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Despite its importance, extracting physically meaningful and predictive features from frequency-domain magnetic signals remains challenging, particularly in scenarios where annotated measurement data are scarce and expensive to obtain. In this study, the challenge of extracting physically meaningful features from limited data is addressed by proposing a complex-valued autoencoder. This architecture is designed to jointly encode magnitude and frequency information into a compact latent representation, thereby preserving phase-sensitive structural dependencies that are typically lost in standard approaches. The method was evaluated on a real-world dataset of high-strength alloys with sparse annotations. It is demonstrated that the proposed complex-valued representations yield significantly improved regression performance, characterized by lower prediction error and reduced variance compared to a classical real-valued baseline. 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