Skip to content

Commit 39e29fd

Browse files
jang1563claude
andcommitted
Complete file listings; drop non-reproducing ESM-IF1 rho
- README Project Structure tree now lists docs/SYSTEM_CARD.md and results/summary_risk_table.csv (were referenced but not in the tree) - HF dataset card file table now lists results/summary_risk_table.csv - HF card: removed Spearman rho = -0.27 from the ESM-IF1 null result. The published esmfold_validation.json per-sequence data (top-10 vs bottom-10 FSI designs) reproduces rho = -0.30, not -0.27; the headline null rests on Mann-Whitney p = 0.85, so the unverifiable secondary stat is dropped rather than published. Restated the MW test scope explicitly. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
1 parent 1ad85d3 commit 39e29fd

2 files changed

Lines changed: 5 additions & 2 deletions

File tree

README.md

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -388,9 +388,11 @@ narrow-model-safety-eval/
388388
├── slurm/ SLURM job scripts (Cayuga HPC)
389389
├── results/
390390
│ ├── figures/ Publication-quality figures (PNG/PDF)
391-
│ └── *.json Aggregate numerical results
391+
│ ├── *.json Aggregate numerical results
392+
│ └── summary_risk_table.csv 8-toxin summary (Hugging Face dataset preview)
392393
├── dashboard/app.py Interactive Streamlit visualization
393394
├── docs/
395+
│ ├── SYSTEM_CARD.md Evaluator-facing system card (metrics, audits, scope)
394396
│ ├── ARCHITECTURE.md Pipeline design rationale
395397
│ ├── DATA_CORRECTIONS.md Accession and annotation correction log
396398
│ ├── FSI_NUMBERING_AUDIT.md Residue-numbering audit

huggingface/README.md

Lines changed: 2 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -189,10 +189,11 @@ The two highest-FSI toxins (BoNT-A and Tetanus LC) both carry the highest physic
189189

190190
### ESM-IF1 structural compatibility (null result)
191191

192-
High-FSI sequences are **not** more backbone-compatible than low-FSI sequences (Mann-Whitney p = 0.85, Spearman ρ = −0.27). This null result confirms that the functional recovery signal captured by FSI is driven by sequence-level constraint at catalytic positions, not by overall structural fitness — important for ruling out a confounder that high-FSI designs might simply be "easier" sequences.
192+
High-FSI sequences are **not** more backbone-compatible than low-FSI sequences (Mann-Whitney p = 0.85 on per-residue ESM-IF1 log-likelihood, top-10 vs bottom-10 FSI designs). This null result confirms that the functional recovery signal captured by FSI is driven by sequence-level constraint at catalytic positions, not by overall structural fitness — important for ruling out a confounder that high-FSI designs might simply be "easier" sequences.
193193

194194
| File | Description |
195195
|------|-------------|
196+
| `results/summary_risk_table.csv` | Curated 8-toxin summary (FSI, FSPE, realizability tier) — powers the dataset preview |
196197
| `results/separability_results.json` | AUROC, accuracy, Precision@k, t-SNE coordinates |
197198
| `results/fspe_results.json` | Per-protein FSPE ratios and entropy distributions |
198199
| `results/fsi_results.json` | Per-design FSI values for all FSI-scored structures |

0 commit comments

Comments
 (0)