Repository Structure

UDS-BOPE/
├── acquisition.py              # Acquisition functions (Random, UCB, EI, LLM-EI)
├── model.py                    # Gaussian Process models (standard GP, preference GP)
├── preference_BO.py            # Preference-guided BO for BH datasets
├── run_amide_coupling_bo.py    # Amide coupling BO workflow
├── amide_llm_interface.py      # LLM interface for amide reactions
└── LLM_survey/                 # Survey generation and execution
    ├── run_llm_survey_BH.py    # Buchwald-Hartwig survey
    ├── run_llm_survey_DA.py    # Direct arylation survey
    └── utils.py                # LLM utilities

Usage

Running Complete BO Workflow

Buchwald-Hartwig datasets (BH1-5):

python preference_BO.py --n_trials 50 --n_start 1 --acc 0.7 --m 100 --beta 2.0

Amide Coupling datasets:

python run_amide_coupling_bo.py --n_trials 50 --n_start 1 --acc 0.8 --m 100 --beta 2.0

Arguments:

• --n_trials: Number of independent BO runs (default: 50)
• --n_start: Number of initial random observations (default: 1)
• --acc: LLM survey accuracy for synthetic preference data (default: 0.7-0.8)
• --m: Number of pairwise comparisons (default: 100)
• --beta: Exploration parameter (not used in LLM-EI)

Running LLM Surveys

python LLM_survey/run_llm_survey_BH.py \
    --questions questions.pkl \
    --exp_database dataset.csv \
    --res_dir results/ \
    --llm_result survey_results.csv \
    --model_type 0

Model types: 0=Claude 3.5 Sonnet, 1=Claude 3 Sonnet, 2=Claude 3 Haiku

Installation

Install Dependencies

pip install -r requirements.txt

Verify Licenses

To check all installed package licenses:

pip install pip-licenses
pip-licenses --format=markdown

For detailed license information, see DEPENDENCIES.md.

License

See the LICENSE file for details.