Open comments for this post
- ran the full pipeline without any caps and regenerated all results.
- updated the interpretations based on the new results.
- updated the README and paper to match the final outputs.
- completed the project (for now) and verified that the code, results, and documentation are all consistent.
image: source control image showing the main changes i did in the paper’s latex.
Open comments for this post
- added frozen DNABERT sequence-head evaluation with AUROC, AUPRC, and accuracy reporting.
- added real null calibration, GC-matched background calibration, and improved the threshold sensitivity analysis.
- regenerated the downstream task performance and threshold sensitivity results.
image: source control image showing the main changes i did in the threshold sensitivity code.
Open comments for this post
- replaced the evidence summary with a clearer evidence table linking each claim to its supporting results and limitations.
- added a section explaining the main lessons for mechanistic interpretability.
- expanded the limitations section with clearer discussion of the study’s scope and assumptions.
image: source control image showing the main changes i did in the paper.
Open comments for this post
- added a glossary for the main biology terms.
- explained why the selected motifs are biologically important.
- simplified the theory section.
- moved detailed proofs to the appendix.
- clearly defined how nucleotide motifs are mapped to tokens.
- added a simple workflow diagram for the full analysis pipeline.
image: source control image showing changes that i made in the code.
Open comments for this post
made the entire pipeline fully reproducible, without any caps, including the threshold analysis and result generation.
image: screenshot of the pipeline being run.
