  An important application of Synthetic Biology is the engineering of the host
cell system to yield useful products. However, an increase in the scale of the
host system leads to huge design space and requires a large number of
validation trials with high experimental costs. A comprehensible machine
learning approach that efficiently explores the hypothesis space and guides
experimental design is urgently needed for the Design-Build-Test-Learn (DBTL)
cycle of the host cell system. We introduce a novel machine learning framework
ILP-iML1515 based on Inductive Logic Programming (ILP) that performs abductive
logical reasoning and actively learns from training examples. In contrast to
numerical models, ILP-iML1515 is built on comprehensible logical
representations of a genome-scale metabolic model and can update the model by
learning new logical structures from auxotrophic mutant trials. The ILP-iML1515
framework 1) allows high-throughput simulations and 2) actively selects
experiments that reduce the experimental cost of learning gene functions in
comparison to randomly selected experiments.
