Searching for Phenotypic Needles in Genomic Haystacks: DNA Language Models for Sex Prediction

In this study, we explore fine-tuning of Genomic Language Models (GLM) to predict phenotypic traits directly from genomic sequence, without prior knowledge about causative loci or molecular mechanisms linking genotype to phenotype. As a case study, we focus on sex prediction, a well-defined genomic feature associated with the presence of the Y chromosome in most mammals. We adapt a pre-trained GENA-LM model for trait prediction by introducing a sequence chunk classification component with cross-attention, enabling the model to process larger genomic contexts. Training and evaluation on human and mouse genomes demonstrate that the model does not require high-quality reference genome assembly and converges even when the fraction of genomic signal associated with phenotype is below 1%. Prediction accuracy improves with increased sequencing depth, highlighting the scalability of GLMs for genome-wide tasks. Furthermore, a multi-species model effectively learns sex-specific signals for both human and mouse, confirming its cross-species predictive ability. Ablation studies demonstrate that the model relies on the Y chromosome for sex prediction, that aligns with real biological principles. Our findings highlight the applicability of GLMs for trait prediction in long and fragmented genomic data.