bioRxiv2025
The rapid advancement of DNA foundation language models has brought about a transformative shift in genomics, allowing for the deciphering of intricate patterns and regulatory mechanisms embedded within DNA sequences. The genomic foundation model Evo2 demonstrates remarkable capabilities in decoding DNA functional patterns through cross-species pretraining. However, despite the great potential of Evo2 in basic genomics research, there is currently no clear and systematic guidance on its specific application scenarios, performance, and optimization directions in the field of tumor genomics, and its performance dependency on specialized hardware (such as FP8 precision on H800 GPUs) has not been empirically benchmarked. Here, we present a focused validation of Evo2 using two independent cancer genomic datasets (Bladder Urothelial Carcinoma and Ovarian Cancer), we tested the downstream tasks of Evo2, including the prediction of tumor pathogenic variants and the prediction of mutational effects, and compared its performance on A100 and H800 GPUs. The results show that critical importance of FP8 precision, enabling the H800 to achieve a 4x faster inference speed than the A100 with stable accuracy (AUC 0.88-0.95). The 7B-parameter model emerged as the top performer, whereas the 40B model experienced a severe performance drop (AUC to 0.48) on non-FP8 hardware like the A100. These findings empirically validated Evo2s hardware specifications and provided practical insights for researchers implementing the model with similar computational resources. Futhermore, our findings provide a framework for the application and optimization of downstream tasks of the DNA language model Evo2 in cancer, and can guide researchers in effectively applying it in genomic studies. Key PointsO_LIHardware Precision Impact: FP8 precision on H800 GPUs is critical for Evo 2s performance, enabling 4x faster inference than A100 (without FP8 support) while maintaining high accuracy (AUC 0.88-0.95). C_LIO_LIModel Scale Optimization: The 7B-parameter model outperformed larger variants (e.g., 40B), which suffered severe accuracy drops (AUC as low as 0.48) on non-FP8 hardware, highlighting a balance between efficiency and performance. C_LIO_LIPractical Guidelines: We provide a framework for deploying Evo 2 in cancer genomics, including hardware recommendations, dataset curation, and downstream task optimization--valuable for researchers with varied computational resources. C_LI