5 papers
Fast and Interpretable Protein Substructure Alignment via Optimal Transport
Zhiyu Wang, Bingxin Zhou, Jing Wang +4
Proteins are essential biological macromolecules that execute life functions. Local structural motifs, such as active sites, are the most critical components for linking structure…
MoRE-GNN: Multi-omics Data Integration with a Heterogeneous Graph Autoencoder
Zhiyu Wang, Sonia Koszut, Pietro Liò +1
The integration of multi-omics single-cell data remains challenging due to high-dimensionality and complex inter-modality relationships. To address this, we introduce MoRE-GNN (Mul…
Topotein: Topological Deep Learning for Protein Representation Learning
Zhiyu Wang, Arian Jamasb, Mustafa Hajij +3
Protein representation learning (PRL) is crucial for understanding structure-function relationships, yet current sequence- and graph-based methods fail to capture the hierarchical…
BioMARS: A Multi-Agent Robotic System for Autonomous Biological Experiments
Yibo Qiu, Zan Huang, Zhiyu Wang +7
Large language models (LLMs) and vision-language models (VLMs) have the potential to transform biological research by enabling autonomous experimentation. Yet, their application re…
OASIS: Open Agent Social Interaction Simulations with One Million Agents
Ziyi Yang, Zaibin Zhang, Zirui Zheng +20
There has been a growing interest in enhancing rule-based agent-based models (ABMs) for social media platforms (i.e., X, Reddit) with more realistic large language model (LLM) agen…