Hello, I’m trying to reproduce Chrombpnet becnhmark from Extended Data Fig 3g and having trouble achieving the reported correlation with Chrombpnet. My command: chrombpnet pred_bw -cm chrombpnet_model.h5 -r bed10.bed -g hg38.fa -c hg38.chrom.sizes -op DNASE/GM12878 -bw ENCFF681PTG.bigWig The mod…

Hi Galina, Thanks for your question. From your description, it looks like there might be an issue with the test intervals that you are using. To help resolve the issue, I’ve made a Colab that recreates the exact test intervals we used for the ChromBPNet GM12878 benchmark in our paper (Fold 0). A …

Hello Vincent, Thank you for your answer! I was able to reproduce the test intervals according to the collab and now the command runs without an error. However, the resulting metrics are still slightly different from those reported in the article. For GM12878, I get log total count pearson r 0.629…

Reproducing Chrombpnet becnhmarks

Help & Support

Vincent_Dutordoir June 26, 2026, 3:56pm 4

Hi, I won’t be able to help with the chrombpnet pred_bw command but these suggestions are likely to resolve the remaining discrepancy. Reproducing AlphaGenome becnhmarks - #4 by Vincent_Dutordoir

Topic		Replies	Views
Can't reproduce alphagenome's benchmarks Help & Support	9	2884	September 20, 2025
Reproducing AlphaGenome becnhmarks Help & Support	4	177	July 6, 2026
Validation of API usage Help & Support	5	1792	September 16, 2025
Interpreting output prediction inconsistency based on the length of input interval Feedback & Feature Requests testing	1	1320	August 19, 2025
Predict_interval throughput/server-side output averaging Feedback & Feature Requests	4	1269	September 5, 2025

Reproducing Chrombpnet becnhmarks

Related topics