Open Problems: Perturbation Prediction

NeurIPS competition & continuing benchmark for single-cell perturbation response prediction under distribution shift.

Composite

91.9

Experimental validation

Retrospective

Stages

Virtual Cell

Modalities

cross-modality

Task types

perturbation-prediction

Size

cells: 240,000
perturbations: 144

License

MIT

First release

2021-06

Last updated

2024-12

Official site

→ project page

Leaderboard

→ leaderboard

Dataset

→ dataset

Code / GitHub

→ repository

HuggingFace

→ HF

Paper

Predicting Cellular Responses to Novel Drug Perturbations at a Single-Cell Resolution · Hetzel L, Boehm S, Kilbertus N, et al. · 2022 · paper · doi:10.48550/arXiv.2204.13545 · 180 citations

Flags

none

Experts

Fabian Theis, Daniel Burkhardt, Malte Luecken

Groups

Open Problems Consortium, Helmholtz Munich (Theis Lab), CZI Science

Hosted by

Open Problems in Single-Cell Analysis, CZI Virtual Cell / CellxGene / VCC

Related benchmarks

CZ Virtual Cell Challenge, scPerturb, LINCS L1000 / CMap

Rubric (7-criterion)

rigor

coverage

maintenance

adoption

quality

accessibility

industry_relevance

Notes

Best-in-class rigor (Viash workflow, hidden test, NeurIPS track).

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