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Abstract Generative models aim to learn the probability distributions underlying data, enabling the generation of new, realistic samples. Quantum-inspired generative models, such as Born machines based on the matrix product state (MPS) framework, have demonstrated remarkable capabilities in unsupervised learning tasks. This study advances the Born machine paradigm by introducing trainable token embeddings through positive operator-valued measurements (POVMs), replacing the traditional approach of static tensor indices. Key technical innovations include encoding tokens as quantum measurement operators with trainable parameters and leveraging QR decomposition to adjust the physical dimensions of the MPS. This approach maximizes the utilization of operator space and enhances the model’s expressiveness. Empirical results on RNA data demonstrate that the proposed method significantly reduces negative log-likelihood compared to one-hot embeddings, with higher physical dimensions further enhancing single-site probabilities and multi-site correlations. The model also outperforms GPT-2 in single-site estimation and achieves competitive correlation modeling, showcasing the potential of trainable POVM embeddings for complex data correlations in quantum-inspired sequence modeling.