├── LICENSE ├── README.md ├── SOBER ├── BASQ │ ├── __init__.py │ ├── _basq.py │ └── _scale_mmlt.py ├── BOLFI │ ├── __init__.py │ ├── _botorch_acquisition.py │ └── _gpytorch_bolfi_model.py ├── FBGP │ ├── __init__.py │ ├── _acquisition_function.py │ ├── _fitbo.py │ ├── _fully_Bayesian_gp.py │ ├── _hyperprior.py │ └── _scale_vbq.py ├── __init__.py ├── _drug_modelling.py ├── _expectation_propagation_lfi.py ├── _gp.py ├── _inverse_modelling.py ├── _kernel.py ├── _pi.py ├── _prior.py ├── _prior_update.py ├── _rchq.py ├── _sampler.py ├── _settings.py ├── _sober.py ├── _sober_wrapper.py ├── _tmvn.py ├── _utils.py ├── _weights.py ├── _wkde.py └── mvnorm │ ├── Phi.py │ ├── __init__.py │ ├── conditioning.py │ ├── integration.py │ └── multivariate_normal_cdf.py ├── benchmarks ├── _batch_bo.py ├── dpp_ts_bo │ ├── gp.py │ ├── snippet_batched.py │ ├── snippet_dppts.py │ └── test_script.py └── gp_sampling │ ├── __init__.py │ ├── base.py │ ├── basis_functions.py │ ├── decoupled_samplers.py │ ├── thompson_samplers.py │ └── utils │ ├── __init__.py │ ├── layer.py │ └── random_gp.py ├── docs ├── animated.gif ├── animated_with_plot.gif ├── equation.png └── visual_explanation.png ├── examples ├── ackley.py ├── hartmann.py ├── ising.py ├── malaria.py ├── maxsat.py ├── pest.py ├── rosenbrock.py ├── shekel.py ├── solvent.py └── svm.py ├── experiments ├── _ackley.py ├── _ecm.py ├── _generate_drug_dataset.py ├── _hartmann.py ├── _ising.py ├── _malaria.py ├── _maxsat.py ├── _pest.py ├── _rosenbrock.py ├── _shekel.py ├── _solvent.py ├── _svm.py ├── _synthetic_function.py └── dataset │ ├── QM9_dipole.csv │ ├── malaria_box_dataset.csv │ └── maxcut-johnson8-2-4.clq.wcnf ├── pyproject.toml ├── requirements.txt ├── setup.cfg └── tutorials ├── 00 Quick start.ipynb ├── 01 How does SOBER work.ipynb ├── 02 Customise prior for various domain type.ipynb ├── 03 Customise acquisition function.ipynb ├── 04 Fast fully Bayesian Gaussian process modelling.ipynb ├── 05 Fast Bayesian inference for simulation-based inference.ipynb ├── 06 Tips for drug discovery.ipynb ├── 07 Compare with Thompson sampling.ipynb ├── 08 Benchmarking against batch BO methods.ipynb └── Advanced 01 BOLFI modelling.ipynb /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ma921/SOBER/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ma921/SOBER/HEAD/README.md -------------------------------------------------------------------------------- /SOBER/BASQ/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ma921/SOBER/HEAD/SOBER/BASQ/__init__.py -------------------------------------------------------------------------------- /SOBER/BASQ/_basq.py: 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