Result provenance and manuscript changes
The original Hugging Face revision is recorded in reproducibility/upstream.json. Original experiment JSON files and trained checkpoints are preserved. The draft reports those measurements with their original preprocessing scope; corrected full-scale tables remain unfilled.
| Manuscript comparison | Source result records |
|---|---|
| Response accuracy and baseline comparison | norman_benchmark.json, norman_distloss.json |
| Single-gene nomination | norman_benchmark.json, norman_nom_improved.json |
| Pair retrieval and residual correlation | norman_combinatorial.json, norman_extra_ablations.json, norman_timing_scaling.json |
| GEARS response and ranking | pivot_vs_gears.json, gears_ranking.json |
| Loss components | norman_ablation_components.json |
| Reward and guidance sweeps | norman_ablation_reward.json, norman_ablation_guidance_steps.json |
| Larger single-gene catalog | replogle_k562_nom_improved.json |
Numerical records are in results/legacy/. The original source is in reproducibility/original_source.zip. It includes the historical GEARS workflows. Extract it into a separate directory when reproducing those experiments and use the corresponding original preprocessing. Historical model weights cannot be loaded with a corrected cache.
The manuscript now leads with population matching and held-out pair nomination. It retains additive ranking and the cell-conditional MLP because they are necessary comparisons for those claims. Secondary experiments and detailed implementation differences appear in the appendix.
Substantive corrections:
- PCA is a lossy projection with an affine reconstruction. Historical expression error and DE correlation used reconstructed observed expression as well as reconstructed predictions.
- Feature selection and PCA were fitted before splitting. Some evaluation routines pooled all cells carrying a test label, creating training-cell overlap in the cell-holdout analysis.
- The original semigroup branch used a state interpolated at a different starting time. The corrected branch recomputes the source state at its sampled time.
- The default historical DE correlation used 20 selected coordinates. It differs from GEARS Pearson correlation on absolute expression.
- The GEARS nomination task used 21 targets and 101 single-gene candidates; PIVOT used 22 and 105. Pair candidate pools were 128 and 131, respectively.
- Several earlier significance statements referred to Top-1 while the underlying calculations used Top-5. Two summary records disagreed on a random-comparison bootstrap result. The draft uses recovery counts and the stored interval without those significance claims.
- Effect clusters are expression-derived groups. They do not establish pathway recovery. Their high random-recovery rate appears in the paper.
- Greedy search returned one set. The duplicated historical Top-5 proxy has been removed.
- The recorded pair residual correlation subtracts the fitted additive baseline from both predicted and observed effects. A confirmatory residual analysis should use independent single-gene response cells, residual MSE, and zero/shuffled residual controls.
- Guidance initialization, backward evaluations, and projection costs must be counted. A best-candidate initialization includes an exhaustive pass.
The shared Figure 1 is schematic. No synthetic performance curves or invented experimental measurements are included.