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CompBioBench item

multiome-match-atac-rna-q1

Question

You are given two gzipped TSVs. Rows are features and columns are 8 pseudo-bulk cell populations (same 8 in both files). multiome.match.atac.rna.q1.rna.tsv.gz: RNA TPM (genes × populations). multiome.match.atac.rna.q1.atac.tsv.gz: ATAC 10kb-bin counts normalized to 1e6 (bins × populations). The ATAC columns have been permuted, but RNA columns are in the correct order. For each RNA column i (0-based), output the 0-based index of the matching ATAC column. Respond with a single semicolon-separated string with no spaces, length 8, e.g. 7;6;5;4;3;2;1;0.

Predicted answer
5;1;4;0;6;3;7;2Most likely answer for this question; not uniquely determined from submitted scores.
Domain
Epigenomics
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

Matches predictionUDT-only
Answer5;1;4;0;6;3;7;2
Workflow
Match multiome RNA ATAC columnsPromoter match multiome RNA ATAC columnsPromoter centered match multiome RNA ATAC columns
Codex GPT-5.5

Replicate 2

RerunMatches predictionUDT-only
Answer5;1;4;0;6;3;7;2
Workflow
Match multiome columns by similarity geometryMatch multiome columns by promoter bins
Total tokens
506.8K
Output
10.8K
Codex GPT-5.5

Replicate 3

Matches predictionUDT-only
Answer5;1;4;0;6;3;7;2
Workflow
Multiome Column Match DiagnosticMultiome Column Match Diagnostic v2UDT Template ProbeUDT Template Probe v2UDT Template Probe v31 more tools
Total tokens
2.3M
Output
21.2K

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches predictionUDT-only
Answer5;1;4;0;6;3;7;2
Workflow
Match RNA and ATAC pseudo-bulk populations
Codex GPT-5.6 Sol

Replicate 2

Matches predictionUDT-only
Answer5;1;4;0;6;3;7;2
Workflow
RNA ATAC population match diagnosticFinal validated RNA ATAC population match
Total tokens
959.2K
Output
11.4K
Codex GPT-5.6 Sol

Replicate 3

Matches predictionUDT + standard tools
Answer5;1;4;0;6;3;7;2
Workflow
Multiome RNA ATAC population matching diagnosticRegex1ChipseekerFilter TabularGroup and aggregate5 more tools
Total tokens
17.7M
Output
31.7K

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches predictionUDT-only
Answer5;1;4;0;6;3;7;2
Workflow
Gene Activity Matching DiagnosticDeviation Matching DiagnosticFinal RNA ATAC Column Match
Total tokens
3.9M
Output
42.2K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches predictionUDT-only
Answer5;1;4;0;6;3;7;2
Workflow
Match Multiome Columns
Total tokens
1.1M
Output
20.0K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches predictionUDT + standard tools
Answer5;1;4;0;6;3;7;2
Workflow
Match columns diagnosticProbe renderMatch Columns Diag V2Filter Tabular
Total tokens
54.3M
Output
129.9K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches predictionUDT-only
Answer5;1;4;0;6;3;7;2
Workflow
Pseudo-bulk Column Match DiagnosticPseudo-bulk Feature-wise Rank Match DiagnosticPseudo-bulk Genomic Column Match DiagnosticPseudo-bulk Genomic Build CheckPseudo-bulk RNA-to-ATAC Column Match Final
Total tokens
2.9M
Output
35.3K
Codex GPT-5.6 Luna

Replicate 2

Matches predictionUDT-only
Answer5;1;4;0;6;3;7;2
Workflow
Multimodal Column Match DiagnosticStreaming Multimodal Column Match DiagnosticGene Bin Multimodal Column Match DiagnosticGene Bin Multimodal Build ControlGene Bin Column Match Final Diagnostic1 more tools
Total tokens
8.0M
Output
47.8K
Codex GPT-5.6 Luna

Replicate 3

Matches predictionUDT-only
Answer5;1;4;0;6;3;7;2
Workflow
Multiome Column Matching DiagnosticMultiome Column Matching Robust DiagnosticUpload1Multiome Column Matching Genomic DiagnosticMultiome Column Matching Cross Feature Diagnostic1 more tools
Total tokens
2.8M
Output
46.4K

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Matches prediction
Answer5;1;4;0;6;3;7;2
Workflow
Local codePythonSciPy
Codex GPT-5.5

Replicate 2

Matches prediction
Answer5;1;4;0;6;3;7;2
Workflow
Local codePython
Codex GPT-5.5

Replicate 3

Matches prediction
Answer5;1;4;0;6;3;7;2
Workflow
Local codePython

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Matches prediction
Answer5;1;4;0;6;3;7;2
Workflow
Local codePythonSciPy
Codex GPT-5.6 Sol

Replicate 2

Matches prediction
Answer5;1;4;0;6;3;7;2
Workflow
Local codePythonSciPy
Codex GPT-5.6 Sol

Replicate 3

Matches prediction
Answer5;1;4;0;6;3;7;2
Workflow
Local codePython

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Matches prediction
Answer5;1;4;0;6;3;7;2
Workflow
Local codePythonSciPyScanpyAnnData
Total tokens
359.1K
Output
11.3K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Matches prediction
Answer5;1;4;0;6;3;7;2
Workflow
Local codePythonSciPyAnnDataScanpy
Total tokens
1.0M
Output
17.3K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Matches prediction
Answer5;1;4;0;6;3;7;2
Workflow
Local codePythonSciPy
Total tokens
935.7K
Output
33.6K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Matches prediction
Answer5;1;4;0;6;3;7;2
Workflow
Local codePythonSciPy
Codex GPT-5.6 Luna

Replicate 2

Matches prediction
Answer5;1;4;0;6;3;7;2
Workflow
Local codePythonSciPyBedtools
Codex GPT-5.6 Luna

Replicate 3

Matches prediction
Answer5;1;4;0;6;3;7;2
Workflow
Local codePythonSciPy

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Matches prediction
Answer5;1;4;0;6;3;7;2
Workflow
Local codePythonSciPy
Total tokens
361.6K
Output
3.7K