Nature Machine Intelligence (2026). DOI: 10.1038/s42256-026-01232-w"> Explainability through analysis of training data. Credit: Nature Machine Intelligence (2026). DOI: 10.1038/s42256-026-01232-w Protein language models are artificial intelligence tools which help engineer proteins with useful properties, including completely new structures never seen before in nature. The technology has huge potential for addressing global challenges, such as synthesizing enzymes that can absorb carbon dioxide from the atmosphere or building catalysts that greatly reduce energy use or toxic waste byproducts in industrial processes. As many of these models begin to shape real-world decisions in biotechnology, a major problem persists. Protein language models (pLMs) largely operate as black boxes, making it hard to understand their decision process and judge whether their predictions are reliable, biased, or even safe to apply in the real world.…