Codex GPT-5.5
replicate 1
pass
Answer
3Workflow
Spearman correlation
- Total tokens
- 903.1K
- Output
- 5.6K
New token-optimization experiment
Three additional GPT-5.6 Sol Galaxy replicates are available separately. Previous results remain unchanged.
Question
How many genes in the provided data show strong positive Spearman correlation between expression and essentiality across cell lines, with a correlation coefficient >= 0.6?
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 3.52M total | 3/3 replicate 1 replicate 2 replicate 3 1.24M total |
| Codex GPT-5.6 Sol | 3/3 replicate 1 replicate 2 replicate 3 2.04M total | 3/3 replicate 1 replicate 2 replicate 3 904.2K total |
| Codex GPT-5.6 Luna | 3/3 replicate 1 replicate 2 replicate 3 6.83M total | 3/3 replicate 1 replicate 2 replicate 3 2.78M total |
| DeepSeek V4 Pro via Codex | 3/3 replicate 1 replicate 2 replicate 3 6.31M total | 3/3 replicate 1 replicate 2 replicate 3 1.75M total |
| DeepSeek V4 Pro via Claude Codesuperseded | 2/3 replicate 1 replicate 2 replicate 3 4.02M total | 3/3 replicate 1 replicate 2 replicate 3 2.68M total |
Execution condition
Galaxy-API code with skills
Codex GPT-5.5
3 primary replicatesCodex GPT-5.5
replicate 2
pass
Answer
3Workflow
Spearman correlation
- Total tokens
- 1.61M
- Output
- 4.8K
Codex GPT-5.5
replicate 3
passUDT-only
Answer
3Workflow
Galaxy UDTSpearman correlationSciPy
- Total tokens
- 1.01M
- Output
- 9.7K
Codex GPT-5.6 Sol
3 primary replicatesCodex GPT-5.6 Sol
replicate 1
pass
Answer
3Workflow
Spearman correlation
- Total tokens
- 715.7K
- Output
- 4.5K
Codex GPT-5.6 Sol
replicate 2
pass
Answer
3Workflow
Spearman correlation
- Total tokens
- 649.7K
- Output
- 4.2K
Codex GPT-5.6 Sol
replicate 3
pass
Answer
3Workflow
Spearman correlation
- Total tokens
- 672.2K
- Output
- 4.0K
Codex GPT-5.6 Luna
3 primary replicatesCodex GPT-5.6 Luna
replicate 1
pass
Answer
3Workflow
Spearman correlationCsv To TabularTp Grep ToolJoin datasets
- Total tokens
- 3.21M
- Output
- 19.5K
Codex GPT-5.6 Luna
replicate 2
pass
Answer
3Workflow
Spearman correlation
- Total tokens
- 2.51M
- Output
- 9.4K
Codex GPT-5.6 Luna
replicate 3
pass
Answer
3Workflow
Spearman correlation
- Total tokens
- 1.11M
- Output
- 9.4K
DeepSeek V4 Pro via Codex
3 primary replicatesDeepSeek V4 Pro via Codex
replicate 1
pass
Answer
3Workflow
Galaxy via BioBlendSciPySpearman correlation
- Total tokens
- 1.54M
- Output
- 11.8K
DeepSeek V4 Pro via Codex
replicate 2
pass
Answer
3Workflow
Galaxy via BioBlendSciPySpearman correlation
- Total tokens
- 3.54M
- Output
- 29.0K
DeepSeek V4 Pro via Codex
replicate 3
pass
Answer
3Workflow
Spearman correlation
- Total tokens
- 1.23M
- Output
- 11.4K
DeepSeek V4 Pro via Claude CodeSuperseded
3 primary replicatesDeepSeek V4 Pro via Claude Code
replicate 1
fail
Why it missed
Scientific interpretation errorThis run applied the positive-correlation threshold to the raw CRISPR score and returned zero genes. Using the biological essentiality direction produces the accepted three genes.
Answer
0Workflow
Show Beginning1Spearman correlation
- Total tokens
- 1.76M
- Output
- 12.6K
DeepSeek V4 Pro via Claude Code
replicate 2
pass
Answer
3Workflow
Spearman correlation
- Total tokens
- 1.25M
- Output
- 13.6K
History isolation noteReplicate 3 created this history first; replicate 2 found and adopted it 15 seconds later. They submitted separate jobs, so this is a history-isolation violation without detected output reuse.
DeepSeek V4 Pro via Claude Code
replicate 3
pass
Answer
3Workflow
Spearman correlation
- Total tokens
- 1.01M
- Output
- 11.9K
Execution condition
Open-ended code with skills
Codex GPT-5.5
3 primary replicatesCodex GPT-5.5
replicate 1
pass
Answer
3Workflow
Local analysisSciPySpearman correlationmean summary
- Total tokens
- 399.4K
- Output
- 5.8K
Codex GPT-5.5
replicate 2
pass
Answer
3Workflow
Local analysisSpearman correlationSciPy
- Total tokens
- 370.9K
- Output
- 6.7K
Codex GPT-5.5
replicate 3
pass
Answer
3Workflow
Local analysisSciPySpearman correlationmean summary
- Total tokens
- 468.5K
- Output
- 8.2K
Codex GPT-5.6 Sol
3 primary replicatesCodex GPT-5.6 Sol
replicate 1
pass
Answer
3Workflow
Local analysis
- Total tokens
- 280.5K
- Output
- 6.1K
Codex GPT-5.6 Sol
replicate 2
pass
Answer
3Workflow
Local analysis
- Total tokens
- 363.2K
- Output
- 7.3K
Codex GPT-5.6 Sol
replicate 3
pass
Answer
3Workflow
Local analysis
- Total tokens
- 260.6K
- Output
- 6.1K
Codex GPT-5.6 Luna
3 primary replicatesCodex GPT-5.6 Luna
replicate 1
pass
Answer
3Workflow
Local analysis
- Total tokens
- 731.1K
- Output
- 25.1K
Codex GPT-5.6 Luna
replicate 2
pass
Answer
3Workflow
Local analysis
- Total tokens
- 1.42M
- Output
- 15.2K
Codex GPT-5.6 Luna
replicate 3
pass
Answer
3Workflow
Local analysis
- Total tokens
- 625.0K
- Output
- 15.2K
DeepSeek V4 Pro via Codex
3 primary replicatesDeepSeek V4 Pro via Codex
replicate 1
pass
Answer
3Workflow
Local analysisSciPyPearson correlationmean summarymedian summary
- Total tokens
- 512.7K
- Output
- 14.2K
DeepSeek V4 Pro via Codex
replicate 2
pass
Answer
3Workflow
Local analysisSciPySpearman correlationmean summarymedian summary
- Total tokens
- 663.6K
- Output
- 17.2K
DeepSeek V4 Pro via Codex
replicate 3
pass
Answer
3Workflow
Local analysisSciPySpearman correlation
- Total tokens
- 574.9K
- Output
- 13.2K
DeepSeek V4 Pro via Claude CodeSuperseded
3 primary replicatesDeepSeek V4 Pro via Claude Code
replicate 1
pass
Answer
3Workflow
Local analysisSciPy
- Total tokens
- 739.3K
- Output
- 9.2K
DeepSeek V4 Pro via Claude Code
replicate 2
pass
Answer
3Workflow
Local analysisSciPySpearman correlationmean summaryAIC model selection
- Total tokens
- 1.65M
- Output
- 37.9K
DeepSeek V4 Pro via Claude Code
replicate 3
pass
Answer
3Workflow
Local analysisSciPy
- Total tokens
- 291.5K
- Output
- 4.6K
bix-16-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
3- Total tokens
- 460.2K
- Input
- 455.8K
- Cached input
- 428.2K
- Output
- 4.5K
Galaxy-API code · October 2026
replicate 2
Correct
Answer
3- Total tokens
- 411.2K
- Input
- 407.3K
- Cached input
- 377.0K
- Output
- 3.9K
Galaxy-API code · October 2026
replicate 3
Correct
Answer
3- Total tokens
- 454.9K
- Input
- 451.0K
- Cached input
- 428.2K
- Output
- 3.8K
Open-ended code averaged 0.30M tokens; previous website Galaxy averaged 0.68M; the new Galaxy runs averaged 0.44M, or 1.47× 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.