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Leveraging generative Artificial Intelligence (AI), we have transformed a dataset comprising 1000 scientific papers focused on biological materials into a comprehensive ontological knowledge graph. Through an in-depth structural analysis of this graph, we have calculated node degrees, identified communities along with their connectivities, and evaluated clustering coefficients and betweenness centrality of pivotal nodes, uncovering fascinating knowledge architectures. We find that the graph has an inherently scale-free nature, shows a high level of connectedness, and can be used as a rich source for downstream graph reasoning by taking advantage of transitive and isomorphic properties to reveal insights into unprecedented interdisciplinary relationships that can be used to answer queries, identify gaps in knowledge, propose never-before-seen material designs, and predict material behaviors. Using a large language embedding model we compute deep node representations and use combinatorial node similarity ranking to develop a path sampling strategy that allows us to link dissimilar concepts that have previously not been related. One comparison revealed detailed structural parallels between biological materials and Beethoven’s 9th Symphony, highlighting shared patterns of complexity through isomorphic mapping. In another example, the algorithm proposed an innovative hierarchical mycelium-based composite based on integrating path sampling with principles extracted from Kandinsky’s ‘Composition VII’ painting. The resulting material integrates an innovative set of concepts that include a balance of chaos and order, adjustable porosity, mechanical strength, and complex patterned chemical functionalization. We uncover other isomorphisms across science, technology and art, revealing a nuanced ontology of immanence that reveal a context-dependent heterarchical interplay of constituents. Because our method transcends established disciplinary boundaries through diverse data modalities (graphs, images, text, numerical data, etc), graph-based generative AI achieves a far higher degree of novelty, explorative capacity, and technical detail, than conventional approaches and establishes a widely useful framework for innovation by revealing hidden connections.