Large language models (LLMs) have recently been proposed as general-purpose agents for experimental design, with claims that they can perform in-context experimental design. We evaluate this hypothesis using both open- and closed-source instruction-tuned LLMs applied to genetic perturbation and molecular property discovery tasks. We find that LLM-based agents show no sensitivity to experimental feedback: replacing true outcomes with randomly permuted labels has no impact on performance. Across benchmarks, classical methods such as linear bandits and Gaussian process optimization consistently outperform LLM agents. We further propose a simple hybrid method, LLM-guided Nearest Neighbour (LLMNN) sampling, that combines LLM prior knowledge with nearest-neighbor sampling to guide the design of experiments. LLMNN achieves competitive or superior performance across domains without requiring significant in-context adaptation. These results suggest that current open- and closed-source LLMs do not perform in-context experimental design in practice and highlight the need for hybrid frameworks that decouple prior-based reasoning from batch acquisition with updated posteriors.

Agents based on large language models have shown great potential in accelerating scientific discovery by leveraging their rich background knowledge and reasoning capabilities. Here, we develop BioDiscoveryAgent, an agent that designs new experiments, reasons about their outcomes, and efficiently navigates the hypothesis space to reach desired solutions. We demonstrate our agent on the problem of designing genetic perturbation experiments, where the aim is to find a small subset out of many possible genes that, when perturbed, result in a specific phenotype (e.g., cell growth). Utilizing its biological knowledge, BioDiscoveryAgent can uniquely design new experiments without the need to train a machine learning model or explicitly design an acquisition function. Moreover, BioDiscoveryAgent achieves an average of 18% improvement in detecting desired phenotypes across five datasets, compared to existing Bayesian optimization baselines specifically trained for this task. Our evaluation includes one dataset that is unpublished, ensuring it is not part of the language model's training data. Additionally, BioDiscoveryAgent predicts gene combinations to perturb twice as accurately as a random baseline, a task so far not explored in the context of closed-loop experiment design. The agent also has access to tools for searching the biomedical literature, executing code to analyze biological datasets, and prompting another agent to critically evaluate its predictions. Overall, BioDiscoveryAgent is interpretable at every stage, representing an accessible new paradigm in the computational design of biological experiments with the potential to augment scientists' capabilities.