5 citations · 9 across the 13 of their papers we have counts for
5 papers · 1 filter
Tool-Augmented On-Policy Distillation for LLM Domain Adaptation in Sequence-Based Omics Tasks
Jie Ying, Zhefan Wang, Zihong Chen +11
Multi-omics sequences contain complex biological patterns, yet deciphering their mechanisms for automated scientific discovery remains challenging. As large language models (LLMs)…
Graph-structured joint-embedding prediction for single-cell transcriptomics
Yuhao Wang, Zelin Zang, Yuxuan Liu +2
Single-cell transcriptomes are sparse, unordered measurements of coordinated biological activity, yet many self-supervised models define their learning target at the level of indiv…
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…