The accurate prediction of origin-destination (OD) flows is essential for advancing sustainable urban mobility and supporting resilient urban planning. However, the inherent heterogeneity of mobility patterns results in complex geographic unit relations, diverse spatial organizational structures, and the long-tailed effect on OD flow distribution. This study proposes a novel OD flow prediction method based on graph-based deep learning (named as HMCG-LGBM). Specifically, 1) a modularity-based graph reconstruction strategy is presented for geographic unit relation augmentation by eliminating weak connections; 2) the heterogeneous spatial organization of OD flows is captured by combining the community detection approach and graph attention mechanism with the introduction of socio-economic and spatial features; and 3) a weighted loss function with distribution smoothing paradigm is developed to enhance the prediction for low-probability mobility events, addressing the challenges posed by long-tailed distributions. Extensive experiments conducted on real-world datasets show that the predictive performance of the proposed method is significantly improved, with the RMSE and MAE reduced from the baselines by 11.1%–33.3% and 14.1%–22.2%, respectively. The results also demonstrate the robustness of the proposed method for dealing with imbalanced OD flow distributions, providing valuable insights for spatial interaction predictive modeling in the context of sustainable urban systems.
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