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CompBioBench item

borzoi-rnaseq-q1

Question

Use the Borzoi model (replicate 0) to predict the total RNA-seq coverage on the forward strand for the experiment ENCFF281BWX, over the genomic interval chr1:70157360-70353968 in the hg38 genome. Return the total predicted RNA-seq coverage over the specified interval, which means reversing any transformations that were applied to RNA-seq coverage before training the Borzoi model. The Borzoi paper is saved as borzoi.rnaseq.q1.pdf. Round the answer to the nearest 10.

Inferred answer
9380Uniquely inferred from submitted scores.
Domain
Machine Learning
Question style
Tooling

An answer can be uniquely inferred for 54 of 100 questions from submitted scores. Green: correct · Red: incorrect. For questions without a uniquely determined answer: Blue: matches prediction · Orange: differs from prediction. These are inferred answer checks, not official per-question grades.

Galaxy

12/12 terminal item results

UDT = user-defined tool: custom code executed by Galaxy. Route badges summarize analysis tools, excluding uploads and automatic conversions. How usage is counted.

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

CorrectUDT-only
Answer9380
Workflow
Borzoi container probeBorzoi PyTorch probeBorzoi RNA-seq interval predictionBorzoi RNA-seq interval prediction correctedGalaxy disk probe2 more tools
Codex GPT-5.5

Replicate 2

CorrectUDT-only
Answer9380
Workflow
Borzoi runtime probeBorzoi RNA-seq Q1 prediction
Total tokens
1.4M
Output
10.2K
Codex GPT-5.5

Replicate 3

RerunCorrectUDT-only
Answer9380
Workflow
Borzoi RNA-seq Q1 diagnosticBorzoi RNA-seq Q1 replicate 0 predictionBorzoi RNA-seq Q1 replicate 0 TensorFlow predictionUDT resource probeBorzoi RNA-seq Q1 replicate 0 TensorFlow prediction highmem13 more tools
Total tokens
9.2M
Output
26.0K

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

CorrectUDT + standard tools
Answer9380
Workflow
Galaxy UDTborzoi_predictBorzoi predictionUDT schema probeTensorFlow container probe5 more tools
Codex GPT-5.6 Sol

Replicate 2

CorrectUDT + standard tools
Answer9380
Workflow
Extract Genomic Dna 1Borzoi replicate 0 RNA-seq count-space coverage
Total tokens
1.8M
Output
9.6K
Codex GPT-5.6 Sol

Replicate 3

CorrectUDT-only
Answer9380
Workflow
Borzoi hg38 input and target diagnosticBorzoi replicate 0 untransformed RNA-seq totalBorzoi replicate 0 untransformed RNA-seq total direct checkpointBorzoi replicate 0 untransformed RNA-seq total direct checkpoint py310
Total tokens
14.2M
Output
16.5K

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

RerunCorrectUDT + standard tools
Answer9380
Workflow
Probe Borzoi ImageProbe Borzoi Image V2Probe Borzoi Image V3Extract Genomic DNAbedtools getfasta6 more tools
Total tokens
6.4M
Output
27.1K
Codex + DeepSeek-v4-pro-0813

Replicate 2

CorrectUDT + standard tools
Answer9380
Workflow
pysamExtract Genomic Dna 1Borzoi RNA forward coverageSciPyBorzoi RNA forward coverage v21 more tools
Total tokens
10.4M
Output
39.2K
Codex + DeepSeek-v4-pro-0813

Replicate 3

CorrectUDT + standard tools
Answer9380
Workflow
pysamBorzoi Runtime Probe v2Borzoi Runtime Probe v3Cat ProbeEcho Probe16 more tools
Total tokens
20.2M
Output
59.0K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

RerunCorrectUDT-only
Answer9380
Workflow
User-defined tool
Total tokens
9.1M
Output
31.6K
Codex GPT-5.6 Luna

Replicate 2

CorrectUDT-only
Answer9380
Workflow
Borzoi runtime probeBorzoi HF network probeBorzoi HF file probeStage Borzoi replicate 0 checkpointStage hg38 Borzoi input window2 more tools
Total tokens
6.8M
Output
30.0K
Codex GPT-5.6 Luna

Replicate 3

CorrectUDT-only
Answer9380
Workflow
Borzoi Runtime ProbeBorzoi Replicate 0 Forward Coverage DiagnosticBorzoi Raw Output CheckBorzoi Replicate 0 Forward Coverage Inverse Sum
Total tokens
4.5M
Output
25.0K

Anycode

13/13 terminal item results

Codex GPT-5.5

3 replicates
Codex GPT-5.5

Replicate 1

Correct
Answer9380
Workflow
Local codePythonSciPy
Codex GPT-5.5

Replicate 2

Correct
Answer9380
Workflow
Local codePythonSciPypysam
Codex GPT-5.5

Replicate 3

Incorrect
Answer8870
Workflow
Local codePythonpysamSciPy

Codex GPT-5.6 Sol

3 replicates
Codex GPT-5.6 Sol

Replicate 1

Correct
Answer9380
Workflow
Local codePythonSciPy
Codex GPT-5.6 Sol

Replicate 2

Correct
Answer9380
Workflow
Local codePython
Codex GPT-5.6 Sol

Replicate 3

Correct
Answer9380
Workflow
Local codePython

Codex + DeepSeek-v4-pro-0813

3 replicates
Codex + DeepSeek-v4-pro-0813

Replicate 1

Incorrect
Answer8870
Workflow
Local codePythonSamtoolspysamSciPy
Total tokens
18.1M
Output
60.7K
Codex + DeepSeek-v4-pro-0813

Replicate 2

Correct
Answer9380
Workflow
Local codePythonSciPySamtoolsBedtools
Total tokens
12.6M
Output
53.1K
Codex + DeepSeek-v4-pro-0813

Replicate 3

Correct
Answer9380
Workflow
Local codePython
Total tokens
13.8M
Output
46.6K

Codex GPT-5.6 Luna

3 replicates
Codex GPT-5.6 Luna

Replicate 1

Correct
Answer9380
Workflow
Local codePython
Codex GPT-5.6 Luna

Replicate 2

Correct
Answer9380
Workflow
Local codePythonpysam
Codex GPT-5.6 Luna

Replicate 3

Correct
Answer9380
Workflow
Local codePython

Codex GPT-6 Astra

1 replicate
Codex GPT-6 Astra

Replicate 1

Correct
Answer9380
Workflow
Local codePythonSciPy
Total tokens
753.7K
Output
4.7K