| # 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. |
|
|
