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arXiv 2011.04832cs.LGcs.ITmath.ITq-bio.GNstat.ML
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秩一模型的自适应学习在高效序列比对中的应用

Adaptive Learning of Rank-One Models for Efficient Pairwise Sequence Alignment

Microsoft Research New England(新英格兰微软研究院);Stanford University(斯坦福大学);University of Illinois, Urbana-Champaign(伊利诺伊大学厄巴纳-香槟分校)

Govinda M. Kamath, Tavor Z. Baharav, Ilan Shomorony

摘要:

DNA测序数据的成对比对是生物信息学中普遍存在的任务,并且通常代表沉重的计算负担。加速该任务的最先进的方法使用散列来识别由读段对共享的短片段(k-mer),然后可以将其用于估计比对分数。然而,当读段的数量很大时,准确地估计所有对的比对分数仍然是非常昂贵的。此外,在实践中,人们只对鉴定具有大比对分数的读段对感兴趣。在这项工作中,我们提出了一种新的方法,成对比对估计的基础上两个关键的新成分。第一个要素是将成对比对估计的问题置于一级众包模型的一般框架下,其中工作者的响应对应于k聚体哈希冲突。这些模型可以通过响应矩阵的谱分解来精确求解。第二个成分是利用多臂bandit算法来自适应地改进该谱估计器,仅用于可能具有大比对的读段对。所得到的算法迭代地执行自适应选择的读取对的子集的响应矩阵的谱分解。

英文摘要:

Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. State-of-the-art approaches to speed up this task use hashing to identify short segments (k-mers) that are shared by pairs of reads, which can then be used to estimate alignment scores. However, when the number of reads is large, accurately estimating alignment scores for all pairs is still very costly. Moreover, in practice, one is only interested in identifying pairs of reads with large alignment scores. In this work, we propose a new approach to pairwise alignment estimation based on two key new ingredients. The first ingredient is to cast the problem of pairwise alignment estimation under a general framework of rank-one crowdsourcing models, where the workers' responses correspond to k-mer hash collisions. These models can be accurately solved via a spectral decomposition of the response matrix. The second ingredient is to utilise a multi-armed bandit algorithm to adaptively refine this spectral estimator only for read pairs that are likely to have large alignments. The resulting algorithm iteratively performs a spectral decomposition of the response matrix for adaptively chosen subsets of the read pairs.

机构、总结、中文摘要均由AI分析而来,可能存在错误,请以论文正文为准。

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