Timestamp calibration for time-series single cell RNA-seq expression data

TL;DR

This paper introduces ScPace, a novel timestamp calibration model for noisy time-series single-cell RNA-seq data, improving annotation accuracy and downstream pseudotime analysis by effectively detecting and handling noisy labels.

Contribution

The paper presents a new latent variable-based calibration method, ScPace, that outperforms existing approaches in handling noisy timestamps in time-series scRNA-seq data.

Findings

ScPace outperforms previous methods in simulated and real datasets.

Calibrated timestamps improve pseudotime analysis accuracy.

The method robustly detects and handles noisy labels across datasets.

Abstract

Timestamp automatic annotation (TAA) is a crucial procedure for analyzing time-series ScRNA-seq data, as they unveil dynamic biological developments and cell regeneration process. However, current TAA methods heavily rely on manual timestamps, often overlooking their reliability. This oversight can significantly degrade the performance of timestamp automatic annotation due to noisy timestamps. Nevertheless, the current approach for addressing this issue tends to select less critical cleaned samples for timestamp calibration. To tackle this challenge, we have developed a novel timestamp calibration model called ScPace for handling noisy labeled time-series ScRNA-seq data. This approach incorporates a latent variable indicator within a base classifier instead of probability sampling to detect noisy samples effectively. To validate our proposed method, we conducted experiments on both simulated and real time-series ScRNA-seq datasets. Cross-validation experiments with different artificial mislabeling rates demonstrate that ScPace outperforms previous approaches. Furthermore, after calibrating the timestamps of the original time-series ScRNA-seq data using our method, we performed supervised pseudotime analysis, revealing that ScPace enhances its performance significantly. These findings suggest that ScPace is an effective tool for timestamp calibration by enabling reclassification and deletion of detected noisy labeled samples while maintaining robustness across diverse ranges of time-series ScRNA-seq datasets. The source code is available at https://github.com/OPUS-Lightphenexx/ScPace.