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. Our code is publicly available at https://github.com/Alistair-Turcan/TusoAI.