SPACE: Your Genomic Profile Predictor Is a Powerful DNA Foundation Model

Abstract

While unsupervised DNA pre-training has shown promise, we argue that supervised genomic profile prediction provides more effective DNA representations, since DNA functions are regulated by genomic profiles like chromatin accessibility. We propose **S**pecies-**P**rofile **A**daptive **C**ollaborative **E**xperts (SPACE), a model that uses Mixture of Experts (MoE) to capture cross-species and multi-profile relationships in genomic data. Through extensive evaluation, SPACE achieves state-of-the-art performance, demonstrating that supervised training with genomic profiles creates powerful DNA representations.