Codex GPT-5.5
replicate 1
passUDT-only
Answer
0Workflow
Galaxy UDTKEGGDESeq2
- Total tokens
- 1.37M
- Output
- 9.9K
New token-optimization experiment
Three additional GPT-5.6 Sol Galaxy replicates are available separately. Previous results remain unchanged.
Question
Using KEGG over-representation analysis (ORA), how many pathways are significantly enriched (absolute value of lfc > 1.5) in the same direction for all three mutant strains (97, 98, and 99), relative to wildtype?
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 4.10M total | 3/3 replicate 1 replicate 2 replicate 3 1.99M total |
| Codex GPT-5.6 Sol | 3/3 replicate 1 replicate 2 replicate 3 8.04M total | 3/3 replicate 1 replicate 2 replicate 3 1.45M total |
| Codex GPT-5.6 Luna | 3/3 replicate 1 replicate 2 replicate 3 33.68M total | 3/3 replicate 1 replicate 2 replicate 3 3.82M total |
| DeepSeek V4 Pro via Codex | 0/3 replicate 1 replicate 2 replicate 3 15.02M total | 0/3 replicate 1 replicate 2 replicate 3 19.52M total |
| DeepSeek V4 Pro via Claude Codesuperseded | 2/3 replicate 1 replicate 2 replicate 3 6.35M total | 2/3 replicate 1 replicate 2 replicate 3 5.29M total |
Execution condition
Galaxy-API code with skills
Codex GPT-5.5
3 primary replicatesCodex GPT-5.5
replicate 2
passUDT-only
Answer
0Workflow
Galaxy UDTKEGGclusterProfilerDESeq2
- Total tokens
- 881.7K
- Output
- 13.6K
Codex GPT-5.5
replicate 3
passUDT + standard tools
Answer
0Workflow
Galaxy UDTKegg OraDESeq2
- Total tokens
- 1.85M
- Output
- 15.0K
Codex GPT-5.6 Sol
3 primary replicatesCodex GPT-5.6 Sol
replicate 1
pass
Answer
0Workflow
Rds To TabularFilter rowsKegg Ora
- Total tokens
- 4.11M
- Output
- 11.2K
Codex GPT-5.6 Sol
replicate 2
pass
Answer
0Workflow
Rds To TabularFilter rowsKegg Ora
- Total tokens
- 2.25M
- Output
- 11.4K
Codex GPT-5.6 Sol
replicate 3
pass
Answer
0Workflow
Rds To TabularKegg Ora
- Total tokens
- 1.68M
- Output
- 11.9K
Codex GPT-5.6 Luna
3 primary replicatesCodex GPT-5.6 Luna
replicate 1
passUDT + standard tools
Answer
0Workflow
Rds To TabularKegg OraGalaxy UDTGprofiler Gost
- Total tokens
- 17.56M
- Output
- 64.4K
Codex GPT-5.6 Luna
replicate 2
pass
Answer
0Workflow
Rds To TabularFilter rowsSelect columnsKegg Ora
- Total tokens
- 12.52M
- Output
- 43.1K
Codex GPT-5.6 Luna
replicate 3
passUDT + standard tools
Answer
0Workflow
Rds To TabularAdd derived columnGalaxy UDTKegg Ora
- Total tokens
- 3.60M
- Output
- 27.1K
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
2Workflow
Rds To TabularFilter rowsSelect columnsKegg Ora
- Total tokens
- 6.87M
- Output
- 43.4K
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
2Workflow
Rds To TabularFilter rowsKegg Ora
- Total tokens
- 3.12M
- Output
- 28.1K
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
2Workflow
Rds To TabularFilter rowsKegg Ora
- Total tokens
- 5.03M
- Output
- 39.5K
DeepSeek V4 Pro via Claude CodeSuperseded
3 primary replicatesDeepSeek V4 Pro via Claude Code
replicate 1
pass
Answer
0Workflow
Rds To TabularKegg Ora
- Total tokens
- 2.74M
- Output
- 40.0K
DeepSeek V4 Pro via Claude Code
replicate 2
fail
Why it missed
Multiple-testing scope changedThis run corrected only pathways with foreground hits, which made pau01110 and pau01310 pass. Correcting across the full tested KEGG pathway family leaves no pathway significant in the same direction across all mutants.
Answer
2Workflow
Rds To TabularKegg Ora
- Total tokens
- 1.86M
- Output
- 23.6K
DeepSeek V4 Pro via Claude Code
replicate 3
pass
Answer
0Workflow
Rds To TabularKegg OraDESeq2
- Total tokens
- 1.75M
- Output
- 29.3K
Execution condition
Open-ended code with skills
Codex GPT-5.5
3 primary replicatesCodex GPT-5.5
replicate 1
pass
Answer
0Workflow
Local analysisDESeq2clusterProfilerKEGGEnrichr
- Total tokens
- 654.5K
- Output
- 8.2K
Codex GPT-5.5
replicate 2
pass
Answer
0Workflow
Local analysisclusterProfilerKEGGDESeq2
- Total tokens
- 645.2K
- Output
- 8.0K
Codex GPT-5.5
replicate 3
pass
Answer
0Workflow
Local analysisclusterProfilerDESeq2
- Total tokens
- 690.4K
- Output
- 9.4K
Codex GPT-5.6 Sol
3 primary replicatesCodex GPT-5.6 Sol
replicate 1
pass
Answer
0Workflow
Local analysis
- Total tokens
- 453.8K
- Output
- 8.0K
Codex GPT-5.6 Sol
replicate 2
pass
Answer
0Workflow
Local analysis
- Total tokens
- 593.6K
- Output
- 10.1K
Codex GPT-5.6 Sol
replicate 3
pass
Answer
0Workflow
Local analysis
- Total tokens
- 400.5K
- Output
- 8.9K
Codex GPT-5.6 Luna
3 primary replicatesCodex GPT-5.6 Luna
replicate 1
pass
Answer
0Workflow
Local analysis
- Total tokens
- 1.69M
- Output
- 21.6K
Codex GPT-5.6 Luna
replicate 2
pass
Answer
0Workflow
Local analysis
- Total tokens
- 1.05M
- Output
- 15.7K
Codex GPT-5.6 Luna
replicate 3
pass
Answer
0Workflow
Local analysis
- Total tokens
- 1.08M
- Output
- 23.6K
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
2Workflow
Local analysisGSEApystatsmodelsKEGGSciPyclusterProfiler
- Total tokens
- 4.33M
- Output
- 42.5K
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
2Workflow
Local analysisclusterProfilerKEGGSciPyDESeq2
- Total tokens
- 4.69M
- Output
- 29.0K
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
2Workflow
Local analysisSciPystatsmodelsBiopythonGSEApyscikit-learn
- Total tokens
- 10.50M
- Output
- 46.7K
DeepSeek V4 Pro via Claude CodeSuperseded
3 primary replicatesDeepSeek V4 Pro via Claude Code
replicate 1
fail
Why it missed
Scientific route errorThis run first intersected 59 genes that changed in the same direction and performed one pooled ORA. The requested route runs ORA per mutant and direction, then intersects significant pathway sets; that result is zero.
Answer
3Workflow
Local analysisDESeq2GSEApyKEGGSciPyFisher exact test
- Total tokens
- 1.75M
- Output
- 16.9K
DeepSeek V4 Pro via Claude Code
replicate 2
pass
Answer
0Workflow
Local analysisDESeq2clusterProfilerGSEApyKEGGstatsmodels
- Total tokens
- 2.05M
- Output
- 24.1K
DeepSeek V4 Pro via Claude Code
replicate 3
pass
Answer
0Workflow
Local analysisDESeq2KEGGSciPyFisher exact teststatsmodels
- Total tokens
- 1.50M
- Output
- 30.0K
bix-32-q2 · 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
Incorrect
Answer
2- Total tokens
- 1.31M
- Input
- 1.30M
- Cached input
- 1.20M
- Output
- 12.0K
Galaxy-API code · October 2026
replicate 2
Correct
Answer
0- Total tokens
- 1.38M
- Input
- 1.37M
- Cached input
- 1.30M
- Output
- 7.6K
Galaxy-API code · October 2026
replicate 3
Incorrect
Answer
2- Total tokens
- 1.42M
- Input
- 1.41M
- Cached input
- 1.31M
- Output
- 9.8K
Open-ended code averaged 0.48M tokens; previous website Galaxy averaged 2.68M; the new Galaxy runs averaged 1.37M, or 2.83× 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.