Mechanist: AI as a Scientific Instrument for Discovering the Mechanisms of Intelligence

Abstract

AI models are increasingly used in scientific discovery and human decision-making. Yet how AI models work and what risks they pose remain poorly understood. As AI development becomes faster and more automated, research on the mechanisms underlying AI remains largely manual. To bridge this gap, we introduce Mechanist, an agentic system that uses AI as a scientific instrument for the autonomous discovery of mechanisms underlying AI. To ground novel mechanism hypotheses, we construct a scientific knowledge graph of 13,000 studies on AI mechanisms, alongside a multidisciplinary database of 43 million papers spanning 26 fields. For reliable experiment execution, we curate a library of 32 foundational methods for mechanism analysis. Compared with Claude Code and existing AI-scientist systems, Mechanist generates higher-quality mechanism hypotheses and executes experiments more reliably. Across four case studies, Mechanist autonomously discovers new model behaviors and their underlying mechanisms, and translates these discoveries into mechanism-guided interventions and interdisciplinary design. Specifically, Mechanist first uncovers a counterintuitive safety risk in scientific laboratories, showing that unsafe traits can transfer to fine-tuned student models through apparently safe training data and emerge across modalities. Mechanist then develops a mechanism theory of belief, revealing how models represent world knowledge, form beliefs, infer the beliefs of others, and how these mechanisms emerge during pretraining. Building on this theory, Mechanist develops targeted interventions that improve model performance across diverse scenarios. Finally, Mechanist can also advance interdisciplinary discovery through mechanistic design, providing an alternative to the computationally intensive generate-and-rerank paradigm.