# Worked domain examples

The repository's `examples/` directory contains complete, runnable
scripts that apply Mergen end to end in several fields. Each is
self-contained and produces a design, a quality report, and plots.
They are the fastest way to see the whole workflow on a realistic
problem close to your own.

## Wet-lab biology

An enzyme-assay design over pH, incubation temperature, buffer type,
and substrate concentration. Buffer type is a nominal factor, so the
design is scored with $\mathrm{MaxPro_{QQ}}$; a held-out validation set is
reserved for checking the fitted response on unseen conditions. See
`examples/11_wetlab_biology.py`.

## CFD engineering

A computational-fluid-dynamics parameter study on a purely numeric,
continuous space, illustrating a projection-based criterion where any
subset of the inputs may drive the response. See
`examples/12_cfd_engineering.py`.

## Machine-learning hyperparameters

A hyperparameter design over learning rate, batch size, optimiser, and
weight decay. The learning rate is placed on a logarithmic ladder of
explicit levels and the optimiser is a nominal factor, so a QQ-type
criterion is used. See `examples/13_ml_hyperparameters.py`.

## High-energy physics phenomenology

A parameter scan of a beyond-the-Standard-Model two-Higgs-doublet
model, the kind of high-dimensional, constrained scan for which
space-filling coverage is essential. See
`examples/14_bsm_2hdm_phenomenology.py`.

## Accelerator beamline optics

A beamline-optics tuning design, showing Mergen on an
instrument-configuration problem. See
`examples/15_beamline_optics.py`.

## The full set

| Script | Focus |
|---|---|
| `01_quickstart.py` | The five-statement workflow, end to end |
| `02_parameter_types.py` | All five factor types in one space |
| `03_advanced_design.py` | Prescribed points, focus region, exclusion zone |
| `04_choosing_criteria.py` | `compare()` across criteria, saving the winner |
| `05_choosing_algorithm.py` | One criterion, three optimisers, score vs time |
| `06_sample_size.py` | Budget choices around the 10 x d guideline |
| `07_extra_sets.py` | External labelled sets and validation hold-outs |
| `08_resume_existing.py` | `load_design`: reusing a previous campaign |
| `09_sequential_workflow.py` | extend, run_order, subsample, k_fold_split |
| `10_outputs_and_reports.py` | Every export format and the quality report |
| `11_wetlab_biology.py` | Enzyme assay with a nominal buffer factor |
| `12_cfd_engineering.py` | Continuous CFD parameter study |
| `13_ml_hyperparameters.py` | Log-ladder learning rate, nominal optimiser |
| `14_bsm_2hdm_phenomenology.py` | Constrained high-dimensional physics scan |
| `15_beamline_optics.py` | Instrument-configuration tuning |

## Running them

Each script runs directly:

```bash
python examples/11_wetlab_biology.py
```

The lower-numbered scripts (`01` through `10`) build up the same
features tutorial by tutorial, from the quickstart to full export and
reporting.