scFTAT: a novel cell annotation method integrating FFT and transformer

Abstract

Background: Advancements in high-throughput sequencing and deep learning have boosted single-cell RNA studies. However, current methods for annotating single-cell data face challenges due to high data sparsity and tedious manual annotation on large-scale data. Results: Thus, we proposed a novel annotation model integrating FFT (Fast Fourier Transform) and an enhanced Transformer, named scFTAT. Initially, it reduces data sparsity using LDA (Linear Discriminant Analysis). Subsequently, automatic cell annotation is achieved through a proposed module integrating FFT and an enhanced Transformer. Moreover, the model is fine-tuned to improve training performance by effectively incorporating such techniques as kernel approximation, position encoding enhancement, and attention enhancement modules. Compared to existing popular annotation tools, scFTAT maintains high accuracy and robustness on six typical datasets. Specifically, the model achieves an accuracy of 0.93 on the human kidney data, with an F1 score of 0.84, precision of 0.96, recall rate of 0.80, and Matthews correlation coefficient of 0.89. The highest accuracy of the compared methods is 0.92, with an F1 score of 0.71, precision of 0.75, recall rate of 0.73, and Matthews correlation coefficient of 0.85. The compiled codes and supplements are available at: https://github.com/gladex/scFTAT. Conclusion: In summary, the proposed scFTAT effectively integrates FFT and enhanced Transformer for automatic feature learning, addressing the challenges of high sparsity and tedious manual annotation in single-cell profiling data. Experiments on six typical scRNA-seq datasets from human and mouse tissues evaluate the model using five metrics as accuracy, F1 score, precision, recall, and Matthews correlation coefficient. Performance comparisons with existing methods further demonstrate the efficiency and robustness of our proposed method.