Dataset Information

More efficient approximation of smoothing splines via space-filling basis selection.

ABSTRACT: We consider the problem of approximating smoothing spline estimators in a nonparametric regression model. When applied to a sample of size [Formula: see text], the smoothing spline estimator can be expressed as a linear combination of [Formula: see text] basis functions, requiring [Formula: see text] computational time when the number [Formula: see text] of predictors is two or more. Such a sizeable computational cost hinders the broad applicability of smoothing splines. In practice, the full-sample smoothing spline estimator can be approximated by an estimator based on [Formula: see text] randomly selected basis functions, resulting in a computational cost of [Formula: see text]. It is known that these two estimators converge at the same rate when [Formula: see text] is of order [Formula: see text], where [Formula: see text] depends on the true function and [Formula: see text] depends on the type of spline. Such a [Formula: see text] is called the essential number of basis functions. In this article, we develop a more efficient basis selection method. By selecting basis functions corresponding to approximately equally spaced observations, the proposed method chooses a set of basis functions with great diversity. The asymptotic analysis shows that the proposed smoothing spline estimator can decrease [Formula: see text] to around [Formula: see text] when [Formula: see text]. Applications to synthetic and real-world datasets show that the proposed method leads to a smaller prediction error than other basis selection methods.

SUBMITTER: Meng C

PROVIDER: S-EPMC7430945 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Similar Datasets

Project description:BackgroundNext-generation sequencing has been used by investigators to address a diverse range of biological problems through, for example, polymorphism and mutation discovery and microRNA profiling. However, compared to conventional sequencing, the error rates for next-generation sequencing are often higher, which impacts the downstream genomic analysis. Recently, Wang et al. (BMC Bioinformatics 13:185, 2012) proposed a shadow regression approach to estimate the error rates for next-generation sequencing data based on the assumption of a linear relationship between the number of reads sequenced and the number of reads containing errors (denoted as shadows). However, this linear read-shadow relationship may not be appropriate for all types of sequence data. Therefore, it is necessary to estimate the error rates in a more reliable way without assuming linearity. We proposed an empirical error rate estimation approach that employs cubic and robust smoothing splines to model the relationship between the number of reads sequenced and the number of shadows.ResultsWe performed simulation studies using a frequency-based approach to generate the read and shadow counts directly, which can mimic the real sequence counts data structure. Using simulation, we investigated the performance of the proposed approach and compared it to that of shadow linear regression. The proposed approach provided more accurate error rate estimations than the shadow linear regression approach for all the scenarios tested. We also applied the proposed approach to assess the error rates for the sequence data from the MicroArray Quality Control project, a mutation screening study, the Encyclopedia of DNA Elements project, and bacteriophage PhiX DNA samples.ConclusionsThe proposed empirical error rate estimation approach does not assume a linear relationship between the error-free read and shadow counts and provides more accurate estimations of error rates for next-generation, short-read sequencing data.

Dataset Information

More efficient approximation of smoothing splines via space-filling basis selection.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets