Jian Tang

GENERator-v2: Reconciling Coarse Tokenization with Single-Nucleotide Resolution in Genomic Language Modeling

This paper introduces improved genomic language models that balance long-range context with single-nucleotide resolution, achieving better performance and efficiency than prior methods.

Rapid De Novo Antibody Design with GeoFlow-V3

GeoFlow-V3 designs nanobodies de novo with high hit rates, reducing experimental screening needs and improving antibody discovery efficiency.

Bering: joint cell segmentation and annotation for spatial transcriptomics with transferred graph embeddings

Bering improves cell segmentation and annotation in spatial transcriptomics by using graph embeddings and transfer learning, achieving better accuracy across different technologies and tissues.

Pretrainable Geometric Graph Neural Network for Antibody Affinity Maturation

This paper introduces GearBind, a geometric graph neural network for in silico antibody affinity maturation, achieving significant improvements in binding affinity.

Path-based reasoning in biomedical knowledge graphs with BioPathNet

BioPathNet improves link prediction in biomedical knowledge graphs by using path-based reasoning, outperforming existing methods and identifying novel drug indications and gene interactions.

Learning interpretable cellular and gene signature embeddings from single-cell transcriptomic data

This paper introduces scETM, a model that learns interpretable gene and cell type embeddings from scRNA-seq data, showing cross-tissue and cross-species transferability.