bix-26-q3 | Current BixBench results

New token-optimization experiment

Three additional GPT-5.6 Sol Galaxy replicates are available separately. Previous results remain unchanged.

View the October 2026 batch and its run records

Question

Among significantly upregulated genes in the iron-depleted glucose condition (FeMinus), how many genes contribute to the enrichment of the 'ABC transporters' term after conducting KEGG pathway enrichment analysis? Use an absolute log2 fold change cut off 1.5 and an adjusted p-value threshold of 0.05.

Accepted answer: 11
Domain: transcriptomics

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 8.03M total	3/3 replicate 1 replicate 2 replicate 3 1.18M total
Codex GPT-5.6 Sol	3/3 replicate 1 replicate 2 replicate 3 4.23M total	3/3 replicate 1 replicate 2 replicate 3 770.6K total
Codex GPT-5.6 Luna	3/3 replicate 1 replicate 2 replicate 3 20.92M total	3/3 replicate 1 replicate 2 replicate 3 3.13M total
DeepSeek V4 Pro via Codex	3/3 replicate 1 replicate 2 replicate 3 10.45M total	3/3 replicate 1 replicate 2 replicate 3 4.78M total
DeepSeek V4 Pro via Claude Codesuperseded	3/3 replicate 1 replicate 2 replicate 3 6.18M total	3/3 replicate 1 replicate 2 replicate 3 4.28M total

Execution condition

Galaxy-API code with skills

Codex GPT-5.5

3 primary replicates

Codex GPT-5.5

replicate 1

passUDT + standard tools

Answer11

Workflow

Kegg OraGalaxy UDTclusterProfilerDESeq2

Total tokens: 2.76M
Output: 18.1K

Galaxy history Run trace

Codex GPT-5.5

replicate 2

passUDT + standard tools

Answer11

Workflow

Galaxy UDTKegg OraDESeq2fold-change calculation

Total tokens: 2.31M
Output: 21.9K

Galaxy history Run trace

Codex GPT-5.5

replicate 3

pass

Answer11

Workflow

Kegg Ora

Total tokens: 2.96M
Output: 17.6K

Galaxy history Run trace

Codex GPT-5.6 Sol

3 primary replicates

Codex GPT-5.6 Sol

replicate 1

passUDT-only

Answer11

Workflow

Galaxy UDTclusterProfilerfold-change calculationKEGG

Total tokens: 2.05M
Output: 16.8K

Galaxy history Run trace

Codex GPT-5.6 Sol

replicate 2

pass

Answer11

Workflow

Rds To TabularFilter rowsKegg Ora

Total tokens: 1.15M
Output: 5.8K

Galaxy history Run trace

Codex GPT-5.6 Sol

replicate 3

pass

Answer11

Workflow

Rds To TabularKegg Ora

Total tokens: 1.03M
Output: 7.8K

Galaxy history Run trace

Codex GPT-5.6 Luna

3 primary replicates

Codex GPT-5.6 Luna

replicate 1

passUDT + standard tools

Answer11

Workflow

Rds To TabularGalaxy UDTKegg Ora

Total tokens: 12.34M
Output: 39.8K

Galaxy history Run trace

Codex GPT-5.6 Luna

replicate 2

pass

Answer11

Workflow

Rds To TabularFilter rowsSelect columnsKegg Ora

Total tokens: 4.99M
Output: 25.6K

Galaxy history Run trace

Codex GPT-5.6 Luna

replicate 3

pass

Answer11

Workflow

Rds To TabularFilter rowsKegg Ora

Total tokens: 3.60M
Output: 19.2K

Galaxy history Run trace

DeepSeek V4 Pro via Codex

3 primary replicates

DeepSeek V4 Pro via Codex

replicate 1

pass

Answer11

Workflow

Galaxy via BioBlendKEGGDESeq2

Total tokens: 3.81M
Output: 30.4K

Galaxy history Run trace

DeepSeek V4 Pro via Codex

replicate 2

pass

Answer11

Workflow

Galaxy via BioBlendclusterProfilerKEGGSciPy

Total tokens: 3.90M
Output: 22.3K

Galaxy history Run trace

DeepSeek V4 Pro via Codex

replicate 3

pass

Answer11

Workflow

Galaxy via BioBlendDESeq2KEGGclusterProfiler

Total tokens: 2.74M
Output: 24.6K

Galaxy history Run trace

DeepSeek V4 Pro via Claude CodeSuperseded

3 primary replicates

DeepSeek V4 Pro via Claude Code

replicate 1

pass

Answer11

Workflow

Rds To TabularKegg Orafold-change calculation

Total tokens: 1.35M
Output: 12.3K

Galaxy history Run trace

DeepSeek V4 Pro via Claude Code

replicate 2

pass

Answer11

Workflow

Rds To TabularKegg Orafold-change calculation

Total tokens: 1.26M
Output: 13.9K

Galaxy history Run trace

DeepSeek V4 Pro via Claude Code

replicate 3

pass

Answer11

Workflow

Rds To TabularKegg Orafold-change calculation

Total tokens: 3.57M
Output: 32.7K

Galaxy history Run trace

Execution condition

Open-ended code with skills

Codex GPT-5.5

3 primary replicates

Codex GPT-5.5

replicate 1

pass

Answer11

Workflow

Local analysisclusterProfilerKEGGEnrichr

Total tokens: 328.8K
Output: 5.4K

Run trace

Codex GPT-5.5

replicate 2

pass

Answer11

Workflow

Local analysis

Total tokens: 418.8K
Output: 6.2K

Run trace

Codex GPT-5.5

replicate 3

pass

Answer11

Workflow

Local analysisKEGGDESeq2

Total tokens: 433.5K
Output: 8.0K

Run trace

Codex GPT-5.6 Sol

3 primary replicates

Codex GPT-5.6 Sol

replicate 1

pass

Answer11

Workflow

Local analysis

Total tokens: 236.1K
Output: 4.0K

Run trace

Codex GPT-5.6 Sol

replicate 2

pass

Answer11

Workflow

Local analysis

Total tokens: 290.6K
Output: 4.3K

Run trace

Codex GPT-5.6 Sol

replicate 3

pass

Answer11

Workflow

Local analysis

Total tokens: 244.0K
Output: 5.4K

Run trace

Codex GPT-5.6 Luna

3 primary replicates

Codex GPT-5.6 Luna

replicate 1

pass

Answer11

Workflow

Local analysis

Total tokens: 1.27M
Output: 11.8K

Run trace

Codex GPT-5.6 Luna

replicate 2

pass

Answer11

Workflow

Local analysis

Total tokens: 1.06M
Output: 10.0K

Run trace

Codex GPT-5.6 Luna

replicate 3

pass

Answer11

Workflow

Local analysis

Total tokens: 793.8K
Output: 10.1K

Run trace

DeepSeek V4 Pro via Codex

3 primary replicates

DeepSeek V4 Pro via Codex

replicate 1

pass

Answer11

Workflow

Local analysisDESeq2clusterProfilerReactomefold-change calculationKEGG

Total tokens: 984.0K
Output: 13.0K

Run trace

DeepSeek V4 Pro via Codex

replicate 2

pass

Answer11

Workflow

Local analysisKEGGedgeRSciPyGSEApyDESeq2

Total tokens: 2.06M
Output: 19.3K

Run trace

DeepSeek V4 Pro via Codex

replicate 3

pass

Answer11

Workflow

Local analysisclusterProfilerKEGGDESeq2SciPy

Total tokens: 1.74M
Output: 18.6K

Run trace

DeepSeek V4 Pro via Claude CodeSuperseded

3 primary replicates

DeepSeek V4 Pro via Claude Code

replicate 1

pass

Answer11

Workflow

Local analysisDESeq2clusterProfilerstatsmodelsSciPyfold-change calculation

Total tokens: 1.19M
Output: 14.1K

Run trace

DeepSeek V4 Pro via Claude Code

replicate 2

pass

Answer11

Workflow

Local analysisGSEApyDESeq2fold-change calculationKEGGSciPy

Total tokens: 1.66M
Output: 17.5K

Run trace

DeepSeek V4 Pro via Claude Code

replicate 3

pass

Answer11

Workflow

Local analysisfold-change calculationDESeq2clusterProfilerKEGGGSEApy

Total tokens: 1.43M
Output: 14.0K

Run trace

bix-26-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

Answer11

Total tokens: 722.3K
Input: 717.2K
Cached input: 678.0K
Output: 5.1K

Run trace Final answer Galaxy history

Galaxy-API code · October 2026

replicate 2

Correct

Answer11

Total tokens: 778.1K
Input: 771.6K
Cached input: 733.3K
Output: 6.6K

Run trace Final answer Galaxy history

Galaxy-API code · October 2026

replicate 3

Correct

Answer11

Total tokens: 1.48M
Input: 1.47M
Cached input: 1.41M
Output: 9.6K

Run trace Final answer Galaxy history

Open-ended code averaged 0.26M tokens; previous website Galaxy averaged 1.41M; the new Galaxy runs averaged 0.99M, or 3.87× 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