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  • poli 🧪: a library of discrete objective functions

Getting started

  • Getting started

The basics

  • What is poli?
  • Defining an observer
  • Isolating black box objective functions

Examples

  • Optimizing protein stability using random mutations

Objective functions

  • All objective functions
  • Albuterol Similarity (using TDC)
  • Aloha objective function
  • Amlodipine MPO (using TDC)
  • Celecoxib Rediscovery (using TDC)
  • Deco Hop (using TDC)
  • dockstring
  • DRD2 Docking (using TDC)
  • DRD3 docking (using TDC)
  • Ehrlich functions
  • Fexofenadine MPO (using TDC)
  • Protein solvent accessibility (using foldx)
  • Protein stability (using foldx)
  • GSK3β (using TDC)
  • Isomer C7H8N2O2 (using TDC)
  • Isomer C9H10N2O2PF2Cl (using TDC)
  • Log-solubility (logP)
  • Median 1 (using TDC)
  • Median 2 (using TDC)
  • Mestranol Similarity (using TDC)
  • Osimetrinib MPO (using TDC)
  • Penalized logP (using lambo)
  • Quantitative Estimate of Druglikeness (QED)
  • Ranolazine MPO (using TDC)
  • Rapid Stability Predictions
  • Synthetic Accessibility (using TDC)
  • Scaffold Hop (using TDC)
  • Sitagliptin MPO (using TDC)
  • Thiothixene Rediscovery (using TDC)
  • Toy continuous objective functions
  • Troglitazone Rediscovery (using TDC)
  • Valsartan SMARTS (using TDC)
  • White Noise objective function
  • Zaleplon MPO (using TDC)

Optimizers

  • Random mutations
  • CMA-ES
  • Line Bayesian Optimization
  • LaMBO2
  • Hvarfner’s Vanilla Bayesian Optimization
  • Sparse Axis-Aligned Subspaces Bayesian Optimization (SAASBO)
  • Adaptive Linear Embedding Bayesian Optimization (ALEBO)
  • Trust Region Bayesian Optimization (Turbo)
  • Adaptively expanding subspaces (BAxUS)
  • Bounce
  • Probabilistic Reparametrization

Contributing

  • Adding a new black box to the repository
  • Adding a new optimizer to poli-baselines

API reference

  • API documentation for poli
    • poli.core
      • poli.core.abstract_benchmark
      • poli.core.abstract_black_box
      • poli.core.abstract_isolated_function
      • poli.core.abstract_problem_factory
      • poli.core.benchmark_information
      • poli.core.black_box_information
      • poli.core.chemistry
        • poli.core.chemistry.data_packages
        • poli.core.chemistry.tdc_black_box
        • poli.core.chemistry.tdc_isolated_function
        • poli.core.chemistry.tdc_problem
      • poli.core.data_package
      • poli.core.exceptions
      • poli.core.lambda_black_box
      • poli.core.multi_objective_black_box
      • poli.core.problem
      • poli.core.proteins
        • poli.core.proteins.data_packages
        • poli.core.proteins.foldx_black_box
        • poli.core.proteins.foldx_isolated_function
      • poli.core.registry
      • poli.core.util
        • poli.core.util.abstract_observer
        • poli.core.util.algorithm_observer_wrapper
        • poli.core.util.alignment
        • poli.core.util.batch
        • poli.core.util.chemistry
        • poli.core.util.default_observer
        • poli.core.util.external_observer
        • poli.core.util.files
        • poli.core.util.inter_process_communication
        • poli.core.util.isolation
        • poli.core.util.objective_management
        • poli.core.util.observer_wrapper
        • poli.core.util.proteins
        • poli.core.util.seeding
    • poli.objective_factory
    • poli.objective_repository
      • poli.objective_repository.albuterol_similarity
        • poli.objective_repository.albuterol_similarity.register
      • poli.objective_repository.aloha
        • poli.objective_repository.aloha.register
      • poli.objective_repository.amlodipine_mpo
        • poli.objective_repository.amlodipine_mpo.register
      • poli.objective_repository.celecoxib_rediscovery
        • poli.objective_repository.celecoxib_rediscovery.register
      • poli.objective_repository.deco_hop
        • poli.objective_repository.deco_hop.register
      • poli.objective_repository.dockstring
        • poli.objective_repository.dockstring.isolated_function
        • poli.objective_repository.dockstring.register
      • poli.objective_repository.drd2_docking
        • poli.objective_repository.drd2_docking.register
      • poli.objective_repository.drd3_docking
        • poli.objective_repository.drd3_docking.register
      • poli.objective_repository.ehrlich
        • poli.objective_repository.ehrlich.register
      • poli.objective_repository.ehrlich_holo
        • poli.objective_repository.ehrlich_holo.register
      • poli.objective_repository.fexofenadine_mpo
        • poli.objective_repository.fexofenadine_mpo.register
      • poli.objective_repository.foldx_rfp_lambo
        • poli.objective_repository.foldx_rfp_lambo.information
        • poli.objective_repository.foldx_rfp_lambo.isolated_function
        • poli.objective_repository.foldx_rfp_lambo.register
      • poli.objective_repository.foldx_sasa
        • poli.objective_repository.foldx_sasa.isolated_function
        • poli.objective_repository.foldx_sasa.register
      • poli.objective_repository.foldx_stability
        • poli.objective_repository.foldx_stability.isolated_function
        • poli.objective_repository.foldx_stability.register
      • poli.objective_repository.foldx_stability_and_sasa
        • poli.objective_repository.foldx_stability_and_sasa.isolated_function
        • poli.objective_repository.foldx_stability_and_sasa.register
      • poli.objective_repository.gfp_cbas
        • poli.objective_repository.gfp_cbas.abstract_vae_wrapper
        • poli.objective_repository.gfp_cbas.cbas_alphabet_preprocessing
        • poli.objective_repository.gfp_cbas.cbas_wrapper
        • poli.objective_repository.gfp_cbas.gfp_gp
        • poli.objective_repository.gfp_cbas.information
        • poli.objective_repository.gfp_cbas.isolated_function
        • poli.objective_repository.gfp_cbas.make_vae
        • poli.objective_repository.gfp_cbas.register
      • poli.objective_repository.gfp_select
        • poli.objective_repository.gfp_select.information
        • poli.objective_repository.gfp_select.isolated_function
        • poli.objective_repository.gfp_select.register
      • poli.objective_repository.gsk3_beta
        • poli.objective_repository.gsk3_beta.register
      • poli.objective_repository.isomer_c7h8n2o2
        • poli.objective_repository.isomer_c7h8n2o2.register
      • poli.objective_repository.isomer_c9h10n2o2pf2cl
        • poli.objective_repository.isomer_c9h10n2o2pf2cl.register
      • poli.objective_repository.jnk3
        • poli.objective_repository.jnk3.register
      • poli.objective_repository.median_1
        • poli.objective_repository.median_1.register
      • poli.objective_repository.median_2
        • poli.objective_repository.median_2.register
      • poli.objective_repository.mestranol_similarity
        • poli.objective_repository.mestranol_similarity.register
      • poli.objective_repository.osimetrinib_mpo
        • poli.objective_repository.osimetrinib_mpo.register
      • poli.objective_repository.penalized_logp_lambo
        • poli.objective_repository.penalized_logp_lambo.isolated_function
        • poli.objective_repository.penalized_logp_lambo.register
      • poli.objective_repository.perindopril_mpo
        • poli.objective_repository.perindopril_mpo.register
      • poli.objective_repository.ranolazine_mpo
        • poli.objective_repository.ranolazine_mpo.register
      • poli.objective_repository.rasp
        • poli.objective_repository.rasp.isolated_function
        • poli.objective_repository.rasp.register
      • poli.objective_repository.rdkit_logp
        • poli.objective_repository.rdkit_logp.register
      • poli.objective_repository.rdkit_qed
        • poli.objective_repository.rdkit_qed.register
      • poli.objective_repository.rfp_foldx_stability
        • poli.objective_repository.rfp_foldx_stability.assets
        • poli.objective_repository.rfp_foldx_stability.register
      • poli.objective_repository.rfp_foldx_stability_and_sasa
        • poli.objective_repository.rfp_foldx_stability_and_sasa.register
      • poli.objective_repository.rfp_rasp
        • poli.objective_repository.rfp_rasp.assets
        • poli.objective_repository.rfp_rasp.register
      • poli.objective_repository.rmf_landscape
        • poli.objective_repository.rmf_landscape.isolated_function
        • poli.objective_repository.rmf_landscape.register
      • poli.objective_repository.rosetta_energy
        • poli.objective_repository.rosetta_energy.information
        • poli.objective_repository.rosetta_energy.register
      • poli.objective_repository.sa_tdc
        • poli.objective_repository.sa_tdc.information
        • poli.objective_repository.sa_tdc.isolated_function
        • poli.objective_repository.sa_tdc.register
      • poli.objective_repository.scaffold_hop
        • poli.objective_repository.scaffold_hop.information
        • poli.objective_repository.scaffold_hop.register
      • poli.objective_repository.sitagliptin_mpo
        • poli.objective_repository.sitagliptin_mpo.information
        • poli.objective_repository.sitagliptin_mpo.register
      • poli.objective_repository.super_mario_bros
        • poli.objective_repository.super_mario_bros.information
        • poli.objective_repository.super_mario_bros.level_utils
        • poli.objective_repository.super_mario_bros.register
      • poli.objective_repository.thiothixene_rediscovery
        • poli.objective_repository.thiothixene_rediscovery.register
      • poli.objective_repository.toy_continuous_problem
        • poli.objective_repository.toy_continuous_problem.definitions
        • poli.objective_repository.toy_continuous_problem.register
        • poli.objective_repository.toy_continuous_problem.toy_continuous_problem
      • poli.objective_repository.troglitazone_rediscovery
        • poli.objective_repository.troglitazone_rediscovery.register
      • poli.objective_repository.valsartan_smarts
        • poli.objective_repository.valsartan_smarts.register
      • poli.objective_repository.white_noise
        • poli.objective_repository.white_noise.register
      • poli.objective_repository.zaleplon_mpo
        • poli.objective_repository.zaleplon_mpo.register

Bibliography

  • References

Appendix: Understanding foldx

  • Installing foldx
  • Computing the energy of a protein and a single mutation
  • Repository
  • Open issue
  • .rst

poli.objective_repository.scaffold_hop

poli.objective_repository.scaffold_hop#

Modules

poli.objective_repository.scaffold_hop.information

poli.objective_repository.scaffold_hop.register

Implements the Scaffold HOP task using the TDC oracles [1].

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poli.objective_repository.scaffold_hop.information

By Center for Basic Machine Learning Research in Life Science

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