Single-Pass CNN–Transformer for Multi-Label 1H NMR Flavor Mixture Identification

Interpreting multi-component 1H NMR spectra is difficult due to peak overlap, concentration variability, and low-abundance signals. We cast mixture identification as a single-pass multi-label task. A compact CNN–Transformer (“Hybrid”) model was trained end-to-end on domain-informed and realistically simulated spectra derived from a 13-component flavor library; the model requires no real mixtures for training. On 16 real formulations, the Hybrid attains micro-F1 = 0.990 and exact-match (subset) accuracy = 0.875, outperforming CNN-only and Transformer-only ablations, while remaining efficient (~0.47 M parameters; ~0.68 ms on GPU, V100). The approach supports abstention and shows robustness to simulated outsiders. Although the evaluation set was small, and the macro-ECE (per-class, 15 bins) was inflated by sparse classes (≈0.70), the micro-averaged Brier is low (0.0179), and temperature scaling had negligible effect (T ≈ 1.0), indicating the good overall probability quality. The pipeline is readily extensible to larger libraries and adjacent applications in food authenticity and targeted metabolomics. Classical chemometric baselines trained on simulation failed to transfer to real measurements (subset accuracy 0.00), while the Hybrid model maintained strong performance.