Decoder (Cov) | configuration

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Evaluations and results

6 evaluations · 12 results. Different protocols are not a single leaderboard.

Sorted by Perturbench RMSE of mean (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	Protocol and dataset	Perturbench RMSE of mean	Perturbench RMSE rank	Perturbench cosine logfc	Perturbench cosine logfc rank	Perturbench matrix distance	Perturbench RMSE transposed rank
Decoder (Cov)Evaluation	PerturBench v4 covariate transfer to a held-out cell line on Srivatsan20, Srivatsan20 (PerturBench v4 covariate-transfer split)	0.023 ± 3 × 10 − 5 (best in column)	0.50 ± 4 × 10 − 2	0.30 ± 1 × 10 − 2 (best in column)	0.47 ± 9 × 10 − 3 (best in column)	Not reported	Not reported
Decoder (Cov)Evaluation	PerturBench CT-RMSE: covariate transfer on Srivatsan20, RMSE of the mean, Srivatsan20 (PerturBench split)	0.023 ± 3 × 10 − 5 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported
Decoder (Cov)Evaluation	PerturBench v4 mode-collapse diagnostics on Srivatsan20, Srivatsan20 (PerturBench v4 covariate-transfer split)	0.026	0.488 (best in column)	Not reported	Not reported	49.9	0.482
Decoder (Cov)Evaluation	PerturBench CT-COSINE: covariate transfer on Srivatsan20, Cosine similarity of log fold change, Srivatsan20 (PerturBench split)	Not reported	Not reported	0.30 ± 1 × 10 − 2 (best in column)	Not reported	Not reported	Not reported
Decoder (Cov)Evaluation	PerturBench CT-COSINE-RANK: covariate transfer on Srivatsan20, Cosine LogFC rank, Srivatsan20 (PerturBench split)	Not reported	Not reported	Not reported	0.47 ± 9 × 10 − 3 (best in column)	Not reported	Not reported
Decoder (Cov)Evaluation	PerturBench CT-RMSE-RANK: covariate transfer on Srivatsan20, RMSE mean rank, Srivatsan20 (PerturBench split)	Not reported	0.50 ± 4 × 10 − 2	Not reported	Not reported	Not reported	Not reported

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
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: 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: Decoder (Cov)	Protocol: PerturBench v4 covariate transfer to a held-out cell line on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.47 ± 9 × 10 − 3 Perturbench cosine logfc rank fraction · lower Uncertainty: SD 0.009 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Decoder (Cov) on PerturBench v4 srivatsan20 lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 2, row 'Decoder (Cov)', column 'Cosine LogFC rank'
Configuration: Decoder (Cov)	Protocol: PerturBench v4 covariate transfer to a held-out cell line on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.30 ± 1 × 10 − 2 Perturbench cosine logfc fraction · higher Uncertainty: SD 0.01 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Decoder (Cov) on PerturBench v4 srivatsan20 lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 2, row 'Decoder (Cov)', column 'Cosine LogFC'
Configuration: Decoder (Cov)	Protocol: PerturBench v4 covariate transfer to a held-out cell line on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.50 ± 4 × 10 − 2 Perturbench RMSE rank fraction · lower Uncertainty: SD 0.04 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Decoder (Cov) on PerturBench v4 srivatsan20 lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 5, row 'Decoder (Cov)', column 'RMSE mean rank'
Configuration: Decoder (Cov)	Protocol: PerturBench v4 covariate transfer to a held-out cell line on Srivatsan20 Dataset subset: Srivatsan20 (PerturBench v4 covariate-transfer split)	0.023 ± 3 × 10 − 5 Perturbench RMSE of mean unit-unreported · lower Uncertainty: SD 0.00003 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Decoder (Cov) on PerturBench v4 srivatsan20 lit-cells-networks-20261011-perturbench-v4-protocol-srivatsan20 Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis (arXiv v4) · Table 5, row 'Decoder (Cov)', column 'RMSE mean'
Configuration: Decoder (Cov)	Task: PerturBench CT-COSINE: covariate transfer on Srivatsan20, Cosine similarity of log fold change Dataset subset: Srivatsan20 (PerturBench split)	0.30 ± 1 × 10 − 2 Perturbench cosine logfc fraction · higher Uncertainty: SD 0.01 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Decoder (Cov) on PerturBench CT-COSINE: covariate transfer on Srivatsan20, Cosine similarity of log fold change Train on some cell types and predict drug effects in a held-out cell type, reported as the mean and one standard deviation over seeds. Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis · Table 2, row(Decoder (Cov)), column(Cosine, log fold change (LogFC))
Configuration: Decoder (Cov)	Task: PerturBench CT-COSINE-RANK: covariate transfer on Srivatsan20, Cosine LogFC rank Dataset subset: Srivatsan20 (PerturBench split)	0.47 ± 9 × 10 − 3 Perturbench cosine logfc rank fraction · lower Uncertainty: SD 0.009 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Decoder (Cov) on PerturBench CT-COSINE-RANK: covariate transfer on Srivatsan20, Cosine LogFC rank Train on some cell types and predict drug effects in a held-out cell type, reported as the mean and one standard deviation over seeds. Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis · Table 2, row(Decoder (Cov)), column(Cosine, LogFC rank)
Configuration: Decoder (Cov)	Task: PerturBench CT-RMSE-RANK: covariate transfer on Srivatsan20, RMSE mean rank Dataset subset: Srivatsan20 (PerturBench split)	0.50 ± 4 × 10 − 2 Perturbench RMSE rank fraction · lower Uncertainty: SD 0.04 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Decoder (Cov) on PerturBench CT-RMSE-RANK: covariate transfer on Srivatsan20, RMSE mean rank Train on some cell types and predict drug effects in a held-out cell type, reported as the mean and one standard deviation over seeds. Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis · Table 2, row(Decoder (Cov)), column(RMSE, mean rank)
Configuration: Decoder (Cov)	Task: PerturBench CT-RMSE: covariate transfer on Srivatsan20, RMSE of the mean Dataset subset: Srivatsan20 (PerturBench split)	0.023 ± 3 × 10 − 5 Perturbench RMSE of mean unit-unreported · lower Uncertainty: SD 0.00003 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Decoder (Cov) on PerturBench CT-RMSE: covariate transfer on Srivatsan20, RMSE of the mean Train on some cell types and predict drug effects in a held-out cell type, reported as the mean and one standard deviation over seeds. Aggregation: Not reported PerturBench: Benchmarking Machine Learning Models for Cellular Perturbation Analysis · Table 2, row(Decoder (Cov)), column(RMSE, mean)

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Stable ID: perturbench-method-decoder-cov

areas: cells-tissues
source locator: Table 2, row(Decoder (Cov))
missing metadata: checkpoint revision: reason: unreported; parameters: reason: unextracted

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