[WIP] Update ablation runner to support additional Tox21 assays

[Copilot]

Thanks for asking me to work on this. I will get started on it and keep this PR's description up to date as I form a plan and make progress.

Update the ablation runner so it can generate ablation results for the other 6 Tox21 assays in the repository, not just the default NR.AhR assay. The current script src/ablation/run_ablation.py already accepts an --assay argument and loads assay-specific files named S_<assay>_tr.csv and S_<assay>_te.csv, but it only runs a single assay per invocation and writes outputs into a shared results directory. Improve the workflow so it is easy to produce ablation results for the six additional Tox21 assays similar to the existing NR.AhR ablation results.

Requirements:

• Preserve the existing single-assay behavior for --assay.
• Add a convenient way to run the ablation pipeline across multiple assays in one invocation, or otherwise provide an ergonomic and reproducible mechanism for generating ablation results for the 6 other Tox21 assays.
• Ensure outputs are organized per assay so results do not overwrite each other.
• Keep the existing ablation metrics and LaTeX/table generation behavior.
• If needed, update documentation or usage comments so it is clear how to run ablations for all supported Tox21 assays.
• The supported assays should include the remaining Tox21 assays beyond NR.AhR, such as NR.AR, NR.AR-LBD, NR.ARE, NR.Aromatase, NR.ER, and NR.ER-LBD.

The following is the prior conversation context from the user's chat exploration (may be truncated):

User: from where did we get the ablation results for the nr ahr assay

Assistant: The NR-AhR ablation results come from the repo’s ablation pipeline, specifically src/ablation/run_ablation.py, which loads the NR-AhR train/test CSVs, runs the model variants under 5-fold stratified CV, and exports the summary table. The paper/LaTeX table is generated from that same output in paper/main_filled.tex and src/ablation/results/paper_table.tex. The key source files are:

load_data(data_root: str, assay: str = "NR.AhR"):
    train_path = os.path.join(data_root, f"S_{assay}_tr.csv")
    test_path  = os.path.join(data_root, f"S_{assay}_te.csv")

    raw = pd.read_csv(train_path).values
    y_full = (raw[:, -1] == 1).astype(int)
    X_raw  = np.maximum(raw[:, :-1], 0)            # clip SMOTE negatives

    raw_te = pd.read_csv(test_path).values
    y_test = (raw_te[:, -1] == 1).astype(int)
    X_test = np.maximum(raw_te[:, :-1], 0)

\caption{Ablation results on Tox21 NR-AhR (5-fold Stratified CV, mean $\pm$ std).}
...
Single MLP & 0.9030 $\pm$ 0.0108 & 0.6265 $\pm$ 0.0503 & ...

\caption{Main ablation results on Tox21 NR-AhR (5-fold Stratified CV, mean $\pm$ std).}

So if you’re asking “where did we get them?”: from the NR-AhR training/test CSVs in data/, processed by run_ablation.py, then summarized into the paper tables.

If you want, I can also trace the exact script path that generates the ablation CSVs and identify which metric file contains the final NR-AhR numbers.

User: i want it for other 6 tox 21 assays similary the ablation results

Assistant: Yes — the same ablation pipeline supports the other Tox21 assays too.

Use the --assay flag in src/ablation/run_ablation.py:

python src/ablation/run_ablation.py --assay NR.AR
python src/ablation/run_ablation.py --assay NR.AR-LBD
python src/ablation/run_ablation.py --assay NR.ARE
python src/ablation/run_ablation.py --assay NR.Aromatase
python src/ablation/run_ablation.py --assay NR.ER
python src/ablation/run_ablation.py --assay NR.ER-LBD

The script reads assay-specific files here:

train_path = os.path.join(data_root, f"S_{assay}_tr.csv")
test_path  = os.path.join(data_root, f"S_{assay}_te.csv")

So for each assay, it expects matching S_<assay>_tr.csv and S_<assay>_te.csv files in data/.

A couple of notes:

• The default assay is NR.AhR.
• The current script writes results to src/ablation/results/, so if you run multiple assays, you’ll want to rename or move the outputs between runs to avoid overwriting.
• The ablation table format is the same: ROC-AUC, PR-AUC, F1, MCC, ECE, Brier.

If you want, I can also help you make this script automatically loop over all 6 NR assays and save each assay’s ablation results into separate folders.

User: yes

Assistant: I’m waiting for your confirmation to continue.