Question
perturb.seq.align.q1.ref.h5ad contains a scRNA-seq matrix from a small scale Perturb-seq experiment in a cell type. perturb.seq.align.q1.query.h5ad contains a scRNA-seq matrix from a Perturb-seq experiment using the same guides in a different cell type. However, the targets of the guides are missing. Can you find the guides corresponding to the following target genes: PABPC1, NUDT21, LEO1. Return the answer as a comma separate list in the format: "guide1,guide2,guide3".
- Inferred answer
guide18,guide13,guide14Uniquely inferred from submitted scores.
- Domain
- Single-cell
- Question style
- Metadata Recovery
An answer can be uniquely inferred for 54 of 100 questions from submitted scores. Green: correct · Red: incorrect. For questions without a uniquely determined answer: Blue: matches prediction · Orange: differs from prediction. These are inferred answer checks, not official per-question grades.
Galaxy
12/12 terminal item results
UDT = user-defined tool: custom code executed by Galaxy. Route badges summarize analysis tools, excluding uploads and automatic conversions. How usage is counted.
Codex GPT-5.5
3 replicates
Codex GPT-5.5
Replicate 1
CorrectUDT + standard tools
Answerguide18,guide13,guide14
WorkflowAnndata Export→H5AD metadata diagnostic→Perturb-seq guide alignment→H5AD matrix scale diagnostic→H5AD structure diagnostic
Codex GPT-5.5
Replicate 2
RerunCorrectUDT-only
Answerguide18,guide13,guide14
WorkflowPerturb-seq guide target lookup→Perturb-seq guide target lookup metadata→Perturb-seq guide lookup diagnostics→Perturb-seq signature guide alignment→Perturb-seq signature guide alignment report→1 more tools
- Total tokens
- 920.0K
- Output
- 17.3K
Codex GPT-5.5
Replicate 3
RerunIncorrectUDT-only
Answerguide16,guide15,guide14
WorkflowPerturb guide target metadata map q1→Perturb guide target metadata map q1 v2→Perturb signature guide alignment q1→Perturb signature guide alignment q1 v2→Perturb global guide alignment q1→3 more tools
- Total tokens
- 1.7M
- Output
- 25.8K
Codex GPT-5.6 Sol
3 replicates
Codex GPT-5.6 Sol
Replicate 1
CorrectUDT + standard tools
Answerguide18,guide13,guide14
WorkflowAnndata Inspect→Perturb-seq alignment diagnostic→Perturb-seq signature alignment
- Total tokens
- 2.4M
- Output
- 17.5K
Codex GPT-5.6 Sol
Replicate 2
CorrectUDT + standard tools
Answerguide18,guide13,guide14
WorkflowAnndata Inspect→SciPy→AnnData→Perturb-seq target knockdown diagnostic→Grep→5 more tools
- Total tokens
- 7.7M
- Output
- 28.9K
Codex GPT-5.6 Sol
Replicate 3
CorrectUDT + standard tools
Answerguide18,guide13,guide14
WorkflowAnndata Inspect→Perturb-seq cross-cell-type alignment diagnostic→Perturb-seq validated guide assignment
- Total tokens
- 3.5M
- Output
- 15.1K
Codex + DeepSeek-v4-pro-0813
3 replicates
Codex + DeepSeek-v4-pro-0813
Replicate 1
CorrectUDT + standard tools
Answerguide18,guide13,guide14
WorkflowAnndata Inspect→Anndata Export→Probe Python 3.11→AnnData→Probe Path→3 more tools
- Total tokens
- 6.3M
- Output
- 49.0K
Codex + DeepSeek-v4-pro-0813
Replicate 2
CorrectUDT + standard tools
Answerguide18,guide13,guide14
WorkflowAnndata Inspect→SciPy→Perturb Probe Minimal→Import Probe→Perturb Seq Guide Alignment→1 more tools
- Total tokens
- 11.4M
- Output
- 54.2K
Codex + DeepSeek-v4-pro-0813
Replicate 3
CorrectUDT + standard tools
Answerguide18,guide13,guide14
WorkflowAnndata Inspect→Anndata Export→Group and aggregate→SciPy→AnnData→1 more tools
- Total tokens
- 7.5M
- Output
- 60.0K
Codex GPT-5.6 Luna
3 replicates
Codex GPT-5.6 Luna
Replicate 1
CorrectUDT + standard tools
Answerguide18,guide13,guide14
WorkflowAnndata Inspect→Filter Tabular→Group and aggregate→Grep→Scanpy Find Markers→3 more tools
- Total tokens
- 10.2M
- Output
- 48.0K
Codex GPT-5.6 Luna
Replicate 2
CorrectUDT + standard tools
Answerguide18,guide13,guide14
WorkflowAnndata Inspect→Filter Tabular→Filter rows→Group and aggregate→Select columns→11 more tools
- Total tokens
- 12.5M
- Output
- 77.1K
Codex GPT-5.6 Luna
Replicate 3
CorrectUDT + standard tools
Answerguide18,guide13,guide14
WorkflowAnndata Inspect→Guide match runtime probe→Guide match H5AD runtime probe→Guide match dependency probe→H5AD structure probe→7 more tools