ABSTRACT Investigating the relationship, particularly the lead–lag effect, between time series is a common question across various disciplines, especially when uncovering biological processes. However, analyzing time series presents several challenges. Firstly, due to technical reasons, the time points at which observations are made are not at uniform intervals. Secondly, some lead–lag effects are transient, necessitating time-lag estimation based on a limited number of time points. Thirdly, external factors also impact these time series, requiring a similarity metric to assess the lead–lag relationship. To counter these issues, we introduce a model grounded in the Gaussian process, affording the flexibility to estimate lead–lag effects for irregular time series. In addition, our method outputs dissimilarity scores, thereby broadening its applications to include tasks such as ranking or clustering multiple pairwise time series when considering their strength of lead–lag effects with external factors. Crucially, we offer a series of theoretical proofs to substantiate the validity of our proposed kernels and the identifiability of kernel parameters. Our model demonstrates advances in various simulations and real-world applications, particularly in the study of dynamic chromatin interactions, compared to other leading methods.

Gaussian processes for time series with lead–lag effects with applications to biology data