2 citations · 2 across the 7 of their papers we have counts for
5 papers · 1 filter
Language-encoded network topology enables large language models to reason about complex networks
Ucchwas Talukder Utsha, Sakib Mostafa, James Zou +1
Networks describe systems in biology and beyond, from protein interactions and social relationships to power grids and citation records. Reasoning about such systems requires under…
A vision foundation model for single-cell biology via spatial gene cartography
Ridvan Yesiloglu, Sakib Mostafa, James Zou +5
Most single-cell foundation models are adapted from language models, representing each cell as a sequence of gene tokens. This discards the relationships among genes and often the…
Knowledge Graph Modulated Deep Learning for Limited-Sample Clinical Data Analysis
Yuwei Xue, Sakib Mostafa, James Zou +5
Biological systems are governed by structured molecular interactions, where pathways, regulatory circuits, and functional gene relationships shape cellular behavior and disease pro…
Toward a universal foundation model for graph-structured data
Sakib Mostafa, Lei Xing, Md. Tauhidul Islam
Graphs are a central representation in biomedical research, capturing molecular interaction networks, gene regulatory circuits, cell--cell communication maps, and knowledge graphs.…
Vision-based Deep Learning Analysis of Unordered Biomedical Tabular Datasets via Optimal Spatial Cartography
Sakib Mostafa, Tarik Massoud, Maximilian Diehn +2
Tabular data are central to biomedical research, from liquid biopsy and bulk and single-cell transcriptomics to electronic health records and phenotypic profiling. Unlike images or…