DecoderOnly (+ perturbations)
DecoderOnly (+ perturbations): Selected per dataset and task by Optuna HPO (at least 60 trials), then retrained with 5 seeds.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
1 evaluation · 4 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 |
|---|---|---|---|---|
| DecoderOnly (+ perturbations)Evaluation | 40.6 | 0.021 | 0.116 | 0.232 |
All 4 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| 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 checkedMethods, coverage and sourceDecoderOnly (+ 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 checkedMethods, coverage and sourceDecoderOnly (+ 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 checkedMethods, coverage and sourceDecoderOnly (+ 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 checkedMethods, coverage and sourceDecoderOnly (+ 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' |
Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.
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Evidence
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Evidence table
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Sources and history
Release 2026-10-23-5347695500ed · Record review: source checked
1 source record and release history
- 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)
Technical metadata and extraction receipts
Stable ID: lit-cells-networks-20261011-perturbench-v4-config-decoderonly-plus-perturbations
- areas
- single-cell
- contexts
- research
- method types
- supervised_machine_learning
- reported name
- DecoderOnly (+ perturbations)
- source locator
- Appendix C.7, Table 12
- foundation model eligible
- false
- hyperparameters
- Selected per dataset and task by Optuna HPO (at least 60 trials), then retrained with 5 seeds (Section 4.3)
- access reuse
- Code in the PerturBench repository (github.com/altoslabs/perturbench)
- missing metadata
- version: reason: unreported; note: No code commit is printed for the v4 runs
- provenance note
- PerturBench Decoder-only baseline with cell line and perturbations as input (Appendix C.7.1; Figure C.2B), as named in the mode-collapse Table 12. The source does not say whether this is the 'Decoder' row of Tables 2 and 5.