Mitigating Bias in Spatial Transcriptomic Pipelines via Human Feedback

Abstract Biological discovery from experimental data, particularly large-scale assays, requires extensive preprocessing, during which raw outputs (e.g., images, sequences) are processed into structured forms that are more amenable to analysis. While statistical methods for such processed data are at the core of computational biology, the problem of coping with uncertainties introduced during preprocessing is a significant and underexplored issue. We address this issue in the context of differential expression analysis in spatial transcriptomics, which depends on a series of preprocessing steps, including demarcation of cell regions (segmentation), quantification of gene expression in cells, and cell-type annotation. We introduce Corrected Spatial Differential Expression (CSDE), a method that builds on Prediction-Powered Inference to leverage a small set of expert-validated data points (cells) to account for uncertainty due to preprocessing errors. Using two case studies, we demonstrate that CSDE produces more reliable and calibrated estimates of differential expression compared to the prevalent approach that neglects the impact of preprocessing. CSDE incorporates an efficient workflow to generate the required expert-annotated data, and is available as open-source at https://github.com/YosefLab/CSDE .