TY - JOUR T1 - Pretraining on Matter: Conceptual Limits of Foundation Models for Materials Science AU - Claire Dupont AU - Julien Martin JF - Journal of Computational and Data-Driven Materials Engineering JO - J. Comput. Data-Driven Mater. Eng. SN - 3149-9368 Y1 - 2024 VL - 3 IS - 2 SP - 115 N2 - The advent of foundation models, large-scale pre-trained architectures adapted from natural language processing paradigms, has permeated computational materials science, promising accelerated discovery through data-driven inference. In materials engineering, these models leverage multimodal datasets encompassing atomic structures, properties, and simulations to enable representation learning across scales. However, inherent conceptual limits arise from the interplay between materials' physical hierarchies—spanning quantum to macroscopic levels—and the inductive biases embedded in pretraining strategies. This manuscript synthesizes recent advancements in machine learning architectures, such as graph neural networks and multimodal integration, within materials informatics ecosystems. It identifies epistemic boundaries where foundation models falter in capturing causality, uncertainty, and domain-specific invariances, potentially leading to misaligned discovery pipelines. To address these, we introduce the Matter Pretraining Boundary Framework (MPBF), a conceptual architecture that delineates layers of data assimilation, representational abstraction, and inference steering to mitigate limits in autonomous materials design. Implications extend to high-throughput computation, inverse design, and simulation-experiment coupling, fostering more robust computational workflows in materials engineering. By interpreting these limits through systems-level dynamics, the framework guides infrastructure trade-offs, enhancing the reliability of data-driven paradigms without empirical validation. UR - https://iamrp.net/e254915106 ER -