Question
differential.composition.q1.1.mtx.gz and differential.composition.q1.2.mtx.gz contain raw scRNA counts matrices derived from retinal samples of two individuals (one per file, each column is a unique barcode that passes QC). differential.composition.q1.genes.txt.gz is the list of common genes. One of the cell types is severely depleted in one of the two individuals. What is this cell type? Return only the name of the depleted cell type from this list: astrocyte, microglial cell, RPE cell, cone cell, rod cell, horizontal cell, bipolar cell, RGC, T cells, macrophage, Schwann cell, Pericyte, B cell, fibroblast, endothelial cell, muller glia cell.
- Predicted answer
horizontal cellMost likely answer for this question; not uniquely determined from submitted scores.
- Domain
- Single-cell
- Question style
- Synthetic/Augmented Data
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
Matches predictionUDT-only
Answerhorizontal cell
WorkflowRetina marker diagnostics→Retina composition marker analysis→Retina composition marker analysis v2→Retina composition HVG validation
Codex GPT-5.5
Replicate 2
Matches predictionUDT-only
Answerhorizontal cell
WorkflowRetina marker diagnostic→Retina depleted cell type final→Retina depleted cell type final v2
- Total tokens
- 487.6K
- Output
- 9.6K
Codex GPT-5.5
Replicate 3
Matches predictionUDT + standard tools
Answerhorizontal cell
WorkflowRetina marker depletion diagnostic→Retina marker diagnostic v2→Retina marker diagnostic v3→UDT copy probe v1→UDT copy probe v2→2 more tools
- Total tokens
- 7.2M
- Output
- 38.6K
Codex GPT-5.6 Sol
3 replicates
Codex GPT-5.6 Sol
Replicate 1
Matches predictionUDT-only
Answerhorizontal cell
WorkflowRetina composition diagnostic→Retina composition marker analysis→Retina composition focused check→Retina rare cell depth check
- Total tokens
- 1.6M
- Output
- 17.4K
Codex GPT-5.6 Sol
Replicate 2
Matches predictionUDT + standard tools
Answerhorizontal cell
WorkflowRetina composition input and marker diagnostic→Retina joint clustering and marker report→Retina MatrixMarket to preprocessed h5ad→Scanpy Cluster Reduce Dimension→Scanpy Find Markers→3 more tools
- Total tokens
- 4.8M
- Output
- 21.2K
Codex GPT-5.6 Sol
Replicate 3
Matches predictionUDT + standard tools
Answerhorizontal cell
WorkflowRetina candidate cell-type marker screen→Retina marker depletion comparison→Prepare retinal AnnData metadata→Anndata Import→Anndata Manipulate→8 more tools
- Total tokens
- 11.0M
- Output
- 27.1K
Codex + DeepSeek-v4-pro-0813
3 replicates
Codex + DeepSeek-v4-pro-0813
Replicate 1
RerunMatches predictionUDT + standard tools
Answerhorizontal cell
WorkflowSelect first→Cut→Import Anndata→Inspect AnnData→Scanpy normalize→11 more tools
- Total tokens
- 26.3M
- Output
- 87.1K
Codex + DeepSeek-v4-pro-0813
Replicate 2
Matches predictionStandard tools only
Answerhorizontal cell
WorkflowScanpy Read 10X→Scanpy Normalise Data→Scanpy Find Variable Genes→Scanpy Run Pca→Scanpy Compute Graph→4 more tools
- Total tokens
- 7.1M
- Output
- 45.7K
Codex + DeepSeek-v4-pro-0813
Replicate 3
Matches predictionStandard tools only
Answerhorizontal cell
WorkflowTp Text File With Recurring Lines
- Total tokens
- 24.9M
- Output
- 60.6K
Codex GPT-5.6 Luna
3 replicates
Codex GPT-5.6 Luna
Replicate 1
Matches predictionUDT-only
Answerhorizontal cell
WorkflowRetinal marker composition diagnostic→Retinal marker co-detection diagnostic→Retinal pseudo-bulk marker differential diagnostic→Retinal marker pair composition diagnostic→Retinal final core-marker composition comparison
- Total tokens
- 1.7M
- Output
- 33.9K
Codex GPT-5.6 Luna
Replicate 2
Matches predictionUDT-only
Answerhorizontal cell
WorkflowRetinal marker diagnostic→Retinal marker validation→Retinal depletion ranking
- Total tokens
- 2.6M
- Output
- 30.7K
Codex GPT-5.6 Luna
Replicate 3
Matches predictionUDT + standard tools
Answerhorizontal cell
WorkflowRetinal marker availability diagnostic→UDT representation probe→Tp Text File With Recurring Lines→Nl→Scipy Sparse→14 more tools
- Total tokens
- 23.3M
- Output
- 56.2K