Biocompiler: Compiling Spatial Network Optimization Problems into Living Solvers with Digital Fabrication System

Living systems, such as Physarum polycephalum (slime mold), have shown great potential in solving network-optimization problems, such as shortest paths, in response to their environmental constraints. While this phenomenon has been well-documented, it has yet to be generated on demand as usable, machine-readable data from user-specified physical constraints. To this end, we introduce Biocompiler, a digital fabrication pipeline that treats P. polycephalum as a design and fabrication interface. Our system comprises three operations split between machine and living organism: our user interface translates an optimization problem into physical constraints embedded into the organism's environment, the organism responds to them through its own growth, and our machine decodes the resulting morphology through computer vision into a machine-readable format that serves as the answer to the optimization problem. We use a CNC-based laser scanning system to fabricate the physical growth-constrained environment and a camera to sense the resulting topology. Our results show that a compiled dynamic light barrier changes the growth paths of the organism, and demonstrate the feasibility of the end-to-end workflow across three problem types.