Hello, I'm Yafi.

Research Interest

I am interested in applying artificial intelligence in bioinformatics, with a focus on single-cell RNA sequencing, spatial transcriptomics, and visualizing high-dimensional data. I am also interested in developing and optimizing machine learning algorithms for these problems.

Areas of interest:

• Computational Biology
• Single-Cell & Spatial Transcriptomics
• Bioinformatics
• Machine Learning

scGIST: Gene Panel Design for Spatial Transcriptomics with Prioritized Gene Sets

First author · Published in Genome Biology in February 2024

Yafi, M., Hisham, M., Grisanti, F. et al. scGIST: gene panel design for spatial transcriptomics with prioritized gene sets. Genome Biology 25, 57 (2024).

The initial goal of the project was to modify a simple linear programming algorithm to include prioritized genes, which we achieved in a short period of time. After that, we challenged ourselves to achieve even better results. Through several iterations and experiments, we developed scGIST.

• Developed a deep-learning tool for designing single-cell spatial transcriptomics gene panels.
• Created a custom loss function for constrained feature selection, optimizing both cell type detection and inclusion of prioritized genes.
• Achieved high accuracy in cell type identification across multiple datasets, outperforming existing methods, especially for small panel sizes.
• Enabled researchers to systematically prioritize genes of interest, including easy-to-target genes and receptor-ligand complexes, without sacrificing accuracy.