bix-49-q4 | 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

What is the total number of significantly differentially expressed genes (padj < 0.05) when performing DESeq2 differential gene expression analysis with apeglm LFC shrinkage, comparing ASXL1 mutation (disease) vs control, while controlling for sex as a covariate?

Accepted answer: 2118 or 2106
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 8.52M total	3/3 replicate 1 replicate 2 replicate 3 5.58M total
Codex GPT-5.6 Sol	3/3 replicate 1 replicate 2 replicate 3 7.40M total	3/3 replicate 1 replicate 2 replicate 3 3.04M total
Codex GPT-5.6 Luna	3/3 replicate 1 replicate 2 replicate 3 49.80M total	3/3 replicate 1 replicate 2 replicate 3 11.48M total
DeepSeek V4 Pro via Codex	3/3 replicate 1 replicate 2 replicate 3 22.29M total	3/3 replicate 1 replicate 2 replicate 3 28.65M total
DeepSeek V4 Pro via Claude Codesuperseded	3/3 replicate 1 replicate 2 replicate 3 11.35M total	1/3 replicate 1 replicate 2 replicate 3 4.95M total

Execution condition

Galaxy-API code with skills

Codex GPT-5.5

3 primary replicates

Codex GPT-5.5

replicate 1

passUDT + standard tools

Answer2106

Workflow

Galaxy UDTExcel to tabularDESeq2apeglm

Total tokens: 4.82M
Output: 23.1K

Galaxy history Run trace

Codex GPT-5.5

replicate 2

pass

Answer2118

Workflow

DESeq2

Total tokens: 1.83M
Output: 12.8K

Galaxy history Run trace

Codex GPT-5.5

replicate 3

pass

Answer2118

Workflow

DESeq2apeglm

Total tokens: 1.87M
Output: 12.1K

Galaxy history Run trace

Codex GPT-5.6 Sol

3 primary replicates

Codex GPT-5.6 Sol

replicate 1

pass

Answer2118

Workflow

DESeq2apeglm

Total tokens: 2.24M
Output: 19.3K

Galaxy history Run trace

Codex GPT-5.6 Sol

replicate 2

passUDT + standard tools

Answer2106

Workflow

Excel to tabularGalaxy UDTDESeq2apeglm

Total tokens: 3.70M
Output: 17.3K

Galaxy history Run trace

Codex GPT-5.6 Sol

replicate 3

passUDT + standard tools

Answer2106

Workflow

Excel to tabularGalaxy UDTDESeq2apeglm

Total tokens: 1.45M
Output: 11.9K

Galaxy history Run trace

Codex GPT-5.6 Luna

3 primary replicates

Codex GPT-5.6 Luna

replicate 1

pass

Answer2118

Workflow

Excel to tabularSelect columnsDESeq2apeglm

Total tokens: 10.02M
Output: 29.5K

Galaxy history Run trace

Codex GPT-5.6 Luna

replicate 2

pass

Answer2118

Workflow

Excel to tabularDatamash TransposeTp Split On Columnmore stepsDESeq2apeglm

Total tokens: 15.00M
Output: 49.0K

Galaxy history Run trace

Codex GPT-5.6 Luna

replicate 3

passUDT + standard tools

Answer2106

Workflow

Excel to tabularSelect columnsBuild ListDESeq2Galaxy UDTapeglm

Total tokens: 24.79M
Output: 78.9K

Galaxy history Run trace

DeepSeek V4 Pro via Codex

3 primary replicates

DeepSeek V4 Pro via Codex

replicate 1

pass

Answer2118

Workflow

DESeq2

Total tokens: 5.32M
Output: 35.7K

Galaxy history Run trace

DeepSeek V4 Pro via Codex

replicate 2

pass

Answer2118

Workflow

Select columnsExcel to tabularBuild ListRelabel From FileDESeq2apeglm

Total tokens: 13.44M
Output: 57.4K

Galaxy history Run trace

DeepSeek V4 Pro via Codex

replicate 3

pass

Answer2118

Workflow

Select columnsExcel to tabularDESeq2

Total tokens: 3.53M
Output: 24.2K

Galaxy history Run trace

DeepSeek V4 Pro via Claude CodeSuperseded

3 primary replicates

DeepSeek V4 Pro via Claude Code

replicate 1

pass

Answer2118

Workflow

DESeq2apeglmfold-change calculation

Total tokens: 1.91M
Output: 22.8K

Galaxy history Run trace

DeepSeek V4 Pro via Claude Code

replicate 2

pass

Answer2118

Workflow

Excel to tabularUpload datasetDESeq2apeglm

Total tokens: 4.17M
Output: 40.7K

Galaxy history Run trace

DeepSeek V4 Pro via Claude Code

replicate 3

pass

Answer2118

Workflow

Copy HistoryDESeq2apeglm

Total tokens: 5.27M
Output: 57.8K

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

Answer2106

Workflow

Local analysisDESeq2apeglm

Total tokens: 2.29M
Output: 11.1K

Run trace

Codex GPT-5.5

replicate 2

pass

Answer2106

Workflow

Local analysisDESeq2apeglm

Total tokens: 1.59M
Output: 8.3K

Run trace

Codex GPT-5.5

replicate 3

pass

Answer2106

Workflow

Local analysisDESeq2apeglmSciPystatsmodelsPyDESeq2

Total tokens: 1.70M
Output: 12.1K

Run trace

Codex GPT-5.6 Sol

3 primary replicates

Codex GPT-5.6 Sol

replicate 1

pass

Answer2106

Workflow

Local analysis

Total tokens: 1.08M
Output: 9.0K

Run trace

Codex GPT-5.6 Sol

replicate 2

pass

Answer2106

Workflow

Local analysis

Total tokens: 1.02M
Output: 8.1K

Run trace

Codex GPT-5.6 Sol

replicate 3

pass

Answer2106

Workflow

Local analysis

Total tokens: 938.4K
Output: 8.1K

Run trace

Codex GPT-5.6 Luna

3 primary replicates

Codex GPT-5.6 Luna

replicate 1

pass

Answer2106

Workflow

Local analysis

Total tokens: 8.71M
Output: 20.9K

Run trace

Codex GPT-5.6 Luna

replicate 2

pass

Answer2118

Workflow

Local analysis

Total tokens: 1.67M
Output: 16.6K

Run trace

Codex GPT-5.6 Luna

replicate 3

pass

Answer2118

Workflow

Local analysis

Total tokens: 1.10M
Output: 16.7K

Run trace

DeepSeek V4 Pro via Codex

3 primary replicates

DeepSeek V4 Pro via Codex

replicate 1

pass

Answer2118

Workflow

Local analysisDESeq2apeglm

Total tokens: 15.37M
Output: 32.4K

Run trace

DeepSeek V4 Pro via Codex

replicate 2

pass

Answer2118

Workflow

Local analysisDESeq2apeglm

Total tokens: 3.29M
Output: 25.8K

Run trace

DeepSeek V4 Pro via Codex

replicate 3

pass

Answer2106

Workflow

Local analysisDESeq2apeglmPyDESeq2SciPy

Total tokens: 9.99M
Output: 40.7K

Run trace

DeepSeek V4 Pro via Claude CodeSuperseded

3 primary replicates

DeepSeek V4 Pro via Claude Code

replicate 1

pass

Answer2118

Workflow

Local analysisapeglmDESeq2PyDESeq2

Total tokens: 2.25M
Output: 16.9K

Run trace

DeepSeek V4 Pro via Claude Code

replicate 2

fail

Why it missed

Named method was replacedThis run used PyDESeq2's alpha=0.05 path instead of the requested R DESeq2 plus apeglm workflow and returned 2100. The requested R implementation reproduces the paper-supported 2118.

Answer2100

Workflow

Local analysisDESeq2apeglmPyDESeq2

Total tokens: 1.08M
Output: 10.5K

Run trace

DeepSeek V4 Pro via Claude Code

replicate 3

fail

Why it missed

Answer2100

Workflow

Local analysisapeglmDESeq2PyDESeq2

Total tokens: 1.61M
Output: 12.9K

Run trace

bix-49-q4 · 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

Answer2118

Total tokens: 1.32M
Input: 1.31M
Cached input: 1.20M
Output: 10.4K

Run trace Final answer Galaxy history

Galaxy-API code · October 2026

replicate 2

Correct

Answer2118

Total tokens: 3.36M
Input: 3.34M
Cached input: 3.23M
Output: 21.7K

Run trace Final answer Galaxy history

Galaxy-API code · October 2026

replicate 3

Correct

Answer2106

Total tokens: 1.98M
Input: 1.96M
Cached input: 1.88M
Output: 19.6K

Run trace Final answer Galaxy history

Open-ended code averaged 1.01M tokens; previous website Galaxy averaged 2.47M; the new Galaxy runs averaged 2.22M, or 2.20× 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