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To improve the quality of track maintenance work, it is a desire to estimate vehicle dynamic behavior from track geometry irregularities. This paper proposes a deep learning model to predict vehicle responses (e.g., vertical wheel-rail forces, wheel unloading rate, and car body vertical acceleration) using deep learning techniques. In the proposed CA-CNN-MUSE model, convolutional neural networks (CNNs) are used to learn features of track irregularities, and multiscale self-attention mechanisms (MUSE) are employed to capture the long-term and short-term trends of sequences. Coordinate attention (CA) is introduced into CNN to focus on important interchannel relationships and important spatial mileage points. The experiments were performed on a multibody simulation model of the vehicle system and the measured data of the actual high-speed line. The results show that the CA-CNN-MUSE has high prediction accuracy for vertical vehicle responses and fast computation speed. The predicted time-domain waveforms and power spectral densities (PSDs) agree well with the actual vehicle responses. The main features of the lateral vehicle responses can also be captured by the proposed method, yet the results are not as good as the vertical ones.