xSiGra: explainable model for single-cell spatial data elucidation.
Aishwarya BudhkarZiyang TangXiang LiuXuhong ZhangJing SuQianqian SongPublished in: Briefings in bioinformatics (2024)
Recent advancements in spatial imaging technologies have revolutionized the acquisition of high-resolution multichannel images, gene expressions, and spatial locations at the single-cell level. Our study introduces xSiGra, an interpretable graph-based AI model, designed to elucidate interpretable features of identified spatial cell types, by harnessing multimodal features from spatial imaging technologies. By constructing a spatial cellular graph with immunohistology images and gene expression as node attributes, xSiGra employs hybrid graph transformer models to delineate spatial cell types. Additionally, xSiGra integrates a novel variant of gradient-weighted class activation mapping component to uncover interpretable features, including pivotal genes and cells for various cell types, thereby facilitating deeper biological insights from spatial data. Through rigorous benchmarking against existing methods, xSiGra demonstrates superior performance across diverse spatial imaging datasets. Application of xSiGra on a lung tumor slice unveils the importance score of cells, illustrating that cellular activity is not solely determined by itself but also impacted by neighboring cells. Moreover, leveraging the identified interpretable genes, xSiGra reveals endothelial cell subset interacting with tumor cells, indicating its heterogeneous underlying mechanisms within complex cellular interactions.
Keyphrases
- single cell
- high resolution
- induced apoptosis
- gene expression
- rna seq
- cell cycle arrest
- convolutional neural network
- cell therapy
- big data
- stem cells
- endothelial cells
- artificial intelligence
- cell death
- electronic health record
- computed tomography
- oxidative stress
- magnetic resonance imaging
- lymph node
- endoplasmic reticulum stress
- copy number
- pi k akt
- pain management