Leveraging Lineage Barcodes as Natural Augmentations for Contrastive Learning of Cell Fate in scRNA-seq Data

Abstract

Deciphering how cells commit to future fates is essential for developing precision therapeutics that can reprogram stem cells or modulate immune functions. However, isolating these fate-determining signals in single-cell lineage tracing (scLT) remains challenging because differentiation programs are often confounded by unrelated processes like the cell cycle. To address this, we introduce Lineage-aware Contrastive Learning (LCL), a framework that treats inheritable lineage barcodes as a "natural" data augmentation to isolate subtle, lineage-specific signals. LCL utilizes a semi-supervised architecture to align unlabeled cells, facilitating the transfer of lineage structures to clinical datasets where explicit barcoding is unavailable. We demonstrate LCL’s utility by predicting future cell-type compositions from early-time points, effectively modeling longitudinal fate commitment from cross-sectional data. Benchmarking on hematopoietic and fibroblast systems shows that LCL significantly outperforms standard models like scVI, establishing contrastive learning as a scalable paradigm for understanding and potentially manipulating cellular differentiation.