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CompBioBench item

ep-interactions-q1

Question

You are given two complementary datasets describing eight candidate distal regulatory element–promoter interactions (EP1–EP8): (1) a Hi-C–like chromatin contact dataset measuring 3D proximity between each element–promoter pairs (ep.interactions.q1.hic.csv) and (2) a CRISPR perturbation dataset measuring the effect of element disruption on promoter expression (ep.interactions.q1.expr.csv). Which E–P pair is least consistent with being a true causal regulatory element–promoter interaction when integrating both datasets? Choose exactly one: A) EP1 B) EP2 C) EP3 D) EP4 E) EP5 F) EP6 G) EP7. Reply with a single letter (A-G).

Inferred answer
CUniquely inferred from submitted scores.
Domain
Epigenomics
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

IncorrectUDT-only
AnswerF
Workflow
EP Q1 Integrated Causal ScoreEP Q1 Regulatory Sensitivity
Total tokens
520.1K
Output
8.3K
Codex GPT-5.5

Replicate 2

IncorrectUDT + standard tools
AnswerF
Workflow
EP integration analysisUDT render probeUDT render probe v2Datamash Ops
Total tokens
1.4M
Output
18.0K
Codex GPT-5.5

Replicate 3

IncorrectUDT + standard tools
AnswerF
Workflow
EP integration analysisEP integration analysis v2EP integration analysis v3Csv To TabularDatamash Ops
Total tokens
1.4M
Output
13.3K

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

CorrectUDT-only
AnswerC
Workflow
EP Hi-C distance-adjusted diagnosticEP CRISPR expression diagnosticEP integrated causal-consistency sensitivity analysis
Total tokens
642.0K
Output
7.9K
Codex GPT-5.6 Sol

Replicate 2

CorrectUDT-only
AnswerC
Workflow
EP interaction diagnostic summaryFinal integrated EP causal assessment
Total tokens
486.0K
Output
9.1K
Codex GPT-5.6 Sol

Replicate 3

CorrectUDT + standard tools
AnswerC
Workflow
EP integrated diagnosticsEP integrated diagnostics v2Csv To TabularDatamash OpsFilter Tabular
Total tokens
2.5M
Output
13.0K

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

CorrectStandard tools only
AnswerC
Workflow
Add A Column1
Total tokens
8.9M
Output
41.4K
Codex + DeepSeek-v4-pro-0813

Replicate 2

CorrectUDT + standard tools
AnswerC
Workflow
Datamash OpsEP interactions integrationEP interactions meta-analysis
Total tokens
8.8M
Output
67.7K
Codex + DeepSeek-v4-pro-0813

Replicate 3

CorrectUDT + standard tools
AnswerC
Workflow
EP integrated analysisUDT probe hiUDT cat probeUDT probe hi v2UDT cat probe v22 more tools
Total tokens
18.9M
Output
63.9K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

CorrectStandard tools only
AnswerC
Workflow
Csv To TabularDatamash OpsGroup and aggregate
Total tokens
1.5M
Output
18.6K
Codex GPT-5.6 Luna

Replicate 2

CorrectStandard tools only
AnswerC
Workflow
Csv To TabularDatamash Ops
Total tokens
14.3M
Output
42.2K
Codex GPT-5.6 Luna

Replicate 3

CorrectUDT + standard tools
AnswerC
Workflow
Csv To TabularEP interaction integration diagnosticEP interaction integration sensitivity diagnosticsEP interaction final rank discordance decision
Total tokens
1.2M
Output
24.9K

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Incorrect
AnswerF
Workflow
Local codePythonSciPy
Codex GPT-5.5

Replicate 2

Incorrect
AnswerF
Workflow
Local codePython
Codex GPT-5.5

Replicate 3

Incorrect
AnswerF
Workflow
Local codePythonSciPy

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Incorrect
AnswerF
Workflow
Local codePythonSciPyR
Codex GPT-5.6 Sol

Replicate 2

Correct
AnswerC
Workflow
Local codePythonSciPy
Codex GPT-5.6 Sol

Replicate 3

Correct
AnswerC
Workflow
Local codePythonSciPy

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Incorrect
AnswerF
Workflow
Local codePythonSciPy
Total tokens
595.4K
Output
22.0K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Correct
AnswerC
Workflow
Local codePythonSciPy
Total tokens
4.4M
Output
39.9K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Correct
AnswerC
Workflow
Local codePythonSciPy
Total tokens
2.8M
Output
29.7K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Correct
AnswerC
Workflow
Local codePython
Codex GPT-5.6 Luna

Replicate 2

Correct
AnswerC
Workflow
Local code
Codex GPT-5.6 Luna

Replicate 3

Correct
AnswerC
Workflow
Local codePython

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Correct
AnswerC
Workflow
Local code
Total tokens
27.0K
Output
89