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Beef up GaussianProcessSurrogate#745

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AdrianSosic wants to merge 162 commits intomainfrom
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Beef up GaussianProcessSurrogate#745
AdrianSosic wants to merge 162 commits intomainfrom
dev/gp

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@AdrianSosic AdrianSosic commented Feb 10, 2026

Rough agenda:

#743 (Cleanup)

  • Clean up GP code

#746 (GP Components)

  • Extract current GP setting into preset
  • Add EDBO / SMOOTHED_EDBO preset
  • Generalize kernel machinery into component machinery using generics
  • Add configurability for mean / likelihood
  • Turn current mean / noise factories into serializable classes using new generic mechanism
  • Add low-level support for gpytorch GP components

#747 (Index Kernel)

  • Add BayBE IndexKernel class
  • Add BayBE PositiveIndexKernel class

#763 (Kernel Arithmetic)

  • improved + and * operations for Kernels

#748 (Active Dimensions)

  • Enable active dimension control for kernels
  • Absorb hardcoded IndexKernel logic into kernel factory
  • Implement deprecation mechanism for breaking change

#776 (Kernel Factory Validation)

  • Ensure kernel factories check if they support their given parameters

#752 (CHEN Preset)

  • Add CHEN preset

#757 (BoTorch Preset)

  • Add BOTORCH preset

Must TODO

  • Add decorator for extending presets to apply mechanism they don't cover themselves (e.g. transfer learning)
  • Stratification for multitask likelihoods
  • Decide on new BayBE defaults (i.e. do we use BOTORCH, CHEN, etc, or some heuristic on top)
  • Documentation

Optional TODO

  • Add HVARFNER preset
  • Enable serialization for gpytorch GP components
  • Add preset Setting attribute

To be added but out of scope

  • Make optimizer configurable

AdrianSosic and others added 4 commits February 10, 2026 17:18
* Cleans up the `GaussianProcessSurrogate` class
* Adds transfer learning tests asserting that the mechanism works
regardless of which tasks are represented in the training data
@AdrianSosic AdrianSosic self-assigned this Feb 10, 2026
@AdrianSosic AdrianSosic added enhancement Expand / change existing functionality new feature New functionality on hold PR progress is awaiting for something else to continue refactor and removed on hold PR progress is awaiting for something else to continue labels Feb 10, 2026
AdrianSosic and others added 27 commits April 15, 2026 14:42
The new parameter kind validation step guards us
Until we are certain that we keep it
DevPR, parent is #745

Adds a validation mechanism to ensure kernel factories only produce
kernels for search spaces they are intended for.
This is achieved via a new `_ParameterKind` flag enum that factories can
use to signal which parameter types they support.
DevPR, parent is #745 

Add an adaptive hyper-prior for GP proposed in the paper: 
**Guanming Chen**, **Maximilian Fleck**, **Thijs Stuyver**. Leveraging
Hidden-Space Representations Effectively in Bayesian Optimization for
Experiment Design through Dimension-Aware Hyperpriors. ChemRxiv. 09
February 2026.
DOI: https://doi.org/10.26434/chemrxiv.10001986/v2

<img width="1203" height="439" alt="image"
src="https://github.com/user-attachments/assets/2e4cece7-103f-4f84-8b71-4c0eb3eabfed"
/>
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5 participants