Learning to Discover Regulatory Elements for Gene Expression Prediction
Authors: name: Xingyu Su; name: Haiyang Yu; name: Degui Zhi; name: Shuiwang Ji
Published: 2025-02-19 03:25:49

Abstract: We consider the problem of predicting gene expressions from DNA sequences. A
key challenge of this task is to find the regulatory elements that control gene
expressions. Here, we introduce Seq2Exp, a Sequence to Expression network
explicitly designed to discover and extract regulatory elements that drive
target gene expression, enhancing the accuracy of the gene expression
prediction. Our approach captures the causal relationship between epigenomic
signals, DNA sequences and their associated regulatory elements. Specifically,
we propose to decompose the epigenomic signals and the DNA sequence conditioned
on the causal active regulatory elements, and apply an information bottleneck
with the Beta distribution to combine their effects while filtering out
non-causal components. Our experiments demonstrate that Seq2Exp outperforms
existing baselines in gene expression prediction tasks and discovers
influential regions compared to commonly used statistical methods for peak
detection such as MACS3. The source code is released as part of the AIRS
library (https://github.com/divelab/AIRS/).