MLP baseline (raw control expression + gene co-expression input, Eq. 3)
A 1-hidden-layer MLP probe (same architecture family as the scFM-embedding probes, Eq. 4) whose input ZGE = Xc (+) Gc (Eq. 3) concatenates the log-normalized raw control-expression matrix Xc with a gene co-expression matrix Gc computed between the perturbed gene(s) and the highly variable genes -- not raw expression data alone. Isolates whether an scFM embedding adds information beyond this fixed, non-learned-embedding representation; distinct from the five scFM-embedding MLP probes (Geneformer/scBERT/scFoundation/scGPT/UCE) in the same table, which share this MLP architecture but take scFM-generated embeddings (Eq. 2) as input instead.
Overview
A 1-hidden-layer MLP probe (same architecture family as the scFM-embedding probes, Eq. 4) whose input ZGE = Xc (+) Gc (Eq. 3) concatenates the log-normalized raw control-expression matrix Xc with a gene co-expression matrix Gc computed between the perturbed gene(s) and the highly variable genes -- not raw expression data alone. Isolates whether an scFM embedding adds information beyond this fixed, non-learned-embedding representation; distinct from the five scFM-embedding MLP probes (Geneformer/scBERT/scFoundation/scGPT/UCE) in the same table, which share this MLP architecture but take scFM-generated embeddings (Eq. 2) as input instead.
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Evaluations and results
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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). |
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Release 2026-10-07-1448159e6a81 · Record review: source checked
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- PertEval-scFM (Wenteler et al., ICML 2025), full text · Original source · PMLR v267 wenteler25a (as served by the PMLR-affiliated mlresearch/v267 GitHub mirror; ETag "ed9f0fe44cf6edc939ee6950d024f65dcd8dd6f16414bd9f5297cda9395d6e58" at retrieval)
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Stable ID: perteval-scfm-2025-method-mlp-baseline
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- cells-spatial-multiomics
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- Table 1, row MLP baseline, Norman single-gene section; Section 2.1 ('Raw expression data', Eq. 3); Section 2.2 ('MLP baseline', Eq. 4).