Comparator predictions on the tan70 test fold
This directory carries per-compound prediction probabilities for the two external comparators used in the reverse-leak audit and the head-to-head comparison (manuscript Tables 3, 3b, S2, S3, and Figure 4).
| file | comparator | citation |
|---|---|---|
ctoxpred2_tan70_predictions.csv |
CToxPred2 | Arab et al. 2024 — https://github.com/issararab/CToxPred2 |
cardiogenai_tan70_predictions.csv |
CardioGenAI | Kyro et al. 2025 — https://github.com/gregory-kyro/CardioGenAI |
Both files were generated by running each comparator's released code with
its default checkpoints on the tan70 test fold SMILES from this repository
(data/compounds/compounds.csv joined to data/splits/tan70.csv on
row_idx). The reverse-leak audit (manuscript line 199 and following) is
computed against the InChI-keys in these files vs. each comparator's
training-set InChI-keys.
Schema (both files)
| column | dtype | notes |
|---|---|---|
row_idx |
int | canonical row index — joins to data/compounds/compounds.csv and data/labels/labels_v1.csv |
inchikey |
str | 27-character standard InChI-key (duplicated here so this file is self-contained) |
valid |
bool | did the comparator successfully score this compound? (compounds that fail comparator-specific SMILES parsing get valid=false and the prob columns are filled with whatever the comparator emitted — usually NaN or 0.0) |
herg_prob |
float | hERG blocker probability (post-sigmoid output of the comparator) |
nav15_prob |
float | Nav1.5 blocker probability |
cav12_prob |
float | Cav1.2 blocker probability |
All probabilities are matched against the manuscript's deployed CardioSafe
output thresholds (default = 0.5) for the head-to-head MCC computation.
The hERG probability head from both comparators is trained at the 10 µM
threshold, so it is compared against our herg_blocker_10um label; the
1 µM CardioSafe head has no direct comparator equivalent (see Table S2
hERG 1 µM rows: the comparator probability is used for both 10 µM and 1 µM
matched against our respective ground truths, by paper convention).
Coverage
| comparator | n total | n valid |
|---|---|---|
| CToxPred2 | 46,326 | 46,326 |
| CardioGenAI | 46,326 | 46,230 |
(CardioGenAI fails to score 96 of the 46,326 tan70 test compounds — these are filtered out before any aggregate metric computation.)
Reproducing the head-to-head numbers
Tables S2 and S3 (the comparator panels pre- and post-de-leak) are built
on top of these CSVs. The full paired-bootstrap output is shipped at
data/supplementary/tables_s2_s3_paired_bootstrap.json so you can verify
the aggregated numbers without re-running the bootstrap.