold and residual error in the presence of noise. Our findings carry implications for radio-frequency photonic sensors and microwave dark matter haloscopes.