Transformer Model Generated Bacteriophage Genomes are Compositionally Distinct from Natural Sequences

Abstract

Novel applications of language models in genomics promise to have a large impact on the field. The megaDNA model is the first publicly available generative model for creating synthetic viral genomes. To evaluate megaDNA’s ability to recapitulate the nonrandom genome composition of viruses and assess whether synthetic genomes can be algorithmically detected, compositional metrics for 4,969 natural bacteriophage genomes and 1,002de novosynthetic bacteriophage genomes were compared. Transformer-generated sequences had varied but realistic genome lengths and 58% were classified as viral by geNomad. However, the sequences demonstrated consistent differences in various compositional metrics when compared to natural bacteriophage genomes by rank-sum tests and principal component analysis. A simple neural network trained to detect transformer-generated sequences on global compositional metrics alone displayed a median sensitivity of 93.0% and specificity of 97.9% (n = 12 independent models). Overall, these results demonstrate that megaDNA does not yet generate bacteriophage genomes with realistic compositional biases and that genome composition is a reliable method for detecting sequences generated by this model. While the results are specific to the megaDNA model, the evaluate framework described here could be applied to any generative model for genomic sequences.