arXiv:2606. 18672v1 Announce Type: cross Abstract: Single-cell RNA sequencing (scRNA-seq) serves a pivotal role in characterizing gene expression at the cellular level, enabling the identification of cell types and advancing the understanding of cellular heterogeneity.
arXiv:2606. 13007v1 Announce Type: cross Abstract: Clustering is fundamental to scRNA-seq analysis, serving as a cornerstone for identifying cell populations and resolving tissue heterogeneity.
arXiv:2606. 28459v1 Announce Type: new Abstract: Single-cell RNA sequencing (scRNA-seq) clustering is essential for identifying cell types, but high dimensionality, sparsity, dropout, and technical noise hinder robust expression representation and cell graph construction.
arXiv:2606. 14734v1 Announce Type: cross Abstract: Motivation: Gene regulatory network inference from single-cell RNA sequencing (scRNA-seq) data is important for uncovering cell-state-specific transcriptional programs.
arXiv:2606. 07676v1 Announce Type: cross Abstract: Spatial transcriptomics (ST) is a powerful tool for exploring biological properties dependent on structure, proximity, and interaction in tissue.
arXiv:2506. 11152v4 Announce Type: replace-cross Abstract: Single-cell transcriptomics and proteomics have become a great source for data-driven insights into biology, enabling the use of advanced deep learning methods to understand cellular heterogeneity and gene expression at the single-cell level.
arXiv:2607. 14410v1 Announce Type: new Abstract: Spatially resolved omics studies increasingly combine transcriptomic and epigenomic assays, yet downstream analysis is often still performed using single-modality pipelines.
arXiv:2606. 09558v1 Announce Type: cross Abstract: Motivation: Transformer-based models are increasingly applied to large-scale single-cell transcriptomics, showing strong performance through self-supervised learning on millions of cells.
arXiv:2607. 13120v1 Announce Type: cross Abstract: Inferring gene regulatory networks (GRNs) from single-cell transcriptomic data is crucial for biological discovery, yet existing approaches suffer from a fundamental misalignment with real-world needs.
arXiv:2506. 22228v2 Announce Type: replace-cross Abstract: Single-cell sequencing is revolutionizing biology by enabling detailed investigations of cell-state transitions.
arXiv:2608. 05928v1 Announce Type: new Abstract: Single-cell transcriptomes are sparse observations of coordinated biological programmes, yet most self-supervised models learn by reconstructing individual genes.
arXiv:2607. 29043v1 Announce Type: cross Abstract: Single-cell RNA sequencing (scRNA-seq) has become an essential tool in modern cellular biology, and generating accurate synthetic scRNA-seq data is becoming increasingly important.
Single-cell transcriptomes are sparse observations of coordinated biological programmes, yet most self-supervised models learn by reconstructing individual genes. Here we present BioM-JEPA, a joint-embedding predictive architecture that instead predicts aggregate representations of graph-connected gene blocks defined by protein-association and corpus-derived coexpression evidence.