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bioRxiv · 10.64898/2026.03.09.708388

HAETAE: A highly accurate and efficient epigenome transformer for tissue-specific histone modification prediction

Park, S.-J.·Im, S.-H.·Kim, S.-Y.·Kim, J.-Y.
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Abstract

While genomic models trained on four bases often fail to capture cell-type specificity, we introduce HAETAE, which integrates 5-methylcytosine from long-read sequencing into a 5-base framework. By explicitly modeling epigenetic context, HAETAE achieves state-of-the-art accuracy (>0.95) with orders of magnitude fewer parameters, challenging the prevailing scaling-law paradigm. Furthermore, HAETAE deciphers tissue-specific regulatory logic, as demonstrated by revealing the distinct, context-dependent functional impact of the TERT promoter mutation across diverse tissues.

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Park, S.-J., Im, S.-H., Kim, S.-Y., Kim, J.-Y.. 2026-03-11. HAETAE: A highly accurate and efficient epigenome transformer for tissue-specific histone modification prediction. https://doi.org/10.64898/2026.03.09.708388

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