Differential expression classification benchmark for perturbation models (Sun et al. 2026)
Three-class (non-DE, up, down) differential expression prediction for unseen genetic perturbations within a cell line and for seen perturbations in a held-out cell line, on K562, RPE1, HepG2 and Jurkat essential-gene Perturb-seq screens.
Results are recorded on the linked protocols, tasks or configurations listed below. Their settings and evaluations are kept separate.
Overview
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Results on linked records
This benchmark has no results of its own in this release. 2 linked records have results. They are not assigned to the underlying benchmark: each record keeps its own settings and evaluations, and its scores are on its own page.
- Sun et al. 2026 cellular-context DE classification (cross cell line) Protocol · part of this benchmark · 45 evaluations · 90 results
- Sun et al. 2026 unseen-perturbation DE classification (within cell line) Protocol · part of this benchmark · 40 evaluations · 80 results
Methods and evaluation design
Procedure, tasks and evaluated configurations
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Baseline coverage
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0 of 4 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
Baseline status by linked protocol
- Sun et al. 2026 cellular-context DE classification (cross cell line) · 0/2 roles measured
- Sun et al. 2026 unseen-perturbation DE classification (within cell line) · 0/2 roles measured
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-23-5347695500ed. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
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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
- Beyond Expression Prediction: Benchmarking Differential Expression Classification in Single-Cell Perturbation Models · Original source · bioRxiv preprint version 1, posted 2026-07-24
Technical metadata and extraction receipts
Stable ID: lit-cells-networks-20261011-sun2026de-benchmark-de-classification
- areas
- single-cell
- contexts
- research
- entity level
- suite
- version
- bioRxiv v1 (2026-07-24)
- task
- Prediction of differential expression status after genetic perturbation
- scope note
- DE labels from Wilcoxon rank-sum tests with Benjamini-Hochberg correction per perturbation (adjusted p < 0.01) on observed and predicted expression alike.
- source locator
- Sections 1, 3.1-3.3; Tables 1-5