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In the evolving landscape of computational and data-driven materials engineering, innovation is increasingly driven by the interplay between algorithmic advancements and chemical discoveries. Traditional metrics often conflate these dimensions, overlooking how machine learning architectures, such as graph neural networks and representation learning, enable high-throughput computation while potentially prioritizing computational efficiency over substantive material breakthroughs. This conceptual gap hinders a nuanced understanding of progress in materials informatics, where autonomous discovery systems and closed-loop experimentation integrate simulation-experiment coupling with uncertainty quantification. Here, we introduce the Algorithmic-Chemical Novelty Duality Framework (ACNDF), a novel interpretive structure that disentangles algorithmic novelty—encompassing innovations in deep learning architectures and multimodal datasets—from chemical novelty, focused on inverse design and emergent material properties. By emphasizing systems-level insights into representation-inference interactions and epistemic risk structures, ACNDF reorients innovation metrics toward balanced discovery steering logics. This framework highlights infrastructure trade-offs in foundation models for science, fostering more integrative workflows. Implications extend to enhancing predictive analytics and transfer learning across small data regimes, ultimately guiding computational ecosystems toward sustainable innovation in materials engineering.