For reliable large-scale quantum computation, a quantum error correction (QEC) scheme must effectively resolve physical errors to protect logical information. Leveraging recent advances in deep learning, neural network-based decoders have emerged as a promising approach to enhance the reliability of QEC. We propose the Hierarchical Qubit-Merging Transformer (HQMT), a novel and general decoding framework that explicitly leverages the structural graph of stabilizer codes to learn error correlations across multiple scales. Our architecture first computes attention locally on structurally related groups of stabilizers and then systematically merges these qubit-centric representations to build a global view of the error syndrome. The proposed HQMT achieves substantially lower logical error rates for surface codes by integrating a dedicated qubit-merging layer within the transformer architecture. Across various code distances, HQMT significantly outperforms previous neural network-based QEC decoders as well as a powerful belief propagation with ordered statistics decoding (BP+OSD) baseline. This hierarchical approach provides a scalable and effective framework for surface code decoding, advancing the realization of reliable quantum computing.
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