提出可并行计算的精准对齐算法,大幅缩短长序列对齐时间。
A Study of Parallelizable Alternatives to Dynamic Time Warping for Aligning Long Sequences

- 将代价矩阵分块或沿对角线处理,实现GPU并行加速
- 新算法在长序列上提速1.5至200倍,保持精确对齐
- 适合需要快速对齐长音频/时序数据的研究者使用
本文研究了若干可并行化的替代动态时间规整(DTW)的算法,用于估计两条长序列间的对齐。不同于以往降低总计算量或内存消耗的工作,本文聚焦于利用支持并行处理的硬件(如GPU)减少实际运行时间。提出了四种并行化对齐算法:前三者通过将成对代价矩阵分割为矩形区域并行处理,得到DTW近似;第四种则沿对角线处理代价矩阵,实现精确的DTW对齐。在音频-音频对齐任务上评估性能,并为表现最佳的两种算法——弱序分段DTW(WSDTW)和并行对角线DTW(ParDTW)——开发了基于GPU的实现。实验表明,ParDTW是四者中最实用有效的:能实现精确对齐,且在长序列上相比现有方法运行时间缩短1.5至2个数量级。
原文摘要 · Abstract (English)
This article investigates several parallelizable alternatives to DTW for estimating the alignment between two long sequences. Whereas most previous work has focused on reducing the total computation and/or memory costs of DTW, our focus is instead on reducing wall clock time by utilizing common hardware like GPUs that are optimized for parallel processing. We propose and study four different parallelizable alignment algorithms: the first three algorithms compute approximations of DTW by breaking the pairwise cost matrix into rectangular regions and processing the regions in parallel, and the fourth algorithm computes an exact DTW alignment by processing the cost matrix along diagonals rather than rows or columns. We characterize the performance of our proposed alignment algorithms on an audio-audio alignment task, and we develop GPU-based implementations for the two best-performing algorithms, which we call weakly-ordered Segmental DTW (WSDTW) and Parallelized Diagonal DTW (ParDTW). Our experiments indicate that ParDTW is the most practical and useful of the four algorithms: it computes an exact DTW alignment and reduces runtime by 1.5 to 2 orders of magnitude on long sequences compared to current alternatives. We present a comprehensive evaluation and study of the alignment accuracy, runtime, and practical limitations of the proposed alignment algorithms.
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