No abstract

The emerging field of Genome-NLP (Natural Language Processing) aims to analyse biological sequence data using machine learning (ML), offering significant advancements in data-driven diagnostics. Three key challenges exist in Genome-NLP. First, long biomolecular sequences require "tokenisation" into smaller subunits, which is non-trivial since many biological "words" remain unknown. Second, ML methods are highly nuanced, reducing interoperability and usability. Third, comparing models and reproducing results are difficult due to the large volume and poor quality of biological data. To tackle these challenges, we developed the first automated Genome-NLP workflow that integrates feature engineering and ML techniques. The workflow is designed to be species and sequence agnostic. In this workflow: a) We introduce a new transformer-based model for genomes calledgenomicBERT, which empirically tokenises sequences while retaining biological context. This approach minimises manual preprocessing, reduces vocabulary sizes, and effectively handles out-of-vocabulary "words". (b) We enable the comparison of ML model performance even in the absence of raw data. To facilitate widespread adoption and collaboration, we have madegenomicBERTavailable as part of the publicly accessible conda package calledZiran. We have successfully demonstrated the application ofZiranon multiple case studies, showcasing its effectiveness in the field of Genome-NLP.