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All objective functions

These are all the objective functions available on poli. Click on one of them to get a minimal working example of how to use it.

Toy problems

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:::{grid-item-card} White noise :link: ./using_poli/objective_repository/white_noise.html :columns: 6 White noise drawn from a unit Gaussian :::

:::{grid-item-card} Aloha :link: ./using_poli/objective_repository/aloha.html :columns: 6 A toy example about optimizing 5-letter words to spell "ALOHA" :::

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Small molecules

Most of our problems are based on the PMO benchmark, by Gao et al [TODO: add cite].

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:::{grid-item-card} Quantitative Estimate of Druglikeness (QED) :link: ./using_poli/objective_repository/rdkit_qed.html :columns: 6 Computing the QED using RDKit. :::

:::{grid-item-card} Log-solubility (LogP) :link: ./using_poli/objective_repository/rdkit_logp.html :columns: 6 Computing the log-quotient of solubilities using RDKit. :::

:::{grid-item-card} TDC oracles [WIP] :link: ./using_poli/objective_repository/tdc_oracles.html :columns: 6 Some of the oracles provided by the Therapeutics Data Commons. [WIP] :::

:::{grid-item-card} GuacaMol [WIP] :link: ./using_poli/objective_repository/tdc_oracles.html :columns: 6 Some of the oracles provided by GuacaMol. [WIP] :::

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Proteins

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:::{grid-item-card} Protein Stability (using foldx) :link: ./using_poli/objective_repository/foldx_stability.html :columns: 6 Stability of mutations of a wildtype using foldx :::

:::{grid-item-card} Protein SASA score (using foldx) :link: ./using_poli/objective_repository/foldx_sasa.html :columns: 6 Solvent accessibility of mutations of a wildtype using foldx :::

:::{grid-item-card} Protein Stability (using RaSP) [WIP] :link: ./using_poli/objective_repository/RaSP.html :columns: 6 Rapid Stability Predictions of single mutations from a wildtype. [WIP] :::

:::{grid-item-card} RFP Fluorescence Protein Stability (using lambo) :link: ./using_poli/objective_repository/foldx_rfp_lambo.html :columns: 6 LaMBO Fluorescence (RFP) by stability and solvent-accessible surface area. :::

:::{grid-item-card} GFP Fluorescence Protein Surrogate (using CBas) :link: ./using_poli/objective_repository/gfp_cbas.html :columns: 6 CBas Fluorescence (GFP) median brightness by latent encoding surrogate under the assumption that the encoder mean correlates sufficiently with target brightness. :::

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Other

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:::{grid-item-card} Mario jumps :link: ./using_poli/objective_repository/super_mario_bros.html :columns: 6 Optimizing the number of jumps on a Super Mario Bros level :::