DCAFA: Differential Community Abundance and Feature Analysis for Histological Images

Abstract

Histological images are composed of diverse local structures such as cells, glands, or tissue patches, whose organisation and relative abundance reflect underlying biological processes. While most computational approaches focus on analysing individual features, many clinically relevant signals arise from changes in the composition of these structures rather than isolated measurements. This motivates the need for explicitly modelling how groups of similar instances vary across samples and relate to outcomes. We present DCAFA (Differential Community Abundance and Feature Attribution Analysis), a regression-based framework for analysing hierarchical biomedical data through both compositional and feature-level perspectives. DCAFA groups instances into latent communities representing recurring morphological or phenotypic patterns, and then performs two complementary analyses: (i) community composition analysis, which identifies groups that are enriched or depleted across outcomes, and (ii) feature attribution analysis, which quantifies how instance-level features relate to outcomes directly or within specific communities. Both use generalised linear and mixed-effects models, enabling covariate adjustment and inference through effect sizes, confidence intervals, and false discovery rate control. We demonstrate the utility of DCAFA across multiple biomedical settings, including endometrial histopathology, spatial transcriptomics, multiplex immunofluorescence imaging, and predefined cell-type analyses in colorectal cancer. These examples identify interpretable compositional shifts and context-specific feature associations that are not captured by conventional feature-based approaches. By unifying differential abundance testing and feature attribution within a single statistical framework, DCAFA serves as an openly available toolbox that provides a practical and interpretable means of linking tissue composition with clinical or molecular outcomes in biomedical imaging data. Code available at: https://github.com/wgrgwrght/DCAFA