Question
You are given a single cell transcriptomic counts data generated from primary human tumor samples from patients with lung cancer (lung.cancer.sc.h5ad). This file has been cleaned for doublets and low quality cells already. Each sample is from a patient with lung adenocarcinoma (LUAD) or lung squamous cell carcinoma (LUSC). Out of samples Patient_005, Patient_006, Patient_007, Patient_018, and Patient_040, identify the LUSC sample with the highest proportion of dendritic cells out of all cells in that sample? Secondly, what percentage, to the nearest 20 percent, of all non-immune cells across all samples are malignant basal cells from LUSC patients? Expected answer format: Patient_006;20.
- Inferred answer
Patient_018;40Uniquely inferred from submitted scores.
- Domain
- Single-cell
- Question style
- Routine Analysis
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
IncorrectUDT-only
AnswerPatient_018;20
WorkflowGalaxy dataset inspection
- Total tokens
- 7.1M
- Output
- 33.2K
Codex GPT-5.5
Replicate 2
CorrectUDT + standard tools
AnswerPatient_018;40
WorkflowAnndata Inspect→H5AD Diagnostic→H5AD Diagnostic Quay→H5AD Diagnostic Quay Simple→H5AD Diagnostic No Shell Vars→6 more tools
- Total tokens
- 6.3M
- Output
- 22.6K
Codex GPT-5.5
Replicate 3
Rerun ยท standard service (no fast)CorrectUDT-only
AnswerPatient_018;40
WorkflowH5AD obs diagnostic→H5AD structure diagnostic→Lung marker diagnostic→H5AD index preview→Lung final marker analysis
- Total tokens
- 2.0M
- Output
- 20.7K
Codex GPT-5.6 Sol
3 replicates
Codex GPT-5.6 Sol
Replicate 1
CorrectUDT + standard tools
AnswerPatient_018;40
WorkflowAnndata Inspect→Xlsx2Tsv→Lung source barcode mapping diagnostic→Lung source barcode mapping diagnostic v2→Lung source barcode mapping diagnostic v3→1 more tools
- Total tokens
- 8.8M
- Output
- 17.9K
Codex GPT-5.6 Sol
Replicate 2
CorrectUDT + standard tools
AnswerPatient_018;40
WorkflowAnndata Inspect→Lung cancer AnnData marker diagnostic→CellTypist lung reference prediction→CellTypist lung airway reference prediction→Aggregate lung annotation evidence→1 more tools
- Total tokens
- 5.1M
- Output
- 20.6K
Codex GPT-5.6 Sol
Replicate 3
CorrectUDT + standard tools
AnswerPatient_018;40
WorkflowAnndata Inspect→Lung cancer barcode mapping diagnostic→Lung cancer final cell composition counts
- Total tokens
- 4.0M
- Output
- 14.4K
Codex + DeepSeek-v4-pro-0813
3 replicates
Codex + DeepSeek-v4-pro-0813
Replicate 1
CorrectUDT + standard tools
AnswerPatient_018;40
WorkflowAnndata Inspect→Remove Beginning1→Group and aggregate→Lung cancer diagnostic→Lung cancer cluster analysis→1 more tools
- Total tokens
- 5.5M
- Output
- 44.1K
Codex + DeepSeek-v4-pro-0813
Replicate 2
IncorrectUDT + standard tools
AnswerPatient_018;20
WorkflowAnndata Inspect→Anndata Export→AnnData→Scanpy→SciPy
- Total tokens
- 18.6M
- Output
- 59.3K
Codex + DeepSeek-v4-pro-0813
Replicate 3
RerunCorrectUDT + standard tools
AnswerPatient_018;40
WorkflowAnnData inspection→Sample and marker counts→Cell-type signature scoring→Malignant basal-cell analysis
- Total tokens
- 8.2M
- Output
- 47.1K
Codex GPT-5.6 Luna
3 replicates
Codex GPT-5.6 Luna
Replicate 1
CorrectUDT-only
AnswerPatient_018;40
WorkflowLung cancer H5AD runtime probe→Lung cancer expression diagnostic→Lung cancer cluster diagnostic→Lung cancer cluster marker mapping→Lung cancer final proportion analysis→1 more tools
- Total tokens
- 6.3M
- Output
- 46.6K
Codex GPT-5.6 Luna
Replicate 2
CorrectUDT + standard tools
AnswerPatient_018;40
WorkflowAnndata Inspect→Lung runtime probe→Lung H5AD structure→Lung marker diagnostic→Lung marker summary→7 more tools
- Total tokens
- 14.6M
- Output
- 59.4K
Codex GPT-5.6 Luna
Replicate 3
CorrectUDT + standard tools
AnswerPatient_018;40
WorkflowH5AD inspection→Marker score diagnostic→Filter Tabular→Match lung cancer metadata→Match anonymized cell barcodes to source metadata→6 more tools
- Total tokens
- 11.3M
- Output
- 61.9K