21 citations · 45 across the 11 of their papers we have counts for
11 papers
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…
PhyloGen: Language Model-Enhanced Phylogenetic Inference via Graph Structure Generation
ChenRui Duan, Zelin Zang, Siyuan Li +2
Phylogenetic trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths)…
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.…
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…
Non-equispaced Fourier Neural Solvers for PDEs
Haitao Lin, Lirong Wu, Yongjie Xu +4
Solving partial differential equations is difficult. Recently proposed neural resolution-invariant models, despite their effectiveness and efficiency, usually require equispaced sp…
Protein Language Models and Structure Prediction: Connection and Progression
Bozhen Hu, Jun Xia, Jiangbin Zheng +4
The prediction of protein structures from sequences is an important task for function prediction, drug design, and related biological processes understanding. Recent advances have…
EVNet: An Explainable Deep Network for Dimension Reduction
Zelin Zang, Shenghui Cheng, Linyan Lu +7
Dimension reduction (DR) is commonly utilized to capture the intrinsic structure and transform high-dimensional data into low-dimensional space while retaining meaningful propertie…
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…
Unsupervised Deep Manifold Attributed Graph Embedding
Zelin Zang, Siyuan Li, Di Wu +3
Unsupervised attributed graph representation learning is challenging since both structural and feature information are required to be represented in the latent space. Existing meth…
Conditional Local Convolution for Spatio-temporal Meteorological Forecasting
Haitao Lin, Zhangyang Gao, Yongjie Xu +3
Spatio-temporal forecasting is challenging attributing to the high nonlinearity in temporal dynamics as well as complex location-characterized patterns in spatial domains, especial…