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In this paper, we propose a novel graph-based data augmentation method that can generally be applied to medical waveform data with graph structures. In the process of recording medical waveform data, such as electrocardiogram (ECG) or electroencephalogram (EEG), angular perturbations between the measurement leads exist due to discrepancies in lead positions. The data samples with large angular perturbations often cause inaccuracy in algorithmic prediction tasks. We design a graph-based data augmentation technique that exploits the inherent graph structures within the medical waveform data to improve both performance and robustness. In addition, we show that the performance gain from graph augmentation results from robustness by testing against adversarial attacks. Since the bases of performance gain are orthogonal, the graph augmentation can be used in conjunction with existing data augmentation techniques to further improve the final performance. We believe that our graph augmentation method opens up new possibilities to explore in data augmentation.