Making deep‑learning explanations for DNA more reliable
Reliable post hoc interpretations of deep learning in genomics
This project improves computer methods that explain which parts of DNA control gene activity so researchers — and eventually patients — can better understand genetic effects.
Quick facts
| Grant type | R01 grant |
|---|---|
| Study type | NIH-funded research |
| Funding institution | Cold Spring Harbor Laboratory NIH-funded |
| Lab location | 1 site (Cold Spring Harbor, United States) |
| Project ID | NIH-11333758 on NIH RePORTER |
What this research studies
This work uses deep neural networks trained on genomic data to map which DNA letters matter for gene regulation and cell identity. The team will build methods to pick the best models, reduce noise in nucleotide‑level importance maps, and create benchmarks and best practices for interpreting results. They will test these tools across datasets such as ATAC‑seq and known transcription factor motif collections to ensure consistent, biologically meaningful outputs. The goal is clearer, more trustworthy maps of regulatory DNA that researchers can use to link genetic variants to function.
Who could benefit from this research
Good fit: This project does not appear to recruit patients directly; it mainly uses genomic datasets and collaborations with research labs rather than clinical enrollment.
Not a fit: Patients seeking immediate treatment or clinical benefit are unlikely to gain direct, near‑term benefits from this computational methods project.
Why it matters
Potential benefit: If successful, this could help researchers pinpoint genetic changes that alter gene regulation and speed discovery of disease‑relevant variants and targets for therapy.
How similar studies have performed: Related deep‑learning approaches have improved prediction of regulatory DNA activity, but making their nucleotide‑level explanations reliable is still a largely open challenge.
Where this research is happening
Cold Spring Harbor, United States
- Cold Spring Harbor Laboratory — Cold Spring Harbor, United States (Active)
Researchers
- Principal investigator: Koo, Peter K — Cold Spring Harbor Laboratory
- Study coordinator: Koo, Peter K
About this research
- This is an active NIH-funded research project — typically early-stage science, not a clinical trial accepting patient enrollment.
- Some NIH-funded labs run parallel clinical studies or seek volunteers for related work. To check, contact the principal investigator or institution listed above.
- For full project details, budget, and progress reports, visit the official NIH RePORTER page below.