TusoAI: Agentic Optimization for Scientific Methods

Scientific discovery is often slowed by the manual development of computational tools needed to analyze complex experimental data. Building such tools is costly and time-consuming because scientists must iteratively review literature, test mod- eling and scientific assumptions against empirical data, and implement these in- sights into efficient software. Large language models (LLMs) have demonstrated strong capabilities in synthesizing literature, reasoning with empirical data, and generating domain-specific code, offering new opportunities to accelerate com- putational method development. Existing LLM-based systems either focus on performing scientific analyses using existing computational methods or on de- veloping computational methods or models for general machine learning without effectively integrating the often unstructured knowledge specific to scientific do- mains. Here, we introduce TusoAI, an agentic AI system that takes a scientific task description with an evaluation function and autonomously develops and optimizes computational methods for the application. TusoAI integrates domain knowledge into a knowledge tree representation and performs iterative, domain-specific op- timization and model diagnosis, improving performance over a pool of candidate solutions. We conducted comprehensive benchmark evaluations demonstrating that TusoAI outperforms state-of-the-art expert methods, MLE agents, and scien- tific AI agents across diverse tasks. Applying TusoAI to two key open problems in genetics improved existing computational methods and uncovered new biology missed by previous methods.