9 papers
GLACIER: Rethinking Mass Spectrum Prediction as an Object Detection Problem
Rui-Xi Wang, Runzhong Wang, Connor W. Coley
Predicting tandem mass spectra (MS/MS) from molecular structures represents a central task in analytical chemistry with direct relevance to clinical metabolomics, systems biology,…
MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery
Hongxuan Liu, Roman Bushuiev, Ivy Lightheart +12
Reliable benchmarking is critical for developing machine learning models for tandem mass spectrometry (MS/MS) based molecule discovery. Subtle issues in experimental design and mod…
FRIGID: Scaling Diffusion-Based Molecular Generation from Mass Spectra at Training and Inference Time
Montgomery Bohde, Hongxuan Liu, Mrunali Manjrekar +4
Tandem mass spectrometry is prominent in scientific discovery workflows for identifying unknown small molecules, yet high-throughput structural elucidation remains challenging. Whi…
Generative structural elucidation from mass spectra as an iterative optimization problem
Mrunali Manjrekar, Runzhong Wang, Samuel Goldman +2
Liquid chromatography tandem mass spectrometry (LC-MS/MS) is a critical analytical technique for molecular identification across metabolomics, environmental chemistry, and chemical…
Neural Graph Matching Improves Retrieval Augmented Generation in Molecular Machine Learning
Runzhong Wang, Rui-Xi Wang, Mrunali Manjrekar +1
Molecular machine learning has gained popularity with the advancements of geometric deep learning. In parallel, retrieval-augmented generation has become a principled approach comm…
Optimization of Robotic Liquid Handling as a Capacitated Vehicle Routing Problem
Guangqi Wu, Runzhong Wang, Connor W. Coley
We present an optimization strategy to reduce the execution time of liquid handling operations in the context of an automated chemical laboratory. By formulating the task as a capa…