scHyena: Foundation Model for Full-Length Single-Cell RNA-Seq Analysis in Brain

• URL: http://arxiv.org/abs/2310.02713v1
• Date: Wed, 4 Oct 2023 10:30:08 GMT
• Title: scHyena: Foundation Model for Full-Length Single-Cell RNA-Seq Analysis in Brain
• Authors: Gyutaek Oh, Baekgyu Choi, Inkyung Jung, and Jong Chul Ye
• Abstract summary: We introduce scHyena, a foundation model designed to address these challenges and enhance the accuracy of scRNA-seq analysis in the brain. scHyena is equipped with a linear adaptor layer, the positional encoding via gene-embedding, and a bidirectional Hyena operator. This enables us to process full-length scRNA-seq data without losing any information from the raw data.
• Score: 46.39828178736219
• License: http://creativecommons.org/licenses/by-nc-nd/4.0/
• Abstract: Single-cell RNA sequencing (scRNA-seq) has made significant strides in unraveling the intricate cellular diversity within complex tissues. This is particularly critical in the brain, presenting a greater diversity of cell types than other tissue types, to gain a deeper understanding of brain function within various cellular contexts. However, analyzing scRNA-seq data remains a challenge due to inherent measurement noise stemming from dropout events and the limited utilization of extensive gene expression information. In this work, we introduce scHyena, a foundation model designed to address these challenges and enhance the accuracy of scRNA-seq analysis in the brain. Specifically, inspired by the recent Hyena operator, we design a novel Transformer architecture called singe-cell Hyena (scHyena) that is equipped with a linear adaptor layer, the positional encoding via gene-embedding, and a {bidirectional} Hyena operator. This enables us to process full-length scRNA-seq data without losing any information from the raw data. In particular, our model learns generalizable features of cells and genes through pre-training scHyena using the full length of scRNA-seq data. We demonstrate the superior performance of scHyena compared to other benchmark methods in downstream tasks, including cell type classification and scRNA-seq imputation.

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