5 citations · 9 across the 13 of their papers we have counts for
13 papers
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…
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…
A Review of BioTree Construction in the Context of Information Fusion: Priors, Methods, Applications and Trends
Zelin Zang, Yongjie Xu, Chenrui Duan +4
Biological tree (BioTree) analysis is a foundational tool in biology, enabling the exploration of evolutionary and differentiation relationships among organisms, genes, and cells.…
BioKGBench: A Knowledge Graph Checking Benchmark of AI Agent for Biomedical Science
Xinna Lin, Siqi Ma, Junjie Shan +5
Pursuing artificial intelligence for biomedical science, a.k.a. AI Scientist, draws increasing attention, where one common approach is to build a copilot agent driven by Large Lang…
Set-CLIP: Exploring Aligned Semantic From Low-Alignment Multimodal Data Through A Distribution View
Zijia Song, Zelin Zang, Yelin Wang +5
Multimodal fusion breaks through the boundaries between diverse modalities and has already achieved notable performances. However, in many specialized fields, it is struggling to o…
FGBERT: Function-Driven Pre-trained Gene Language Model for Metagenomics
ChenRui Duan, Zelin Zang, Yongjie Xu +6
Metagenomic data, comprising mixed multi-species genomes, are prevalent in diverse environments like oceans and soils, significantly impacting human health and ecological functions…
Must: Maximizing Latent Capacity of Spatial Transcriptomics Data
Zelin Zang, Liangyu Li, Yongjie Xu +5
Spatial transcriptomics (ST) technologies have revolutionized the study of gene expression patterns in tissues by providing multimodality data in transcriptomic, spatial, and morph…
Deep Manifold Transformation for Protein Representation Learning
Bozhen Hu, Zelin Zang, Cheng Tan +1
Protein representation learning is critical in various tasks in biology, such as drug design and protein structure or function prediction, which has primarily benefited from protei…
UDRN: Unified Dimensional Reduction Neural Network for Feature Selection and Feature Projection
Zelin Zang, Yongjie Xu, Linyan Lu +3
Dimensional reduction~(DR) maps high-dimensional data into a lower dimensions latent space with minimized defined optimization objectives. The DR method usually falls into feature…