Recent advances in foundation models have transformed AI for Science, enabling remarkably accurate predictive performance across domains ranging from protein folding to weather forecasting. Yet prediction alone does not constitute scientific discovery. Scientific understanding depends on uncovering the reusable explanatory mechanisms that generate observations, whereas contemporary machine learning remains fundamentally organised around predictive mappings rather than explanatory structure. In this paper, we argue that scientific discovery is fundamentally a problem of knowledge organisation. To this end, we introduce Mechanistic World Models, a new design paradigm that places reusable mechanisms at the centre of representation, computation and learning. Drawing on insights from the philosophy of science, we derive the computational capabilities required for discovery, identify the design principles and inductive pressures that encourage explanatory knowledge to emerge, and formalise the anatomy of a mechanism-centric world model. Finally, we show how diverse research directions including mechanistic interpretability, causal representation learning, equation discovery and modular architectures capture complementary ingredients of this paradigm while lacking a unified framework. We propose Mechanistic World Models as a conceptual foundation and computational blueprint for moving AI beyond predictive forecasting towards autonomous scientific discovery.
Modern Machine Learning (ML) and Artificial Intelligence (AI) models, especially large language models (LLMs), are increasingly used to generate scientific hypotheses and mechanistic explanations from observational data. This position paper argues that in the high-dimensional proxy regimes where modern ML excels, mechanistic learning is generically underdetermined: many incompatible mechanisms induce essentially the same observational relationships on the support of the data, so predictive success and coherent explanations are insufficient evidence of mechanism discovery. This underdetermination becomes uniquely hazardous with large language models (LLMs), which tend to collapse large equivalence classes of explanations into a single fluent narrative. This paper proposes concrete standards for ``mechanistic ML,'' and argues these norms are necessary if LLM-centered workflows are to support science rather than merely simulate it.
AI models have achieved remarkable success across diverse domains, yet the mechanisms underlying their capabilities and the risks they may pose remain poorly understood. As AI development becomes faster and increasingly automated, mechanistic exploration remains largely manual, widening the gap between what models can do and our ability to understand and control them. 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 intelligence. To support autonomous mechanistic discovery, we construct an interpretability-focused knowledge graph of approximately 13,000 papers and integrate it with a multidisciplinary database of 43 million papers spanning 26 fields. We further curate a library of 32 foundational methods for mechanism analysis, causal intervention, and validation. Compared with Claude Code and existing AI-scientist systems, Mechanist generates more valuable mechanism hypotheses and executes experiments more reliably. Mechanist also demonstrates a progression from discovering model behaviors to explaining and controlling AI models. Specifically, Mechanist first uncovers a counterintuitive safety risk in scientific laboratories, showing that unsafe traits can transfer across modalities through apparently safe training data. 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. Finally, Mechanist translates these mechanistic insights into practical interventions that improve model performance across diverse scenarios and steer scientific foundation models toward generating DNA sequences with specified properties.
Deriving governing equations from empirical observations is a longstanding challenge in science. Although artificial intelligence (AI) has demonstrated substantial capabilities in function approximation, the discovery of explainable and extrapolatable equations remains a fundamental limitation of modern AI, posing a central bottleneck for AI-driven scientific discovery. Here, we present machine collective intelligence, a unified paradigm that integrates two fundamental yet distinct traditions in computational intelligence--symbolism and metaheuristics--to enable autonomous and evolutionary discovery of governing equations. It orchestrates multiple reasoning agents to evolve their symbolic hypotheses through coordinated generation, evaluation, critique, and consolidation, enabling scientific discovery beyond single-agent inference. Across scientific systems governed by deterministic, stochastic, or previously uncharacterized dynamics, machine collective intelligence autonomously recovered the underlying governing equations without relying on hand-crafted domain knowledge. Furthermore, the resulting equations reduced extrapolation error by up to six orders of magnitude relative to deep neural networks, while condensing 0.5-1 million model parameters into just 5-40 interpretable parameters. This study marks an important shift in AI toward the autonomous discovery of principled scientific equations.