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.
Mechanist is an agentic system that uses AI as a scientific instrument for the autonomous discovery of mechanisms underlying AI intelligence, and 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.
Mengru Wang, Junfeng Fang, Shuofei Qiao et al.· 0 citations
Scientific discovery has advanced through successive transformations in the organization of knowledge. Observation and experimentation established the empirical foundations of science. Theory made it possible to derive general principles from particular phenomena. Computation extended inquiry into systems beyond direct observation, while data-intensive methods opened new spaces of pattern and prediction. Science now confronts a different frontier. The central challenge is no longer simply to produce more information, but to organize expanding knowledge, reasoning, and evidence into a coherent process of discovery. Here, we introduce Bridging Literature, Agents, and Zero-gap Experimentation (BLAZE), a paradigm of socialized scientific intelligence. BLAZE conceives AI not as an assistant for isolated research tasks, but as an organizational infrastructure for scientific discovery. It connects persistent knowledge, collective reasoning, empirical validation, and human judgment within a continuous research lifecycle, transforming fragmented activities into a cumulative process of inquiry, criticism, and revision. The central premise of BLAZE is that scientific intelligence does not arise from computation alone. It emerges from the sustained interaction among knowledge, hypotheses, experiments, and collective verification. By organizing humans and machines within a shared scientific process, BLAZE makes discovery more traceable, reproducible, and cumulative while preserving human creativity, judgment, and responsibility. Socialized scientific intelligence may provide a foundation for the next era of science. Its purpose is not to replace human discovery, but to extend the scale, depth, and continuity of collective scientific inquiry.
Xinjie Yao, Xingxin Xu, Xiyuan Gao et al.· 0 citations
This article examines the emerging paradigm of agentic AI for scientific discovery, traces the conceptual shift from tools to agents, lays out a six-stage workflow spanning literature synthesis to manuscript generation, and reviews practical systems in chemistry, equation discovery, materials science, and general machine learning research.
Alexander Taktakidze· Longevity Horizon· 0 citations
Artificial intelligence (AI) is shifting scientific discovery from task-specific workflows towards autonomous systems that organize exploration with experimental and human feedback in open-ended candidate spaces. Evolutionary computation (EC) provides a computational basis for feedback-driven discovery because population-based search can maintain diverse scientific candidates while steering exploration through accumulated evidence. However, EC predominantly focuses on candidate refinement for predefined problems, whereas cumulative discovery requires experience retention. To bridge this gap, this review introduces evolutionary intelligence (EI) for scientific discovery. EI characterizes scientific AI systems that sustain exploration by linking candidate refinement with experience retention across evolutionary cycles. We introduce a five-dimensional analytical framework that asks what evolves, how candidates change, why candidates are selected, where feedback originates, and when evolution occurs. This framework clarifies how EI transforms isolated search trajectories into cumulative scientific insight. We further demonstrate this paradigm across diverse discovery modes, from evolving concrete scientific entities to orchestrating automated research workflows. Finally, we identify critical bottlenecks regarding evaluation, process traceability, and shared infrastructure, providing a concrete roadmap for advancing the transition from EC to EI in scientific discovery.
Chao Wang, Lingling Li, Fang Liu et al.· 0 citations
Automation is transforming scientific discovery by enabling systematic exploration of complex hypotheses. Large language models (LLMs) perform well across diverse tasks and promise to accelerate research, but often struggle with logical structures. Here, we present a framework for biological discovery integrating LLM-based agents with laboratory automation, guided by logical scaffolds incorporating symbolic relational learning, structured vocabularies and experimental constraints. This integration improves coherence and reliability in automated workflows. We couple this AI-driven approach to automated cell-culture and metabolomics platforms, enabling integrated hypothesis validation and refinement, yielding a flexible discovery system. The system identified novel interactions in Saccharomyces cerevisiae, including glutamate-induced growth inhibition in spermine-treated cells and aminoadipate's partial rescue of formic-acid stress. All hypotheses, experiments and data are captured in a graph database employing controlled vocabularies. Existing ontologies are extended, and a novel representation of scientific hypotheses is presented using description logics. This work demonstrates the potential for a reliable machine-driven discovery process in systems biology.
Daniel Brunnsåker, Alexander H. Gower, Prajakta Naval et al.· Journal of the Royal Society...· 2 citations
The rapid evolution of Large Language Models (LLMs) has brought unprecedented capabilities across reasoning, coding, and multimodal tasks. However, as performance scales, their opaque ''black-box'' nature raises a critical challenge: How can we trace the origins of emergent intelligence, and more importantly, how can we leverage these internal mechanisms to guide model optimization? This tutorial provides a comprehensive, end-to-end view of LLM interpretability, transitioning from microscopic neural analysis to macroscopic application and deployment. It is systematically organized into five core sections: i) Unlocking the Black Box: We begin with the evolution of LLM interpretability and highlight recent breakthroughs from leading research teams. ii) Methodology: We present a rigorous overview of foundational theories (e.g., mathematical framework for transformer, biological mechanisms in LLMs) and essential methods (e.g., path patching, logit lens, and neuron description). iii) Anatomy of LLMs: Using advanced techniques to decode internal semantic features, neural circuits, and complex behaviors, we interpret how models perform reasoning, factual recall, and in-context learning. iv) Applications: We show how to transfer interpretability insights into actionable improvements across the LLM pipeline, including interpretability-guided data synthesis (data value scoring, corpus filtering, and activation-based data diagnosis). We also present Pinpoint Training and Steering for precise capability gains, and Pinpoint Quantization for extreme low-bit compression with minimal capability loss. v) Advanced Topics: We conclude by exploring how these interpretability paradigms scale and inspire the design of frontier architectures, agentic systems, and thinking models. In this tutorial, researchers and engineers will gain the theoretical frameworks and practical engineering toolkits needed to understand, steer, and efficiently deploy LLMs in real-world production environments.
Wei Zhang, Zhengfu He, Lucia Zhang et al.· Proceedings of the 32nd ACM...· 0 citations