9 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…
ViroBench: Benchmarking Nucleotide Foundation Models on Viral Genomics Tasks
Dongxin Ye, Fang Hu, Han Hu +6
Nucleotide sequences constitute the fundamental genetic basis of biological systems, rendering viral genomic analysis critical for biomedical advancement. Despite progress in biolo…
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…
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…
Learning Cell-Aware Hierarchical Multi-Modal Representations for Robust Molecular Modeling
Mengran Li, Zelin Zang, Wenbin Xing +4
Understanding how chemical perturbations propagate through biological systems is essential for robust molecular property prediction. While most existing methods focus on chemical s…
MergeDNA: Context-aware Genome Modeling with Dynamic Tokenization through Token Merging
Siyuan Li, Kai Yu, Anna Wang +7
Modeling genomic sequences faces two unsolved challenges: the information density varies widely across different regions, while there is no clearly defined minimum vocabulary unit.…