GeneZip: Region-Aware Compression for Long Context DNA Modeling

원문 초록

Long-context DNA modeling is computationally expensive, motivating existing approaches to reduce sequence length through uniform downsampling. However, functional information and sequence redundancy are unevenly distributed across the genome, calling for finer resolution in functionally dense regions and stronger compression of redundant sequence. We introduce GeneZip, a region-aware DNA compression framework that learns where to allocate a limited token budget. Building on H-Net-style dynamic routing, GeneZip combines a Region-Aware Ratio objective, which uses regional labels derived from GENCODE gene annotations to specify compression targets during training, with bounded routing for stable token counts. At inference, it compresses raw DNA without annotations. GeneZip provides three main benefits. First, it preserves predictive utility under high compression: GeneZip-70M achieves 137.6-fold compression with a validation perplexity increase of 0.31 relative to uncompressed Mamba2-84M, and the best average rank across four DNALongBench tasks among compression models with leakage-controlled pretraining. Second, it learns region-aware allocation with emergent repeat-aware compression. Alternative regional priors yield task-dependent performance trade-offs. Without repeat-specific supervision, GeneZip compresses transposable-element-derived and tandem repeats more strongly than matched non-repeat sequence; its tandem-repeat compression preference transfers to a nine-species evaluation panel without further training. Third, it enables efficient long-context modeling: on 450-kb inputs, GeneZip-70M achieves 36.1-fold higher inference throughput than JanusDNA-7.7M on a single H100 GPU.