18 papers
BioM-JEPA: joint-embedding prediction of graph-connected gene blocks in single cells
Yuhao Wang, Zelin Zang, Yuxuan Liu +2
Single-cell transcriptomes are sparse observations of coordinated biological programmes, yet most self-supervised models learn by reconstructing individual genes. Here we present B…
scHelix: Asymmetric Dual-Stream Integration via Explicit Gene-Level Disentanglement
Xichen Yan, Zelin Zang, Changxi Chi +8
A critical challenge in single-cell RNA sequencing (scRNA-seq) integration is resolving the tension between eliminating batch effects and maintaining biological fidelity. While rec…
HDTree: Generative Modeling of Cellular Hierarchies for Robust Lineage Inference
Zelin Zang, WenZhe Li, Yongjie Xu +5
In single-cell research, tracing and analyzing high-throughput single-cell differentiation trajectories is crucial for understanding biological processes. Key to this is the robust…
MAT-Cell: A Multi-Agent Tree-Structured Reasoning Framework for Batch-Level Single-Cell Annotation
Yehui Yang, Zelin Zang, Xienan Zheng +9
Automated single-cell annotation is difficult when the most abundant genes are not the most discriminative ones, or when a target state is poorly covered by a fixed reference atlas…
Doloris: Dual Conditional Diffusion Implicit Bridges with Sparsity Masking Strategy for Unpaired Single-Cell Perturbation Estimation
Changxi Chi, Jun Xia, Yufei Huang +9
Estimating single-cell responses across various perturbations facilitates the identification of key genes and enhances drug screening, significantly boosting experimental efficienc…
SurgMotion: A Video-Native Foundation Model for Universal Understanding of Surgical Videos
Jinlin Wu, Felix Holm, Chuxi Chen +17
While foundation models have advanced surgical video analysis, current approaches rely predominantly on pixel-level reconstruction objectives that waste model capacity on low-level…