DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks.

ABSTRACT: Modeling long-range DNA dependencies is crucial for understanding genome structure and function across a wide range of biological contexts. However, effectively capturing these extensive dependencies, which may span millions of base pairs in tasks such as three-dimensional (3D) chromatin folding prediction, remains a significant challenge. Furthermore, a comprehensive benchmark suite for evaluating tasks that rely on long-range dependencies is notably absent. To address this gap, we introduce DNALongBench, a benchmark dataset encompassing five important genomics tasks that consider long-range dependencies up to 1 million base pairs: enhancer-target gene interaction, expression quantitative trait loci, 3D genome organization, regulatory sequence activity, and transcription initiation signal

SUBMITTER: Cheng W 

PROVIDER: S-EPMC11741265 | biostudies-literature | 2025 Jan

REPOSITORIES: biostudies-literature