Published comparison transcribed from the pinned source; not reproduced.
1 evaluation · 7 results. Different protocols are not a single leaderboard.
Protocol: PerturBench v4 covariate transfer to held-out perturbations in held-out biological states on Jiang24 · Dataset subset: Jiang24 (PerturBench v4 covariate-transfer split)
Sorted by Perturbench cosine logfc (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Perturbench cosine logfc | Perturbench cosine logfc rank | Perturbench energy mmd (gene expression space) | Perturbench energy mmd (PCA space: top 256 principal components fitted on the ground-truth test split) | Perturbench RMSE of mean | Perturbench RMSE rank | Recall (DEG recall: fraction of the top 20 ground-truth DEGs (scanpy t-scores against controls) recalled from predicted cells) |
|---|---|---|---|---|---|---|---|
| SAMS-VAE*Evaluation | 0.59 ± 3 × 10 − 3 | 0.45 ± 9 × 10 − 3 | 4.5 ± 7 × 10 − 3 | 0.32 ± 5 × 10 − 3 | 0.017 ± 2 × 10 − 4 | 0.45 ± 6 × 10 − 3 | 0.000 ± 4 × 10 − 5 |
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: SAMS-VAE* | Protocol: PerturBench v4 covariate transfer to held-out perturbations in held-out biological states on Jiang24 Dataset subset: Jiang24 (PerturBench v4 covariate-transfer split) | 0.45 ± 9 × 10 − 3 Perturbench cosine logfc rank fraction · lower Uncertainty: SD 0.009 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSAMS-VAE ∗ on PerturBench v4 jiang24 lit-cells-networks-20261011-perturbench-v4-protocol-jiang24 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 4, row 'SAMS-VAE ∗', column 'Cosine LogFC rank' |
| Configuration: SAMS-VAE* | Protocol: PerturBench v4 covariate transfer to held-out perturbations in held-out biological states on Jiang24 Dataset subset: Jiang24 (PerturBench v4 covariate-transfer split) | 0.59 ± 3 × 10 − 3 Perturbench cosine logfc fraction · higher Uncertainty: SD 0.003 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSAMS-VAE ∗ on PerturBench v4 jiang24 lit-cells-networks-20261011-perturbench-v4-protocol-jiang24 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 4, row 'SAMS-VAE ∗', column 'Cosine logFC' |
| Configuration: SAMS-VAE* | Protocol: PerturBench v4 covariate transfer to held-out perturbations in held-out biological states on Jiang24 Dataset subset: Jiang24 (PerturBench v4 covariate-transfer split) | 0.000 ± 4 × 10 − 5 Recall (DEG recall: fraction of the top 20 ground-truth DEGs (scanpy t-scores against controls) recalled from predicted cells) fraction · higher Uncertainty: SD 0.00004 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSAMS-VAE ∗ on PerturBench v4 jiang24 lit-cells-networks-20261011-perturbench-v4-protocol-jiang24 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 4, row 'SAMS-VAE ∗', column 'DEG recall' |
| Configuration: SAMS-VAE* | Protocol: PerturBench v4 covariate transfer to held-out perturbations in held-out biological states on Jiang24 Dataset subset: Jiang24 (PerturBench v4 covariate-transfer split) | 0.32 ± 5 × 10 − 3 Perturbench energy mmd (PCA space: top 256 principal components fitted on the ground-truth test split) unit-unreported · lower Uncertainty: SD 0.005 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSAMS-VAE ∗ on PerturBench v4 jiang24 lit-cells-networks-20261011-perturbench-v4-protocol-jiang24 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 4, row 'SAMS-VAE ∗', column 'MMD PCA' |
| Configuration: SAMS-VAE* | Protocol: PerturBench v4 covariate transfer to held-out perturbations in held-out biological states on Jiang24 Dataset subset: Jiang24 (PerturBench v4 covariate-transfer split) | 4.5 ± 7 × 10 − 3 Perturbench energy mmd (gene expression space) unit-unreported · lower Uncertainty: SD 0.007 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSAMS-VAE ∗ on PerturBench v4 jiang24 lit-cells-networks-20261011-perturbench-v4-protocol-jiang24 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 11, row 'SAMS-VAE ∗', column 'MMD' |
| Configuration: SAMS-VAE* | Protocol: PerturBench v4 covariate transfer to held-out perturbations in held-out biological states on Jiang24 Dataset subset: Jiang24 (PerturBench v4 covariate-transfer split) | 0.45 ± 6 × 10 − 3 Perturbench RMSE rank fraction · lower Uncertainty: SD 0.006 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSAMS-VAE ∗ on PerturBench v4 jiang24 lit-cells-networks-20261011-perturbench-v4-protocol-jiang24 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 11, row 'SAMS-VAE ∗', column 'RMSE mean rank' |
| Configuration: SAMS-VAE* | Protocol: PerturBench v4 covariate transfer to held-out perturbations in held-out biological states on Jiang24 Dataset subset: Jiang24 (PerturBench v4 covariate-transfer split) | 0.017 ± 2 × 10 − 4 Perturbench RMSE of mean unit-unreported · lower Uncertainty: SD 0.0002 Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSAMS-VAE ∗ on PerturBench v4 jiang24 lit-cells-networks-20261011-perturbench-v4-protocol-jiang24 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 11, row 'SAMS-VAE ∗', column 'RMSE mean' |
Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.
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PerturBench v4 covariate transfer to held-out perturbations in held-out biological states on Jiang24
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18 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Comparison: adaptation Trained from scratch per dataset with HPO Context-only references | PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) Table 4, row 'SAMS-VAE ∗' Version: arXiv 2408.10609v4, posted 2025-10-24 (NeurIPS 2025 Datasets and Benchmarks Track version) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact bytes of the arXiv HTML rendering of v4 as retrieved; arXiv may regenerate HTML, so the hash describes this retrieval. |
| Comparison: aggregation Mean over 5 seeds Context-only references | PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) Table 4, row 'SAMS-VAE ∗' Version: arXiv 2408.10609v4, posted 2025-10-24 (NeurIPS 2025 Datasets and Benchmarks Track version) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact bytes of the arXiv HTML rendering of v4 as retrieved; arXiv may regenerate HTML, so the hash describes this retrieval. |
| Comparison: budget Optuna HPO, at least 60 trials Context-only references | PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) Table 4, row 'SAMS-VAE ∗' Version: arXiv 2408.10609v4, posted 2025-10-24 (NeurIPS 2025 Datasets and Benchmarks Track version) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact bytes of the arXiv HTML rendering of v4 as retrieved; arXiv may regenerate HTML, so the hash describes this retrieval. |
| Comparison: dataset version Not reported Context-only references | PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) Table 4, row 'SAMS-VAE ∗' Version: arXiv 2408.10609v4, posted 2025-10-24 (NeurIPS 2025 Datasets and Benchmarks Track version) | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact bytes of the arXiv HTML rendering of v4 as retrieved; arXiv may regenerate HTML, so the hash describes this retrieval. |
| Comparison: inputs Control cells with matched covariates and perturbation identity Context-only references | PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) Table 4, row 'SAMS-VAE ∗' Version: arXiv 2408.10609v4, posted 2025-10-24 (NeurIPS 2025 Datasets and Benchmarks Track version) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact bytes of the arXiv HTML rendering of v4 as retrieved; arXiv may regenerate HTML, so the hash describes this retrieval. |
| Comparison: metric implementation PerturBench evaluation module (Section 4.2) Context-only references | PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) Table 4, row 'SAMS-VAE ∗' Version: arXiv 2408.10609v4, posted 2025-10-24 (NeurIPS 2025 Datasets and Benchmarks Track version) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact bytes of the arXiv HTML rendering of v4 as retrieved; arXiv may regenerate HTML, so the hash describes this retrieval. |
| Comparison: population Not reported Context-only references | PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) Table 4, row 'SAMS-VAE ∗' Version: arXiv 2408.10609v4, posted 2025-10-24 (NeurIPS 2025 Datasets and Benchmarks Track version) | missing or unspecified No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact bytes of the arXiv HTML rendering of v4 as retrieved; arXiv may regenerate HTML, so the hash describes this retrieval. |
| Comparison: protocol id lit-cells-networks-20261011-perturbench-v4-protocol-jiang24 Context-only references | PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) Table 4, row 'SAMS-VAE ∗' Version: arXiv 2408.10609v4, posted 2025-10-24 (NeurIPS 2025 Datasets and Benchmarks Track version) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact bytes of the arXiv HTML rendering of v4 as retrieved; arXiv may regenerate HTML, so the hash describes this retrieval. |
| Comparison: split Jiang24 genetic perturbations across cell lines and cytokine treatments, with 70% of perturbations held out in some states. Context-only references | PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) Table 4, row 'SAMS-VAE ∗' Version: arXiv 2408.10609v4, posted 2025-10-24 (NeurIPS 2025 Datasets and Benchmarks Track version) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact bytes of the arXiv HTML rendering of v4 as retrieved; arXiv may regenerate HTML, so the hash describes this retrieval. |
| Origin independent_paper Context-only references | PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) Table 4, row 'SAMS-VAE ∗' Version: arXiv 2408.10609v4, posted 2025-10-24 (NeurIPS 2025 Datasets and Benchmarks Track version) | not individually reviewed No individual claim review recorded independent paper Audit detailsField: Source artifact SHA-256: Hash scope: Exact bytes of the arXiv HTML rendering of v4 as retrieved; arXiv may regenerate HTML, so the hash describes this retrieval. |
Release 2026-10-23-5347695500ed · Record review: source checked
Stable ID: lit-cells-networks-20261011-perturbench-v4-eval-jiang24-sams-vae