BixBench current item

bix-43-q4

Question

After performing differential gene expression analysis comparing CBD/cisplatin treatment vs DMSO control (using padj < 0.05 and |log2FC| ≥ 0.5), followed by enrichment analysis using gseapy with Reactome_2022 gene sets, what is the overlap ratio (DEGs found in pathway / total pathway genes) for the 'TP53 Regulates Transcription Of Cell Cycle Genes' pathway in the enrichment results? Express your answer as a fraction (e.g., X/Y).

Accepted answer
8/49
Domain
transcriptomics

Comparison

Pass counts and token totals across the same three replicates.

AgentGalaxy-API codeOpen-ended code
Codex GPT-5.52/3
replicate 1 replicate 2 replicate 3
4.72M total		3/3
replicate 1 replicate 2 replicate 3
1.65M total
Codex GPT-5.6 Sol3/3
replicate 1 replicate 2 replicate 3
11.06M total		2/3
replicate 1 replicate 2 replicate 3
2.79M total
Codex GPT-5.6 Luna3/3
replicate 1 replicate 2 replicate 3
39.44M total		3/3
replicate 1 replicate 2 replicate 3
9.58M total
DeepSeek V4 Pro via Codex3/3
replicate 1 replicate 2 replicate 3
39.73M total		2/3
replicate 1 replicate 2 replicate 3
21.79M total
DeepSeek V4 Pro via Claude Codesuperseded2/3
replicate 1 replicate 2 replicate 3
7.63M total		3/3
replicate 1 replicate 2 replicate 3
1.96M total

Execution condition

Galaxy-API code with skills

Codex GPT-5.5

3 primary replicates
Codex GPT-5.5

replicate 1

failUDT + standard tools

Why it missed

Gene mapping errorThis run counted one additional mapped gene in the target pathway and returned 9/49. The Reactome enrichment row reports the accepted overlap of 8/49.
Answer9/49
Workflow
Galaxy UDTGSEApy EnrichrReactomeDESeq2
Total tokens
1.25M
Output
9.6K
Galaxy historyRun trace
Codex GPT-5.5

replicate 2

passUDT + standard tools
Answer8/49
Workflow
Galaxy UDTGSEApy EnrichrDESeq2Reactomefold-change calculation
Total tokens
1.31M
Output
10.6K
Galaxy historyRun trace
Codex GPT-5.5

replicate 3

passUDT + standard tools
Answer8/49
Workflow
Galaxy UDTGSEApy EnrichrDESeq2
Total tokens
2.16M
Output
13.7K
Galaxy historyRun trace

Codex GPT-5.6 Sol

3 primary replicates
Codex GPT-5.6 Sol

replicate 1

pass
Answer8/49
Workflow
Csv To TabularSelect columnsDESeq2Filter rowsJoin datasetsGSEApy Enrichr
Total tokens
4.13M
Output
15.3K
Galaxy historyRun trace
Codex GPT-5.6 Sol

replicate 2

pass
Answer8/49
Workflow
Replace textSelect columnsDESeq2Filter rowsJoin datasetsGSEApy Enrichr
Total tokens
5.72M
Output
16.9K
Galaxy historyRun trace
Codex GPT-5.6 Sol

replicate 3

passUDT + standard tools
Answer8/49
Workflow
Galaxy UDTGSEApy EnrichrDESeq2fold-change calculation
Total tokens
1.21M
Output
9.6K
Galaxy historyRun trace

Codex GPT-5.6 Luna

3 primary replicates
Codex GPT-5.6 Luna

replicate 1

pass
Answer8/49
Workflow
Csv To TabularSelect columnsFilter Tabularmore stepsGSEApy EnrichrReactome
Total tokens
9.16M
Output
33.5K
Galaxy historyRun trace
Codex GPT-5.6 Luna

replicate 2

pass
Answer8/49
Workflow
Csv To TabularSelect columnsFilter Tabularmore stepsGSEApy EnrichrReactome
Total tokens
7.57M
Output
27.4K
Galaxy historyRun trace
Codex GPT-5.6 Luna

replicate 3

pass
Answer8/49
Workflow
Csv To TabularFilter TabularSelect columnsmore stepsGSEApy EnrichrReactome
Total tokens
22.71M
Output
50.1K
Galaxy historyRun trace

DeepSeek V4 Pro via Codex

3 primary replicates
DeepSeek V4 Pro via Codex

replicate 1

pass
Answer8/49
Workflow
Galaxy historyGSEApyDESeq2ReactomeEnrichr
Total tokens
9.04M
Output
39.0K
Galaxy historyRun trace
DeepSeek V4 Pro via Codex

replicate 2

pass
Answer8/49
Workflow
Select columnsCsv To TabularDESeq2GSEApy Enrichr
Total tokens
2.64M
Output
22.7K
Galaxy historyRun trace
DeepSeek V4 Pro via Codex

replicate 3

pass
Answer8/49
Workflow
Galaxy via BioBlendReactomeGSEApyDESeq2edgeREnrichr
Total tokens
28.04M
Output
103.7K
Galaxy historyRun trace

DeepSeek V4 Pro via Claude CodeSuperseded

3 primary replicates
DeepSeek V4 Pro via Claude Code

replicate 1

pass
Answer8/49
Workflow
DESeq2fold-change calculationGSEApyEnrichrReactome
Total tokens
2.19M
Output
23.5K
Galaxy historyRun trace
DeepSeek V4 Pro via Claude Code

replicate 2

fail

Why it missed

Answer extraction errorThis run found the correct eight overlapping genes but back-calculated a 47-gene denominator from the odds ratio. The enrichment output reports the pathway size directly as 49, giving 8/49.
Answer8/47
Workflow
DESeq2GSEApy Enrichrfold-change calculationSciPyFisher exact test
Total tokens
3.21M
Output
32.9K
Galaxy historyRun trace
DeepSeek V4 Pro via Claude Code

replicate 3

pass
Answer8/49
Workflow
DESeq2GSEApyfold-change calculationEnrichrReactome
Total tokens
2.23M
Output
20.7K
Galaxy historyRun trace

Execution condition

Open-ended code with skills

Codex GPT-5.5

3 primary replicates
Codex GPT-5.5

replicate 1

pass
Answer8/49
Workflow
Local analysisPyDESeq2GSEApystatsmodelsSciPy
Total tokens
527.7K
Output
6.3K
Run trace
Codex GPT-5.5

replicate 2

pass
Answer8/49
Workflow
Local analysisSciPystatsmodelsGSEApyPyDESeq2
Total tokens
485.2K
Output
6.2K
Run trace
Codex GPT-5.5

replicate 3

pass
Answer8/49
Workflow
Local analysisPyDESeq2GSEApystatsmodelsSciPy
Total tokens
641.5K
Output
8.5K
Run trace

Codex GPT-5.6 Sol

3 primary replicates
Codex GPT-5.6 Sol

replicate 1

pass
Answer8/49
Workflow
Local analysis
Total tokens
851.8K
Output
5.1K
Run trace
Codex GPT-5.6 Sol

replicate 2

pass
Answer8/49
Workflow
Local analysis
Total tokens
928.2K
Output
6.8K
Run trace
Codex GPT-5.6 Sol

replicate 3

fail

Why it missed

DE model included unrelated groupsThis run used all 30 samples in a ten-level dispersion model, which made PLK3 cross the DEG threshold and produced nine pathway hits. The direct six-sample CBD/cisplatin-versus-DMSO comparison gives the accepted overlap 8/49.
Answer9/49
Workflow
Local analysis
Total tokens
1.01M
Output
6.9K
Run trace

Codex GPT-5.6 Luna

3 primary replicates
Codex GPT-5.6 Luna

replicate 1

pass
Answer8/49
Workflow
Local analysis
Total tokens
1.66M
Output
18.0K
Run trace
Codex GPT-5.6 Luna

replicate 2

pass
Answer8/49
Workflow
Local analysis
Total tokens
3.60M
Output
22.3K
Run trace
Codex GPT-5.6 Luna

replicate 3

pass
Answer8/49
Workflow
Local analysis
Total tokens
4.32M
Output
23.6K
Run trace

DeepSeek V4 Pro via Codex

3 primary replicates
DeepSeek 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.
Answer9/49
Workflow
Local analysisSciPystatsmodelsGSEApyPyDESeq2
Total tokens
1.65M
Output
17.2K
Run trace
DeepSeek V4 Pro via Codex

replicate 2

pass
Answer8/49
Workflow
Local analysisSciPystatsmodelsscikit-learnGSEApyDESeq2
Total tokens
1.39M
Output
15.0K
Run trace
DeepSeek V4 Pro via Codex

replicate 3

pass
Answer8/49
Workflow
Local analysisSciPystatsmodelsGSEApyPyDESeq2
Total tokens
18.75M
Output
49.8K
Run trace

DeepSeek V4 Pro via Claude CodeSuperseded

3 primary replicates
DeepSeek V4 Pro via Claude Code

replicate 1

pass
Answer8/49
Workflow
Local analysisGSEApystatsmodelsSciPyPyDESeq2
Total tokens
518.0K
Output
5.5K
Run trace
DeepSeek V4 Pro via Claude Code

replicate 2

pass
Answer8/49
Workflow
Local analysisGSEApyPyDESeq2statsmodelsSciPy
Total tokens
458.4K
Output
7.8K
Run trace
DeepSeek V4 Pro via Claude Code

replicate 3

pass
Answer8/49
Workflow
Local analysisGSEApystatsmodelsSciPyPyDESeq2
Total tokens
985.6K
Output
10.4K
Run trace

bix-43-q4 · October 2026 · three additional replicates

GPT-5.6 Sol · token optimization

Galaxy-API code, high reasoning, Fast service. Previous runs are retained above.

Open-ended code averaged 0.93M tokens; previous website Galaxy averaged 3.69M; the new Galaxy runs averaged 1.63M, or 1.76× 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.

Optimization overview and all 150 runs