arXiv:2607. 23821v1 Announce Type: new Abstract: Identifying therapeutic target genes from single-cell RNA sequencing (scRNA-seq) data remains a fundamental challenge in translational biology.
By Shuyu Chen, Chen Zhu, Ye Zhang, Yang Li, Qiqi Xie, Haohan Wang
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.
By Hiren Madhu, Jo\~ao Felipe Rocha, Tinglin Huang, Siddharth Viswanath, Smita Krishnaswamy, Rex Ying
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.
arXiv:2607. 19400v1 Announce Type: new Abstract: Pre-trained foundation models (FMs) have begun transforming single-cell genomics, but scaling them raises privacy concerns.
By Jiayuan Ding, Jianhui Lin, Ziyang Miao, Nils Mechtel, Shiyu Jiang, Yixin Wang, Zhaoyu Fang, Jorge D. Martin-Rufino, Chen Weng, Reuben Saunders, Weize Xu, Jonathan S. Weissman, Min Li, Jiliang Tang, Wei Ouyang, Yuancheng Ryan Lu, Xiaojie Qiu
arXiv:2506. 22228v2 Announce Type: replace-cross Abstract: Single-cell sequencing is revolutionizing biology by enabling detailed investigations of cell-state transitions.
By Rong Ma, Xi Li, Jingyuan Hu, Bin Yu
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.
By Yuhao Wang, Zelin Zang, Yuxuan Liu, Zhen Lei, Stan Z. Li