Abstract
Artificial intelligence (AI) is changing how biological research is done. Biological foundation models trained on millions of nucleotides, protein, and single-cell measurements predict protein structures, mutation effects, and cellular responses to genetic perturbations. Agentic systems, AI assistants built on large language models, can run multistep analyses from plain-language requests and increasingly call foundation models as tools. Yet it is often unclear when these models' outputs can be trusted. We frame this as a model's knowledge boundary: the range of inputs, tasks, and conditions over which its outputs are reliable. This review explains how foundation models are built and proposes that five design elements (data, architecture, training scheme, evaluation scheme, and post-analysis) define this boundary. We examine evidence on where current models succeed or fail and present standardized descriptions of model limits so that researchers, and the agents acting for them, can use these tools reliably.
Abstract (translated)
URL
https://arxiv.org/abs/2611.17015
