Sequence 06
The Reader of the Great Works
Sent to establish what is already true. To read the great existing models of the genome and rebuild them stone by stone, testing whether their claims hold before any new work is measured against them.
Research Intern Qatar Computing Research Institute (QCRI)
- Baselines lead on a deep learning research project for genomic mutation effect prediction. Evaluated four genomic foundation models (Enformer, Borzoi, Nucleotide Transformer, AlphaGenome) and mapped their transformer architectures to inference requirements.
- Engineered end-to-end Python inference pipelines for large transformer models on hg38 reference sequences up to 524,288 bp, implementing sequence extraction, center-padding logic, and output validation against experimental ground truth via Pearson correlation across 5,313 genomic assay tracks.
- Containerized per-model environments with reproducible conda setups, resolved cross-platform dependency conflicts, and deployed models to remote GPU infrastructure over SSH.