arXiv subjects

Omar Eldaghar

Publications and source records attributed to Omar Eldaghar.

3 recordsLinked to original sources

arXiv2025

SPAC: A Python Package for Spatial Single-Cell Analysis of Multiplex Imaging

Multiplexed immunofluorescence microscopy captures detailed measurements of spatially resolved, multiple biomarkers simultaneously, revealing tissue composition and cellular interactions in situ among single cells. The growing scale and dimensional complexity of these datasets demand reproducible, comprehensive and user-friendly computational tools. To address this need, we developed SPAC (SPAtial single-Cell analysis), a Python-based package and a corresponding shiny application within an integrated, modular SPAC ecosystem (Liu et al., 2025) designed specifically for biologists without extensive coding expertise. Following image segmentation and extraction of spatially resolved single-cell data, SPAC streamlines downstream phenotyping and spatial analysis, facilitating characterization of cellular heterogeneity and spatial organization within tissues. Through scalable performance, specialized spatial statistics, highly customizable visualizations, and seamless workflows from dataset to insights, SPAC significantly lowers barriers to sophisticated spatial analyses.

cs.SE↗

arXiv2025

A spatial hypergraph model to smoothly interpolate between pairwise graphs and hypergraphs to study higher-order structures

We introduce a spatial graph and hypergraph model that smoothly interpolates between a graph with purely pairwise edges and a graph where all connections are in large hyperedges. The key component is a spatial clustering resolution parameter that varies between assigning all the vertices in a spatial region to individual clusters, resulting in the pairwise case, to assigning all the vertices in a spatial region to a single cluster, which results in the large hyperedge case. An important outcome of this model is that the spatial structure is invariant to the choice of hyperedges. Consequently, this model enables us to study clustering coefficients, graph diffusion, and epidemic spread and how their behavior changes as a function of the higher-order structure in the network with a fixed spatial substrate. We hope that our model will find future uses to distill or explain other behaviors in higher-order networks.

cs.SI↗

arXiv2023

Multi-scale Local Network Structure Critically Impacts Epidemic Spread and Interventions

Network epidemic simulation holds the promise of enabling fine-grained understanding of epidemic behavior, beyond that which is possible with coarse-grained compartmental models. Key inputs to these epidemic simulations are the networks themselves. However, empirical measurements and samples of realistic interaction networks typically display properties that are challenging to capture with popular synthetic models of networks. Our empirical results show that epidemic spread behavior is very sensitive to a subtle but ubiquitous form of multi-scale local structure that is not present in common baseline models, including (but not limited to) uniform random graph models (Erdos-Renyi), random configuration models (Chung-Lu), etc. Such structure is not necessary to reproduce very simple network statistics, such as degree distributions or triangle closing probabilities. However, we show that this multi-scale local structure impacts, critically, the behavior of more complex network properties, in particular the effect of interventions such as quarantining; and it enables epidemic spread to be halted in realistic interaction networks, even when it cannot be halted in simple synthetic models. Key insights from our analysis include how epidemics on networks with widespread multi-scale local structure are easier to mitigate, as well as characterizing which nodes are ultimately not likely to be infected. We demonstrate that this structure results from more than just local triangle structure in the network, and we illustrate processes based on homophily or social influence and random walks that suggest how this multi-scale local structure arises.

cs.SI↗