5 papers
SpecBridge: Bridging Mass Spectrometry and Molecular Representations via Cross-Modal Alignment
Yinkai Wang, Yan Zhou Chen, Xiaohui Chen +2
Small-molecule identification from tandem mass spectrometry (MS/MS) remains a bottleneck in untargeted settings where spectral libraries are incomplete. While deep learning offers…
Graph Generative Pre-trained Transformer
Xiaohui Chen, Yinkai Wang, Jiaxing He +4
Graph generation is a critical task in numerous domains, including molecular design and social network analysis, due to its ability to model complex relationships and structured da…
MADGEN: Mass-Spec attends to De Novo Molecular generation
Yinkai Wang, Xiaohui Chen, Liping Liu +1
The annotation (assigning structural chemical identities) of MS/MS spectra remains a significant challenge due to the enormous molecular diversity in biological samples and the lim…
MassSpecGym: A benchmark for the discovery and identification of molecules
Roman Bushuiev, Anton Bushuiev, Niek F. de Jonge +27
The discovery and identification of molecules in biological and environmental samples is crucial for advancing biomedical and chemical sciences. Tandem mass spectrometry (MS/MS) is…
Large Language Model is Secretly a Protein Sequence Optimizer
Yinkai Wang, Jiaxing He, Yuanqi Du +5
We consider the protein sequence engineering problem, which aims to find protein sequences with high fitness levels, starting from a given wild-type sequence. Directed evolution ha…