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I had exactly the same problem: How do I naturally integrate human expertise or manual interventions into automatic hyperparameter optimization process? I ended up writing my own algorithm that helps me achieve that: https://github.com/ar-nowaczynski/spaceopt
This was some time ago but I had some promising results with Bayesian optimization using a Gaussian Process prior. The method was developed by the guys who wrote Spearmint. That library doesn't support parallelization but I implemented the same technique in Scala without too much difficulty.
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