A Super Scalable Algorithm for Short Segment Detection

In many applications such as copy number variant (CNV) detection, the goal is to identify short segments on which the observations have different means or medians from the background. Those segments are usually short and hidden in a long sequence and hence are very challenging to find. We study a super scalable short segment (4S) detection algorithm in this paper. This nonparametric method clusters the locations where the observations exceed a threshold for segment detection. It is computationally efficient and does not rely on Gaussian noise assumption. Moreover, we develop a framework to assign significance levels for detected segments. We demonstrate the advantages of our proposed method by theoretical, simulation, and real data studies.

Automated summary

This paper presents a super scalable short segment detection algorithm that can effectively identify short segments hidden in long sequences and assign significance levels to the detected segments. The algorithm is computationally efficient, does not rely on Gaussian noise assumption, and demonstrates advantages through theoretical, simulation, and real data studies.