Organizations: University of Oxford, Oxford, United Kingdom · Tongji University, Shanghai, China · Hunan University, Changsha, China · University of Cambridge, Cambridge, United Kingdom · Computer Network Information Center, Chinese Academy of Sciences, Beijing, China
Abstract
The rapid growth of single-cell transcriptomic data has enabled the development of foundation models pretrained primarily by reconstructing masked expression values. This objective encourages these models to learn gene dependencies but does not directly optimize whole-cell representations, which are essential for many downstream tasks. To bridge this gap, we propose a contrastive pretraining framework that learns cell representations through complementary transcriptomic views. Since standard contrastive learning is not readily applicable to single-cell pretraining, we introduce specific adaptations along three dimensions --- co-expression-guided gene partitioning, expression-aware contrast-set construction, and competence-gated contrastive onset. Specifically, we first construct two complementary views of each cell by partitioning its genes according to their co-expression structure. Then, to prevent the model from using gene-set identity as a shortcut, we construct hard negatives by permuting expression values while keeping gene identities unchanged. Finally, we introduce a competence-aware controller to determine how the contrastive objective is applied. Experiments on cell-type annotation and gene regulatory network inference demonstrate competitive transfer under the evaluated protocols. In the six-network GRN evaluation, our method records the highest mean AUROC and AUPRC point estimates among the compared variants, while the highest-scoring variant differs across individual networks. These results establish complementary-view contrastive learning as an effective direction for single-cell pretraining beyond gene reconstruction.
Gene regulatory networks (GRNs) capture transcription factor-target interactions and are central to understanding cell-state regulation and disease. Reconstructing GRNs from paired single-cell transcriptomic and chromatin accessibility data is promising but challenging: scATAC is extremely sparse, and most methods rely on fixed peak-to-gene links and weak supervision. We present EpiAwareNet, a prior-guided multi-omic Transformer framework that reconstructs GRNs from paired single-cell data using only lightweight biological priors. In Stage 1, EpiAwareNet learns joint gene-peak representations with a gene-peak cross-attention module, enabling data-driven, gene-specific aggregation of accessibility signals rather than hard-coded peak-to-gene assignments. In Stage 2, EpiAwareNet incorporates a bulk-derived GRN prior as noisy positive edges to provide weak supervision under label scarcity, refining regulatory scores while remaining robust to prior noise. In our experiments, EpiAwareNet improves GRN reconstruction over representative single- and multi-omic baselines and yields GRNs with greater biological plausibility, such as improved recovery of known regulatory interactions, suggesting that lightweight biological priors from bulk data can effectively guide single-cell GRN inference when combined with adaptive cross-modal representation learning. Code and data will be available at https://github.com/tianyang-x/EpiAwareNet_pub.
Single-cell representation learning (SCRL) from gene expression data offers a way to uncover the complex regulatory logic underlying cellular function. Inspired by large language models in natural language modeling, several single-cell pretrained models have recently been proposed that treat genes as tokens and cells as sentences. However, these models are fundamentally limited by the long-tailed nature of cell-type distributions and struggle to generalize under covariate shifts in gene expression data. While fine-tuning is often used to mitigate these issues, we observe that performance remains bounded. To address this challenge, we introduce CellRefine, a post-pretraining method that operates between the pretraining and fine-tuning stages of a single-cell foundation model. CellRefine uses a multi-faceted objective that incorporates marker-gene sets as structural priors to guide post-pretraining and refine the latent embedding manifold of cells. Across multiple computational biology tasks, empirical results show that CellRefine consistently improves downstream performance, yielding gains up to 15%.
Gene Regulatory Network (GRN) inference is essential for understanding complex cellular mechanisms, rendered tractable through single-cell transcriptomic data. With the emergence of single-cell Foundation Models (scFMs), enhanced transcriptomic encoding is widely expected to revolutionize GRN inference. However, we observe that their performance remains far from satisfactory. The primary reason is that the standard reconstruction-based pre-training objectives often fail to explicitly capture latent regulatory signals. To bridge this gap, we first introduce a GRN generalization benchmark designed to evaluate regulatory predictions on unseen genes and datasets, which relies on the zero-shot capabilities of scFMs and is inherently challenging for traditional methods. Furthermore, to unlock the regulatory knowledge within the foundation models, we propose two novel methods, Virtual Value Perturbation and Gradient Trajectory, to distill implicit regulatory information from scFMs into highly generalizable inter-gene features. Extensive experiments demonstrate that our approach significantly outperforms existing methods, establishing a new paradigm for leveraging the potential of scFMs in universal GRN inference.