PertEval-scFM evaluation of the MLP baseline (raw-expression input) on the Norman single-gene, 2,000-HVG, SPECTRA-sparsification AUSPC protocol.
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1 evaluation · 1 result. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: MLP baseline (raw control expression + gene co-expression input, Eq. 3) | Protocol: PertEval-scFM Norman single-gene (2,000 HVGs) AUSPC across SPECTRA sparsification splits Dataset subset: Norman et al. 2019 single-gene perturbations, K562, top 2,000 HVGs (PertEval-scFM Table 1) | 4.484 ± 0.299 AUSPC 10^-2 (printed column header units) · lower Uncertainty: type: author_reported_propagated_standard_error; reported spread: 0.299; note: The source describes this quantity as a standard error (main-text Figure 2 caption: 'Average AUSPC (down-arrow) across sparsification probabilities for each model with standard error bars') and separately gives its own propagation formula (Appendix F.2, Eqs. F3-F5): AUSPC's uncertainty is derived from each split's own MSE uncertainty via the trapezoidal integral's partial derivatives (sigma^2 = sum_i (d/2)^2 * sigma_phi_i^2, where d=0.1 is the fixed sparsification step size). These two author statements describe the same quantity and are not in conflict: a propagated quantity can correctly be reported as a standard error. This is recorded as the author's own reported, propagated uncertainty; the F3-F5 derivation is the authors' own formula and its mathematical correctness has not been independently validated here. It must not be read as an independently resampled model-seed standard deviation or a confidence interval. The underlying per-split uncertainty is attributed by the source to triplicate experiments per model (Appendix I, Figure I1 caption: 'Experiments were carried out in triplicate for each model'), not to the main-text Figure 2 region. Figure I1's own caption separately states '8 train-test splits of increasing difficulty' for this same Norman single-gene evaluation, while Table 1 prints seven S-columns (S0.1-S0.7) and Appendix F.2 describes the sparsification probabilities as spanning 0.1 to 0.7. This 7-vs-8 discrepancy between the Figure I1 caption and the Table 1 / F.2 grid is preserved exactly as printed, not resolved; it must not be read as establishing an eighth Table 1 column or a confirmed n_runs=7, and no significance claim is made from any overlapping error bars. Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMLP baseline on PertEval-scFM Norman single-gene (2,000 HVGs) AUSPC Trapezoidal-rule AUSPC of MSE, scored on the perturbation-effect delta=P-Xc (Eq. 5), across seven SPECTRA sparsification splits (s=0.1..0.7), Norman single-gene, 2,000 HVGs. Aggregation: Not reported PertEval-scFM (Wenteler et al., ICML 2025), full text · Table 1, Norman single-gene section, row MLP baseline, column AUSPC (10^-2). |
Source checking is not independent reproduction. Release 2026-10-07-1448159e6a81.
Trapezoidal-rule AUSPC of MSE, scored on the perturbation-effect delta=P-Xc (Eq. 5), across seven SPECTRA sparsification splits (s=0.1..0.7), Norman single-gene, 2,000 HVGs.
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14 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.adaptation 1-hidden-layer MLP probe; input ZGE = Xc (+) Gc (Eq. 3), concatenating raw control expression with perturbed-gene co-expression features, not raw expression alone; same architecture family as the scFM-embedding probes but without an scFM embedding. Context-only references | PertEval-scFM (Wenteler et al., ICML 2025), full text Table 1, row MLP baseline, Norman single-gene section, column AUSPC (10^-2). Version: PMLR v267 wenteler25a (as served by the PMLR-affiliated mlresearch/v267 GitHub mirror; ETag "ed9f0fe44cf6edc939ee6950d024f65dcd8dd6f16414bd9f5297cda9395d6e58" at retrieval) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.metric_implementation AUSPC (trapezoidal-rule integral of MSE across seven SPECTRA sparsification-probability train-test splits, s=0.1..0.7; Appendix F.2 Eq. F2) Context-only references | PertEval-scFM (Wenteler et al., ICML 2025), full text Table 1, row MLP baseline, Norman single-gene section, column AUSPC (10^-2). Version: PMLR v267 wenteler25a (as served by the PMLR-affiliated mlresearch/v267 GitHub mirror; ETag "ed9f0fe44cf6edc939ee6950d024f65dcd8dd6f16414bd9f5297cda9395d6e58" at retrieval) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.protocol_id perteval-scfm-2025-protocol-norman-single-2000hvg-auspc Context-only references | PertEval-scFM (Wenteler et al., ICML 2025), full text Table 1, row MLP baseline, Norman single-gene section, column AUSPC (10^-2). Version: PMLR v267 wenteler25a (as served by the PMLR-affiliated mlresearch/v267 GitHub mirror; ETag "ed9f0fe44cf6edc939ee6950d024f65dcd8dd6f16414bd9f5297cda9395d6e58" at retrieval) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.evidence_overlap Independent of the GEARS Supplementary Table 6 catalogue entries for this use case. Context-only references | PertEval-scFM (Wenteler et al., ICML 2025), full text Table 1, row MLP baseline, Norman single-gene section, column AUSPC (10^-2). Version: PMLR v267 wenteler25a (as served by the PMLR-affiliated mlresearch/v267 GitHub mirror; ETag "ed9f0fe44cf6edc939ee6950d024f65dcd8dd6f16414bd9f5297cda9395d6e58" at retrieval) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.origin author_reported Context-only references | PertEval-scFM (Wenteler et al., ICML 2025), full text Table 1, row MLP baseline, Norman single-gene section, column AUSPC (10^-2). Version: PMLR v267 wenteler25a (as served by the PMLR-affiliated mlresearch/v267 GitHub mirror; ETag "ed9f0fe44cf6edc939ee6950d024f65dcd8dd6f16414bd9f5297cda9395d6e58" at retrieval) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.protocol Trapezoidal-rule AUSPC of MSE, scored on the perturbation-effect delta=P-Xc (Eq. 5), across seven SPECTRA sparsification splits (s=0.1..0.7), Norman single-gene, 2,000 HVGs. Context-only references | PertEval-scFM (Wenteler et al., ICML 2025), full text Table 1, row MLP baseline, Norman single-gene section, column AUSPC (10^-2). Version: PMLR v267 wenteler25a (as served by the PMLR-affiliated mlresearch/v267 GitHub mirror; ETag "ed9f0fe44cf6edc939ee6950d024f65dcd8dd6f16414bd9f5297cda9395d6e58" at retrieval) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.published_score_reproduction false Context-only references | PertEval-scFM (Wenteler et al., ICML 2025), full text Table 1, row MLP baseline, Norman single-gene section, column AUSPC (10^-2). Version: PMLR v267 wenteler25a (as served by the PMLR-affiliated mlresearch/v267 GitHub mirror; ETag "ed9f0fe44cf6edc939ee6950d024f65dcd8dd6f16414bd9f5297cda9395d6e58" at retrieval) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.source_locator Table 1, row MLP baseline, Norman single-gene section, column AUSPC (10^-2). Context-only references | PertEval-scFM (Wenteler et al., ICML 2025), full text Table 1, row MLP baseline, Norman single-gene section, column AUSPC (10^-2). Version: PMLR v267 wenteler25a (as served by the PMLR-affiliated mlresearch/v267 GitHub mirror; ETag "ed9f0fe44cf6edc939ee6950d024f65dcd8dd6f16414bd9f5297cda9395d6e58" at retrieval) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.suite_complete false Context-only references | PertEval-scFM (Wenteler et al., ICML 2025), full text Table 1, row MLP baseline, Norman single-gene section, column AUSPC (10^-2). Version: PMLR v267 wenteler25a (as served by the PMLR-affiliated mlresearch/v267 GitHub mirror; ETag "ed9f0fe44cf6edc939ee6950d024f65dcd8dd6f16414bd9f5297cda9395d6e58" at retrieval) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| description PertEval-scFM evaluation of the MLP baseline (raw-expression input) on the Norman single-gene, 2,000-HVG, SPECTRA-sparsification AUSPC protocol. Context-only references | PertEval-scFM (Wenteler et al., ICML 2025), full text Table 1, row MLP baseline, Norman single-gene section, column AUSPC (10^-2). Version: PMLR v267 wenteler25a (as served by the PMLR-affiliated mlresearch/v267 GitHub mirror; ETag "ed9f0fe44cf6edc939ee6950d024f65dcd8dd6f16414bd9f5297cda9395d6e58" at retrieval) | not individually reviewed No individual claim review recorded author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
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Release 2026-10-07-1448159e6a81 · Record review: source checked
Stable ID: perteval-scfm-2025-evaluation-mlp-baseline