currybo-benchmarks

usage: currybo-benchmarks [-h] [--options OPTIONS] [--objectives OBJECTIVES [OBJECTIVES ...]] [--final-objective FINAL_OBJECTIVE]
                          [--initial-seed INITIAL_SEED] [--budget BUDGET] [--jobs JOBS] [--workers WORKERS] [--samples SAMPLES [SAMPLES ...]]
                          [--surrogate {SimpleGP,AdditiveStructureGP}] [--kernel {TanimotoKernel}] [--likelihood {GaussianLikelihood}]
                          [--x-utility {Random,SimpleRegret,UncertaintyUtility,QuantileUtility,QuantitativeImprovement,QualitativeImprovement}]
                          [--x-utility-kwargs X_UTILITY_KWARGS]
                          [--w-utility {Random,SimpleRegret,UncertaintyUtility,QuantileUtility}]
                          [--w-utility-kwargs W_UTILITY_KWARGS]
                          [--utility {Random,SimpleRegret,UncertaintyUtility,QuantileUtility,QuantitativeImprovement,QualitativeImprovement}]
                          [--utility-kwargs UTILITY_KWARGS]
                          [--acquisition {SequentialAcquisition,SequentialLookaheadAcquisition,JointLookaheadAcquisition}]
                          [--aggregation {Mean,Sigmoid,MSE,Min}] [--batch-size BATCH_SIZE]
                          [--batch-strategy {QSequentialAcquisition,QProbabilityOfOptimality}] [--qpo-num-samples QPO_NUM_SAMPLES] [--verbose]
                          [--output-dir OUTPUT_DIR]
                          {Denmark,DenmarkMOBO,Cernak,Borylation,Deoxyfluorination,Doyle}
 
Benchmark CLI for currybo
 
positional arguments:
  {Denmark,DenmarkMOBO,Cernak,Borylation,Deoxyfluorination,Doyle}
                        Dataset name (as defined in `datasets/chemistry_datasets/presets.py`)
 
options:
  -h, --help            show this help message and exit
  --options OPTIONS     Options for substrate and condition columns
  --objectives OBJECTIVES [OBJECTIVES ...]
                        Objectives for optimization. Specify [name, threshold, lower_bound, upper_bound, maximize]
  --final-objective FINAL_OBJECTIVE
                        Objective index to optimize when all objectives reached their threshold
  --initial-seed INITIAL_SEED
                        Number of data points to seed the initial run with
  --budget BUDGET       Number of iterations for a single BO campaign
  --jobs JOBS           Number of parallel campaign runs.
  --workers WORKERS     Number of cores to run jobs on. [WARN] CurryBO already runs in parallel, so there's rarely a need to use this!
  --samples SAMPLES [SAMPLES ...]
                        Number of samples for dataset split
  --surrogate {SimpleGP,AdditiveStructureGP}
                        Surrogate Model Type, defaults to `SimpleGP`
  --kernel {TanimotoKernel}
                        Covariance Kernel for the Surrogate Model
  --likelihood {GaussianLikelihood}
                        Likelihood
  --x-utility {Random,SimpleRegret,UncertaintyUtility,QuantileUtility,QuantitativeImprovement,QualitativeImprovement}
                        Utility function Type for x. Defaults to QuantileUtility
  --x-utility-kwargs X_UTILITY_KWARGS
                        Arguments to pass to the x utility, as a keyval string
  --w-utility {Random,SimpleRegret,UncertaintyUtility,QuantileUtility}
                        Utility function Type for w. Defaults to UncertaintyUtility
  --w-utility-kwargs W_UTILITY_KWARGS
                        Arguments to pass to the w utility, as a keyval string
  --utility {Random,SimpleRegret,UncertaintyUtility,QuantileUtility,QuantitativeImprovement,QualitativeImprovement}
                        Utility function for Joint Acquisitions
  --utility-kwargs UTILITY_KWARGS
                        Arguments to pass to the utility, as a keyval string
  --acquisition {SequentialAcquisition,SequentialLookaheadAcquisition,JointLookaheadAcquisition}
                        Acquisition Strategy, defaults to `SequentialAcquisition`
  --aggregation {Mean,Sigmoid,MSE,Min}
                        Aggregation Function, defaults to `Mean`
  --batch-size BATCH_SIZE
                        Batch Size, defaults to 1
  --batch-strategy {QSequentialAcquisition,QProbabilityOfOptimality}
                        Batch Strategy, defaults to QSequentialAcquisition
  --qpo-num-samples QPO_NUM_SAMPLES
                        Nuber of samples for qPO
  --verbose             Verbose Output
  --output-dir OUTPUT_DIR
                        Specify folder to output result files to