2 citations · 2 across the 7 of their papers we have counts for
7 papers
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…
Transformation of Biological Networks into Images via Semantic Cartography for Visual Interpretation and Scalable Deep Analysis
Sakib Mostafa, Lei Xing, Md. Tauhidul Islam
Complex biological networks are fundamental to biomedical science, capturing interactions among molecules, cells, genes, and tissues. Deciphering these networks is critical for und…
On the Evolution of Neuron Communities in a Deep Learning Architecture
Sakib Mostafa, Debajyoti Mondal
Deep learning techniques are increasingly being adopted for classification tasks over the past decade, yet explaining how deep learning architectures can achieve state-of-the-art p…