Protocol

PerturBench v4 mode-collapse diagnostics on Srivatsan20

Mode-collapse diagnostics on the Srivatsan20 covariate-transfer split: RMSE, RMSE rank, transposed rank and matrix distance between predicted and observed cosine similarity matrices.

5 evaluations · 20 results

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5 recorded evaluations, 20 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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5 evaluations · 20 results. Different protocols are not a single leaderboard.

Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 · Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)

Sorted by Perturbench matrix distance (lower 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 matrix distance	Perturbench RMSE of mean	Perturbench RMSE rank	Perturbench RMSE transposed rank
SAMS-VAE* (S)Evaluation	19.3 (best in column)	0.02 (best in column)	0.111	0.179 (best in column)
CPA* (noAdv)Evaluation	32.2	0.021	0.098 (best in column)	0.337
CPA*Evaluation	36.3	0.022	0.104	0.323
DecoderOnly (+ perturbations)Evaluation	40.6	0.021	0.116	0.232
Decoder (Cov)Evaluation	49.9	0.026	0.488	0.482

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CPA*	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	36.3 Perturbench matrix distance unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPA ∗ on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'CPA ∗', column 'Matrix distance'
Configuration: CPA* (noAdv)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	32.2 Perturbench matrix distance unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CPA ∗ (noAdv) on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'CPA ∗ (noAdv)', column 'Matrix distance'
Configuration: CPA* (noAdv)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.098 Perturbench RMSE rank fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CPA ∗ (noAdv) on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'CPA ∗ (noAdv)', column 'RMSE mean rank'
Configuration: CPA* (noAdv)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.021 Perturbench RMSE of mean unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CPA ∗ (noAdv) on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'CPA ∗ (noAdv)', column 'RMSE mean'
Configuration: CPA* (noAdv)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.337 Perturbench RMSE transposed rank fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source CPA ∗ (noAdv) on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'CPA ∗ (noAdv)', column 'RMSE mean transposed-rank'
Configuration: CPA*	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.104 Perturbench RMSE rank fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPA ∗ on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'CPA ∗', column 'RMSE mean rank'
Configuration: CPA*	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.022 Perturbench RMSE of mean unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPA ∗ on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'CPA ∗', column 'RMSE mean'
Configuration: CPA*	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.323 Perturbench RMSE transposed rank fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source CPA ∗ on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'CPA ∗', column 'RMSE mean transposed-rank'
Configuration: Decoder (Cov)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	49.9 Perturbench matrix distance unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DecoderOnly on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'DecoderOnly', column 'Matrix distance'
Configuration: DecoderOnly (+ perturbations)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	40.6 Perturbench matrix distance unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DecoderOnly (+ perturbations) on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'DecoderOnly (+ perturbations)', column 'Matrix distance'
Configuration: DecoderOnly (+ perturbations)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.116 Perturbench RMSE rank fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DecoderOnly (+ perturbations) on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'DecoderOnly (+ perturbations)', column 'RMSE mean rank'
Configuration: DecoderOnly (+ perturbations)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.021 Perturbench RMSE of mean unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DecoderOnly (+ perturbations) on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'DecoderOnly (+ perturbations)', column 'RMSE mean'
Configuration: DecoderOnly (+ perturbations)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.232 Perturbench RMSE transposed rank fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DecoderOnly (+ perturbations) on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'DecoderOnly (+ perturbations)', column 'RMSE mean transposed-rank'
Configuration: Decoder (Cov)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.488 Perturbench RMSE rank fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DecoderOnly on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'DecoderOnly', column 'RMSE mean rank'
Configuration: Decoder (Cov)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.026 Perturbench RMSE of mean unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DecoderOnly on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'DecoderOnly', column 'RMSE mean'
Configuration: Decoder (Cov)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.482 Perturbench RMSE transposed rank fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DecoderOnly on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'DecoderOnly', column 'RMSE mean transposed-rank'
Configuration: SAMS-VAE* (S)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	19.3 Perturbench matrix distance unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source SAMS-VAE ∗ (S) on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'SAMS-VAE ∗ (S)', column 'Matrix distance'
Configuration: SAMS-VAE* (S)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.111 Perturbench RMSE rank fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source SAMS-VAE ∗ (S) on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'SAMS-VAE ∗ (S)', column 'RMSE mean rank'
Configuration: SAMS-VAE* (S)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.02 Perturbench RMSE of mean unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source SAMS-VAE ∗ (S) on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'SAMS-VAE ∗ (S)', column 'RMSE mean'
Configuration: SAMS-VAE* (S)	Protocol: PerturBench v4 mode-collapse diagnostics on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.179 Perturbench RMSE transposed rank fraction · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source SAMS-VAE ∗ (S) on PerturBench v4 srivatsan20-collapse lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 12, row 'SAMS-VAE ∗ (S)', column 'RMSE mean transposed-rank'

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PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Original source · arXiv 2408.10609v4, posted 2025-10-24 (NeurIPS 2025 Datasets and Benchmarks Track version)

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Technical metadata and extraction receipts

Stable ID: lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20-mode-collapse

areas: single-cell
contexts: research
protocol: Mode-collapse diagnostics in Appendix C.7. Single values without spread; the number of runs behind each value is not printed.
version: PerturBench arXiv v4
metric: perturbench-matrix-distance
metric direction: lower
unit: unit-unreported
limitations: No spread or seed count is printed for these tables; values differ from the 5-seed means for the same models in Tables 5 and 8.
source locator: Table 12; Appendix C.7.1-C.7.2

Related records

part of: PerturBench
uses data: Srivatsan20 (PerturBench v4 covariate-transfer split)
assessment: CPA ∗ on PerturBench v4 srivatsan20-collapse
assessment: CPA ∗ (noAdv) on PerturBench v4 srivatsan20-collapse
assessment: DecoderOnly on PerturBench v4 srivatsan20-collapse
assessment: DecoderOnly (+ perturbations) on PerturBench v4 srivatsan20-collapse
assessment: SAMS-VAE ∗ (S) on PerturBench v4 srivatsan20-collapse

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