  Recent advancements in biological research leverage the integration of
molecules, proteins, and natural language to enhance drug discovery. However,
current models exhibit several limitations, such as the generation of invalid
molecular SMILES, underutilization of contextual information, and equal
treatment of structured and unstructured knowledge. To address these issues, we
propose $\mathbf{BioT5}$, a comprehensive pre-training framework that enriches
cross-modal integration in biology with chemical knowledge and natural language
associations. $\mathbf{BioT5}$ utilizes SELFIES for $100%$ robust molecular
representations and extracts knowledge from the surrounding context of
bio-entities in unstructured biological literature. Furthermore,
$\mathbf{BioT5}$ distinguishes between structured and unstructured knowledge,
leading to more effective utilization of information. After fine-tuning, BioT5
shows superior performance across a wide range of tasks, demonstrating its
strong capability of capturing underlying relations and properties of
bio-entities. Our code is available at
$\href{https://github.com/QizhiPei/BioT5}{Github}$.
