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CompBioBench item

subtype-inflammation-q1

Question

subtype.inflammation.q1.1.mtx.gz and subtype.inflammation.q1.2.mtx.gz contain raw scRNA counts matrices from retinal samples from two eyes of an individual (one per file, each column is a unique barcode that passes QC). subtype.inflammation.q1.genes.txt.gz is the list of common genes. One of the cell types is inflammed in one eye compared to the other. What is this cell type? Return only the name of the inflammed 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, muller glia cell, endothelial cell.

Predicted answer
muller glia 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
Answermuller glia cell
Workflow
Retina subtype inflammation analysisRetina matrix format diagnostic
Codex GPT-5.5

Replicate 2

Matches predictionUDT-only
Answermuller glia cell
Workflow
Retina marker diagnosticRetina inflammation classifierRetina glial validation
Total tokens
548.2K
Output
13.5K
Codex GPT-5.5

Replicate 3

Matches predictionUDT + standard tools
Answermuller glia cell
Workflow
Retina inflammation diagnosticUDT copy probeUDT copy probe python containerRemove Beginning1Anndata Import6 more tools
Total tokens
4.3M
Output
22.9K

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches predictionUDT-only
Answermuller glia cell
Workflow
Galaxy UDTretina_inflammationRetina inflammationRetina inflammation joint analysisRetina inflammation joint analysis v22 more tools
Total tokens
2.9M
Output
13.9K
Codex GPT-5.6 Sol

Replicate 2

Matches predictionUDT + standard tools
Answermuller glia cell
Workflow
Retina inflammation marker diagnosticRetina inflammation strict validationPrepare combined retinal AnnData inputsAnndata ImportPrepare combined retinal AnnData inputs corrected5 more tools
Total tokens
8.4M
Output
25.7K
Codex GPT-5.6 Sol

Replicate 3

Matches predictionUDT-only
Answermuller glia cell
Workflow
Retina inflammation marker diagnosticsRetina cell type inflammation full analysisRetina inflammation marker-gate validationRetina inflammation strict lineage validation
Total tokens
3.3M
Output
25.3K

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches predictionUDT + standard tools
Answermuller glia cell
Workflow
Tp Text File With Recurring LinesConvert Characters1NlSelect columnsAnndata Import8 more tools
Total tokens
25.1M
Output
50.2K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches predictionStandard tools only
Answermuller glia cell
Workflow
Scanpy Read 10XAnndata ManipulateAnndata InspectScanpy Normalise DataScanpy Find Variable Genes8 more tools
Total tokens
14.2M
Output
45.4K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches predictionUDT-only
Answermuller glia cell
Workflow
Probe Scanpy RuntimeRetina Inflammation DiagnosticProbe Install Cluster RuntimeRetina Inflammation Diagnostic FullRetina Marker Probe1 more tools
Total tokens
6.4M
Output
41.4K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches predictionUDT-only
Answermuller glia cell
Workflow
Retinal inflammation cell-type diagnosticRetinal inflammation refined validationRetinal inflammation refined validation v2Retinal inflammation final balanced validation
Total tokens
1.6M
Output
37.5K
Codex GPT-5.6 Luna

Replicate 2

Matches predictionUDT-only
Answermuller glia cell
Workflow
Retinal inflammation diagnosticRetinal inflammation focused cell analysisRetinal inflammation anchor validationRetinal inflammation CCL5 identity validation
Total tokens
1.9M
Output
43.5K
Codex GPT-5.6 Luna

Replicate 3

Matches predictionUDT-only
Answermuller glia cell
Workflow
Retinal Marker ScanRetinal Inflammation DiagnosticRetinal Inflammation Diagnostic Assignment CheckRetinal Inflammation Diagnostic Anchor CheckRetinal Inflammation Anchor Focus5 more tools
Total tokens
4.0M
Output
52.0K

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches prediction
Answermuller glia cell
Workflow
Local codePythonSciPyScanpyAnnData
Codex GPT-5.5

Replicate 2

Matches prediction
Answermuller glia cell
Workflow
Local codePythonSciPyScanpyAnnData
Codex GPT-5.5

Replicate 3

Matches prediction
Answermuller glia cell
Workflow
Local codePythonSciPyScanpyAnnData

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches prediction
Answermuller glia cell
Workflow
Local codePythonSciPyScanpyAnnData
Codex GPT-5.6 Sol

Replicate 2

Matches prediction
Answermuller glia cell
Workflow
Local codePythonSciPyAnnDataScanpy
Codex GPT-5.6 Sol

Replicate 3

Matches prediction
Answermuller glia cell
Workflow
Local codePythonSciPyScanpyAnnData

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches prediction
Answermuller glia cell
Workflow
Local codePythonSciPyScanpyAnnData
Total tokens
2.3M
Output
31.8K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches prediction
Answermuller glia cell
Workflow
Local codePythonSciPyScanpyAnnData
Total tokens
1.2M
Output
24.5K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches prediction
Answermuller glia cell
Workflow
Local codePythonScanpyAnnDataSciPy1 more tools
Total tokens
1.1M
Output
17.7K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches prediction
Answermuller glia cell
Workflow
Local codePythonSciPyAnnDataScanpy
Codex GPT-5.6 Luna

Replicate 2

Matches prediction
Answermuller glia cell
Workflow
Local codePythonSciPyScanpyAnnData
Codex GPT-5.6 Luna

Replicate 3

Matches prediction
Answermuller glia cell
Workflow
Local codePythonSciPyScanpyAnnData

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Matches prediction
Answermuller glia cell
Workflow
Local codePythonSciPyScanpyAnnData
Total tokens
363.1K
Output
4.9K