Simulations are a powerful and cost-effective way to demonstrate how
efficiently ProtoLife's Predictive Design Technology (PDT) finds optimal targets
in complex search spaces. The following tests were run on simulated
but realistic experimental search spaces, representing combinations of
a certain number of experimental parameters (e.g., materials or compounds)
chosen from a library of 100, with each parameter in the combination
taking any of 20 different values.1 The response
surfaces for these systems contained several local optima with a range of values
measured in arbitrary units from 0 to 8, with added experimental
noise. These simulations benchmark PDT against established
optimization methods in large and highly synergistic experimental
search spaces, and demonstrate PDT's superiority at identifying the
optimal targets while saving time and resources.
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A simulated system with pairwise
combinations was defined on an experimental
space with a total of 105 experiments.
Exhaustive exploration of such a space in the
laboratory would require a vast effort, and screening even
a fraction of it could be very expensive (e.g., if the
experimental parameters were costly pharmaceuticals or other chemicals).
On this system, standard Design of Experiments (DoE) techniques were
obviously more efficient than exhaustive exploration, but substantially less
efficient than PDT.
PDT found all of the optimal targets after exploring only 3% of the
experimental space, and was more than twice as efficient in doing so than a
standard genetic algorithm (GA).
Higher-order (five-way) combinations
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This simulated system involved all combinations
of up to five experimental parameters, for a huge experimental space of
over 1011 experiments. This system is more
realistic than the one described above,
because unpredictable higher-order synergies often occur in
real-world systems: e.g., chemical systems for protein
crystallization, protein synthesis, combination drug discovery,
formulation of small molecule drugs, complex formulations (such as
siRNA), heterogeneous catalyst discovery, and plastic formulations.
Because of such synergies, standard DoE cannot be used effectively to
find optimal targets; DoE software such as JMP performs only
slightly better than random search in a complex space of these
PDT found all of the optimal targets in this space after exploring
only 4,000 experiments, and was over 3 times more efficient than a
1 Cawse, J, Gazzola, G, and Packard, N. (2011). Efficient discovery and optimization of complex
high-throughput experiments. Catalysis today, 159(1): 55-63.