7 citations · 21 across the 5 of their papers we have counts for
5 papers
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…
One protein is all you need
Anton Bushuiev, Roman Bushuiev, Olga Pimenova +9
Generalization beyond training data remains a central challenge in machine learning for biology. A common way to enhance generalization is self-supervised pre-training on large dat…
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…
Revealing data leakage in protein interaction benchmarks
Anton Bushuiev, Roman Bushuiev, Jiri Sedlar +4
In recent years, there has been remarkable progress in machine learning for protein-protein interactions. However, prior work has predominantly focused on improving learning algori…
Learning to design protein-protein interactions with enhanced generalization
Anton Bushuiev, Roman Bushuiev, Petr Kouba +8
Discovering mutations enhancing protein-protein interactions (PPIs) is critical for advancing biomedical research and developing improved therapeutics. While machine learning appro…