bix-46-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 log2 fold change value rounded to 2 decimal points for the phenazine pathway gene PA14_35160 in the ΔrhlI mutant?

Accepted answer: -4.10
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 4.57M total	3/3 replicate 1 replicate 2 replicate 3 942.6K total
Codex GPT-5.6 Sol	3/3 replicate 1 replicate 2 replicate 3 2.59M total	3/3 replicate 1 replicate 2 replicate 3 921.0K total
Codex GPT-5.6 Luna	3/3 replicate 1 replicate 2 replicate 3 10.83M total	3/3 replicate 1 replicate 2 replicate 3 1.17M total
DeepSeek V4 Pro via Codex	2/3 replicate 1 replicate 2 replicate 3 7.86M total	3/3 replicate 1 replicate 2 replicate 3 25.25M total
DeepSeek V4 Pro via Claude Codesuperseded	3/3 replicate 1 replicate 2 replicate 3 2.53M total	3/3 replicate 1 replicate 2 replicate 3 2.56M total

Execution condition

Galaxy-API code with skills

Codex GPT-5.5

3 primary replicates

Codex GPT-5.5

replicate 1

pass

Answer-4.10

Workflow

Rds To Tabularfold-change calculation

Total tokens: 2.00M
Output: 7.8K

Galaxy history Run trace

Codex GPT-5.5

replicate 2

passUDT + standard tools

Answer-4.10

Workflow

Rds To TabularGalaxy UDTfold-change calculationDESeq2

Total tokens: 1.43M
Output: 7.5K

Galaxy history Run trace

Codex GPT-5.5

replicate 3

passUDT + standard tools

Answer-4.10

Workflow

Rds To TabularGalaxy UDTfold-change calculationDESeq2

Total tokens: 1.14M
Output: 9.9K

Galaxy history Run trace

Codex GPT-5.6 Sol

3 primary replicates

Codex GPT-5.6 Sol

replicate 1

pass

Answer-4.10

Workflow

Rds To Tabularfold-change calculation

Total tokens: 568.1K
Output: 4.5K

Galaxy history Run trace

Codex GPT-5.6 Sol

replicate 2

pass

Answer-4.10

Workflow

Rds To TabularMatch rowsfold-change calculation

Total tokens: 989.9K
Output: 6.4K

Galaxy history Run trace

Codex GPT-5.6 Sol

replicate 3

pass

Answer-4.10

Workflow

Rds To TabularMatch rowsfold-change calculationDESeq2

Total tokens: 1.03M
Output: 6.6K

Galaxy history Run trace

Codex GPT-5.6 Luna

3 primary replicates

Codex GPT-5.6 Luna

replicate 1

passUDT + standard tools

Answer-4.10

Workflow

Rds To TabularGalaxy UDTfold-change calculationDESeq2

Total tokens: 2.07M
Output: 18.1K

Galaxy history Run trace

Codex GPT-5.6 Luna

replicate 2

pass

Answer-4.10

Workflow

Rds To TabularCsv To TabularFilter Tabularfold-change calculation

Total tokens: 6.21M
Output: 29.4K

Galaxy history Run trace

Codex GPT-5.6 Luna

replicate 3

passUDT + standard tools

Answer-4.10

Workflow

Rds To TabularGalaxy UDTFilter Tabularfold-change calculation

Total tokens: 2.55M
Output: 20.0K

Galaxy history Run trace

DeepSeek V4 Pro via Codex

3 primary replicates

DeepSeek V4 Pro via Codex

replicate 1

pass

Answer-4.10

Workflow

Rds To Tabular

Total tokens: 3.56M
Output: 25.5K

Galaxy history Run trace

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.

Answernot produced

Workflow

Rds To Tabular

Total tokens: 876.2K
Output: 9.6K

Galaxy history Run trace

DeepSeek V4 Pro via Codex

replicate 3

pass

Answer-4.10

Workflow

Tp Head ToolRds To TabularFilter TabularCsv To TabularTp Grep Tool

Total tokens: 3.43M
Output: 24.9K

Galaxy history Run trace

DeepSeek V4 Pro via Claude CodeSuperseded

3 primary replicates

DeepSeek V4 Pro via Claude Code

replicate 1

pass

Answer-4.10

Workflow

Rds To TabularDESeq2fold-change calculation

Total tokens: 921.9K
Output: 11.0K

Galaxy history Run trace

DeepSeek V4 Pro via Claude Code

replicate 2

pass

Answer-4.10

Workflow

Rds To Tabularfold-change calculation

Total tokens: 810.0K
Output: 9.9K

Galaxy history Run trace

DeepSeek V4 Pro via Claude Code

replicate 3

pass

Answer-4.10

Workflow

Rds To Tabular

Total tokens: 802.8K
Output: 10.2K

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

Answer-4.10

Workflow

Local analysis

Total tokens: 413.6K
Output: 4.9K

Run trace

Codex GPT-5.5

replicate 2

pass

Answer-4.10

Workflow

Local analysis

Total tokens: 237.6K
Output: 4.4K

Run trace

Codex GPT-5.5

replicate 3

pass

Answer-4.10

Workflow

Local analysisDESeq2

Total tokens: 291.4K
Output: 3.0K

Run trace

Codex GPT-5.6 Sol

3 primary replicates

Codex GPT-5.6 Sol

replicate 1

pass

Answer-4.10

Workflow

Local analysis

Total tokens: 283.4K
Output: 3.9K

Run trace

Codex GPT-5.6 Sol

replicate 2

pass

Answer-4.10

Workflow

Local analysis

Total tokens: 449.8K
Output: 3.4K

Run trace

Codex GPT-5.6 Sol

replicate 3

pass

Answer-4.10

Workflow

Local analysis

Total tokens: 187.8K
Output: 2.3K

Run trace

Codex GPT-5.6 Luna

3 primary replicates

Codex GPT-5.6 Luna

replicate 1

pass

Answer-4.10

Workflow

Local analysis

Total tokens: 369.9K
Output: 6.0K

Run trace

Codex GPT-5.6 Luna

replicate 2

pass

Answer-4.10

Workflow

Local analysis

Total tokens: 307.3K
Output: 6.5K

Run trace

Codex GPT-5.6 Luna

replicate 3

pass

Answer-4.10

Workflow

Local analysis

Total tokens: 492.4K
Output: 7.7K

Run trace

DeepSeek V4 Pro via Codex

3 primary replicates

DeepSeek V4 Pro via Codex

replicate 1

pass

Answer-4.10

Workflow

Local analysisDESeq2

Total tokens: 4.88M
Output: 31.6K

Run trace

DeepSeek V4 Pro via Codex

replicate 2

pass

Answer-4.10

Workflow

Local analysisSpearman correlationmean summarymedian summary

Total tokens: 9.70M
Output: 60.7K

Run trace

DeepSeek V4 Pro via Codex

replicate 3

pass

Answer-4.10

Workflow

Local analysis

Total tokens: 10.67M
Output: 38.5K

Run trace

DeepSeek V4 Pro via Claude CodeSuperseded

3 primary replicates

DeepSeek V4 Pro via Claude Code

replicate 1

pass

Answer-4.10

Workflow

Local analysisDESeq2fold-change calculation

Total tokens: 837.5K
Output: 11.3K

Run trace

DeepSeek V4 Pro via Claude Code

replicate 2

pass

Answer-4.10

Workflow

Local analysisDESeq2

Total tokens: 966.5K
Output: 8.3K

Run trace

DeepSeek V4 Pro via Claude Code

replicate 3

pass

Answer-4.10

Workflow

Local analysisDESeq2fold-change calculation

Total tokens: 754.4K
Output: 10.4K

Run trace

bix-46-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

Answer-4.10

Total tokens: 421.6K
Input: 416.5K
Cached input: 395.6K
Output: 5.1K

Run trace Final answer Galaxy history

Galaxy-API code · October 2026

replicate 2

Correct

Answer-4.10

Total tokens: 675.4K
Input: 665.0K
Cached input: 628.4K
Output: 10.4K

Run trace Final answer Galaxy history

Galaxy-API code · October 2026

replicate 3

Correct

Answer-4.10

Total tokens: 639.7K
Input: 631.7K
Cached input: 594.3K
Output: 8.0K

Run trace Final answer Galaxy history

Open-ended code averaged 0.31M tokens; previous website Galaxy averaged 0.86M; the new Galaxy runs averaged 0.58M, or 1.89× 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