CpG Transformer for imputation of single-cell methylomes
Bioinformatics, 2022•academic.oup.com
Motivation The adoption of current single-cell DNA methylation sequencing protocols is
hindered by incomplete coverage, outlining the need for effective imputation techniques.
The task of imputing single-cell (methylation) data requires models to build an
understanding of underlying biological processes. Results We adapt the transformer neural
network architecture to operate on methylation matrices through combining axial attention
with sliding window self-attention. The obtained CpG Transformer displays state-of-the-art …
hindered by incomplete coverage, outlining the need for effective imputation techniques.
The task of imputing single-cell (methylation) data requires models to build an
understanding of underlying biological processes. Results We adapt the transformer neural
network architecture to operate on methylation matrices through combining axial attention
with sliding window self-attention. The obtained CpG Transformer displays state-of-the-art …
Motivation
The adoption of current single-cell DNA methylation sequencing protocols is hindered by incomplete coverage, outlining the need for effective imputation techniques. The task of imputing single-cell (methylation) data requires models to build an understanding of underlying biological processes.
Results
We adapt the transformer neural network architecture to operate on methylation matrices through combining axial attention with sliding window self-attention. The obtained CpG Transformer displays state-of-the-art performances on a wide range of scBS-seq and scRRBS-seq datasets. Furthermore, we demonstrate the interpretability of CpG Transformer and illustrate its rapid transfer learning properties, allowing practitioners to train models on new datasets with a limited computational and time budget.
Availability and implementation
CpG Transformer is freely available at https://github.com/gdewael/cpg-transformer.
Supplementary information
Supplementary data are available at Bioinformatics online.
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