A Super Scalable Algorithm for Short Segment Detection

Ning Hao, Yue Selena Niu, Feifei Xiao, Heping Zhang

Research output: Contribution to journalArticlepeer-review

1 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)18-33
Number of pages16
JournalStatistics in Biosciences
Issue number1
StatePublished - Apr 2021


  • Copy number variation
  • Inference
  • Nonparametric method
  • Signal detection

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry, Genetics and Molecular Biology (miscellaneous)


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