5 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…
CellScientist: Dual-Space Hierarchical Orchestration for Closed-Loop Refinement of Virtual Cell Models
Mengran Li, Bo Li, Jiaying Wang +12
Virtual Cell Modeling (VCM) requires models that not only predict perturbation responses, but also support targeted revision when predictions fail. Current LLM-assisted modeling wo…
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…
Anatomy-R1: Enhancing Anatomy Reasoning in Multimodal Large Language Models via Anatomical Similarity Curriculum and Group Diversity Augmentation
Ziyang Song, Zelin Zang, Zuyao Chen +6
Multimodal Large Language Models (MLLMs) have achieved impressive progress in natural image reasoning, yet their potential in medical imaging remains underexplored, especially in c…