Codex GPT-5.5
replicate 1
passUDT-only
Answer
0:0Workflow
Galaxy UDTmean summary
- Total tokens
- 1.52M
- Output
- 10.1K
New token-optimization experiment
Three additional GPT-5.6 Sol Galaxy replicates are available separately. Previous results remain unchanged.
Question
What is the ratio of significant (p <= 0.05) differentially expressed miRNAs between patient and control groups identified following Bonferroni correction compared to Benjamini-Yekutieli correction? Provide your answer as a ratio in the format "Bonferroni:Benjamini-Yekutieli".
Comparison
Pass counts and token totals across the same three replicates.
| Agent | Galaxy-API code | Open-ended code |
|---|---|---|
| Codex GPT-5.5 | 3/3 replicate 1 replicate 2 replicate 3 5.56M total | 2/3 replicate 1 replicate 2 replicate 3 896.1K total |
| Codex GPT-5.6 Sol | 3/3 replicate 1 replicate 2 replicate 3 9.42M total | 0/3 replicate 1 replicate 2 replicate 3 1.67M total |
| Codex GPT-5.6 Luna | 3/3 replicate 1 replicate 2 replicate 3 13.90M total | 2/3 replicate 1 replicate 2 replicate 3 4.78M total |
| DeepSeek V4 Pro via Codex | 1/3 replicate 1 replicate 2 replicate 3 21.75M total | 0/3 replicate 1 replicate 2 replicate 3 4.54M total |
| DeepSeek V4 Pro via Claude Codesuperseded | 3/3 replicate 1 replicate 2 replicate 3 8.15M total | 2/3 replicate 1 replicate 2 replicate 3 1.79M total |
Execution condition
Galaxy-API code with skills
Codex GPT-5.5
3 primary replicatesCodex GPT-5.5
replicate 2
passUDT-only
Answer
0:0Workflow
Galaxy UDTSciPystatsmodelsedgeRDESeq2
- Total tokens
- 2.78M
- Output
- 11.6K
Codex GPT-5.5
replicate 3
passUDT + standard tools
Answer
0:0Workflow
Excel to tabularGalaxy UDTmean summary
- Total tokens
- 1.27M
- Output
- 10.6K
Codex GPT-5.6 Sol
3 primary replicatesCodex GPT-5.6 Sol
replicate 1
passUDT + standard tools
Answer
0:0Workflow
Excel to tabularUnivariateGalaxy UDT
- Total tokens
- 3.06M
- Output
- 14.1K
Codex GPT-5.6 Sol
replicate 2
pass
Answer
0:0Workflow
Excel to tabularUnivariate
- Total tokens
- 3.30M
- Output
- 12.8K
Codex GPT-5.6 Sol
replicate 3
passUDT + standard tools
Answer
0:0Workflow
Excel to tabularUnivariateGalaxy UDT
- Total tokens
- 3.06M
- Output
- 18.8K
Codex GPT-5.6 Luna
3 primary replicatesCodex GPT-5.6 Luna
replicate 1
passUDT + standard tools
Answer
0:0Workflow
Excel to tabularGalaxy UDTUnivariateSciPy
- Total tokens
- 4.46M
- Output
- 29.1K
Codex GPT-5.6 Luna
replicate 2
passUDT + standard tools
Answer
0:0Workflow
Excel to tabularFilter TabularRemove headermore stepsGalaxy UDTmean summary
- Total tokens
- 5.12M
- Output
- 31.6K
Codex GPT-5.6 Luna
replicate 3
passUDT + standard tools
Answer
0:0Workflow
Excel to tabularUnivariateGalaxy UDT
- Total tokens
- 4.33M
- Output
- 29.1K
DeepSeek V4 Pro via Codex
3 primary replicatesDeepSeek V4 Pro via Codex
replicate 1
failUDT + standard tools
Evaluation status
Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer
1:0Workflow
Excel to tabularGalaxy UDTSciPymore stepst-testSpearman correlation
- Total tokens
- 13.42M
- Output
- 78.5K
DeepSeek V4 Pro via Codex
replicate 2
passUDT + standard tools
Answer
0:0Workflow
Excel to tabularGalaxy UDTUnivariatestatsmodelsSciPy
- Total tokens
- 3.15M
- Output
- 25.4K
DeepSeek V4 Pro via Codex
replicate 3
failUDT + standard tools
Evaluation status
Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer
1:0Workflow
Excel to tabularGalaxy UDTmean summary
- Total tokens
- 5.17M
- Output
- 31.9K
DeepSeek V4 Pro via Claude CodeSuperseded
3 primary replicatesDeepSeek V4 Pro via Claude Code
replicate 1
passUDT + standard tools
Answer
0:0Workflow
Excel to tabularSciPyt-testmean summary
- Total tokens
- 3.77M
- Output
- 42.6K
DeepSeek V4 Pro via Claude Code
replicate 2
passUDT + standard tools
Answer
0:0Workflow
UnivariateGalaxy UDTt-test
- Total tokens
- 1.58M
- Output
- 17.6K
DeepSeek V4 Pro via Claude Code
replicate 3
passUDT + standard tools
Answer
0:0Workflow
UnivariateGalaxy UDTmean summary
- Total tokens
- 2.80M
- Output
- 33.0K
Execution condition
Open-ended code with skills
Codex GPT-5.5
3 primary replicatesCodex GPT-5.5
replicate 1
pass
Answer
0:0Workflow
Local analysisSciPystatsmodels
- Total tokens
- 285.6K
- Output
- 4.5K
Codex GPT-5.5
replicate 2
pass
Answer
0:0Workflow
Local analysisSciPystatsmodels
- Total tokens
- 286.2K
- Output
- 6.6K
Codex GPT-5.5
replicate 3
fail
Why it missed
Unstated paper workflow addedThis run inferred the source paper from a filename and added sample exclusions, mean-Ct normalization, and a Student t-test that the supplied task does not request. Those extra decisions changed 0:0 to 1:0.
Answer
1:0Workflow
Local analysisSciPystatsmodels
- Total tokens
- 324.2K
- Output
- 7.7K
Codex GPT-5.6 Sol
3 primary replicatesCodex GPT-5.6 Sol
replicate 1
fail
Why it missed
Unstated paper workflow addedThis run inferred the source-paper workflow and added sample exclusions, mean-Ct normalization, and a Student t-test that the self-contained task does not request. Those extra decisions changed the direct supplied-data result from 0:0 to 1:0.
Answer
1:0Workflow
Local analysis
- Total tokens
- 721.6K
- Output
- 6.4K
Codex GPT-5.6 Sol
replicate 2
fail
Why it missed
Unstated paper workflow addedThis run inferred the source-paper workflow and added sample exclusions, mean-Ct normalization, and a Student t-test that the self-contained task does not request. Those extra decisions changed the direct supplied-data result from 0:0 to 1:0.
Answer
1:0Workflow
Local analysis
- Total tokens
- 400.6K
- Output
- 5.4K
Codex GPT-5.6 Sol
replicate 3
fail
Why it missed
Unstated paper workflow addedThis run inferred the source-paper workflow and added sample exclusions, mean-Ct normalization, and a Student t-test that the self-contained task does not request. Those extra decisions changed the direct supplied-data result from 0:0 to 1:0.
Answer
1:0Workflow
Local analysis
- Total tokens
- 548.2K
- Output
- 7.1K
Codex GPT-5.6 Luna
3 primary replicatesCodex GPT-5.6 Luna
replicate 1
pass
Answer
0:0Workflow
Local analysis
- Total tokens
- 637.8K
- Output
- 10.0K
Codex GPT-5.6 Luna
replicate 2
pass
Answer
0:0Workflow
Local analysis
- Total tokens
- 742.7K
- Output
- 14.2K
Codex GPT-5.6 Luna
replicate 3
fail
Why it missed
Unstated paper workflow addedThis run reconstructed source-paper preprocessing instead of answering the supplied-data question directly. The extra exclusions and normalization changed the accepted 0:0 result to 1:0.
Answer
1:0Workflow
Local analysis
- Total tokens
- 3.40M
- Output
- 30.9K
DeepSeek V4 Pro via Codex
3 primary replicatesDeepSeek V4 Pro via Codex
replicate 1
fail
Evaluation status
Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer
1:0Workflow
Local analysisSciPystatsmodelst-testmean summary
- Total tokens
- 1.38M
- Output
- 14.3K
DeepSeek V4 Pro via Codex
replicate 2
fail
Evaluation status
Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer
1:0Workflow
Local analysisSciPystatsmodelsmean summaryt-test
- Total tokens
- 2.59M
- Output
- 28.2K
DeepSeek V4 Pro via Codex
replicate 3
fail
Evaluation status
Manual review pendingThe evaluator marked this answer incorrect. The answer, workflow summary, usage, and available run records are linked, but a manual root-cause audit has not yet been added.
Answer
1:0Workflow
Local analysisstatsmodelsSciPyt-testmean summary
- Total tokens
- 574.0K
- Output
- 13.5K
DeepSeek V4 Pro via Claude CodeSuperseded
3 primary replicatesDeepSeek V4 Pro via Claude Code
replicate 1
pass
Answer
0:0Workflow
Local analysisSciPyt-test
- Total tokens
- 463.3K
- Output
- 10.7K
DeepSeek V4 Pro via Claude Code
replicate 2
fail
Why it missed
Unstated paper workflow addedThis run reconstructed source-paper preprocessing instead of answering the self-contained data question. Excluding two samples and adding mean-Ct normalization changed 0:0 to 1:0.
Answer
1:0Workflow
Local analysisSciPyt-testmean summary
- Total tokens
- 889.5K
- Output
- 17.7K
DeepSeek V4 Pro via Claude Code
replicate 3
pass
Answer
0:0Workflow
Local analysisSciPystatsmodelst-testMann-Whitney Umedian summary
- Total tokens
- 437.3K
- Output
- 8.9K
bix-30-q3 · October 2026 · three additional replicates
GPT-5.6 Sol · token optimization
Galaxy-API code, high reasoning, Fast service. Previous runs are retained above.
Galaxy-API code · October 2026
replicate 1
Correct
Answer
0:0- Total tokens
- 2.22M
- Input
- 2.21M
- Cached input
- 2.12M
- Output
- 11.2K
Galaxy-API code · October 2026
replicate 2
Correct
Answer
0:0- Total tokens
- 1.31M
- Input
- 1.30M
- Cached input
- 1.24M
- Output
- 9.1K
Galaxy-API code · October 2026
replicate 3
Correct
Answer
0:0- Total tokens
- 808.7K
- Input
- 801.7K
- Cached input
- 759.6K
- Output
- 7.0K
Open-ended code averaged 0.56M tokens; previous website Galaxy averaged 3.14M; the new Galaxy runs averaged 1.44M, or 2.59× Open-ended code. Each mean covers three replicates of this same task with GPT-5.6 Sol.
Cached input is already included in input tokens. Full nested tool/job evidence is in each HF run's galaxy_execution_records.tar.gz, with an accompanying member index.