Learning to design protein-protein interactions with enhanced generalization. - Anton Bushuiev; Roman Bushuiev; Petr Kouba; Anatolii Filkin; Marketa Gabrielova; Michal Gabriel; Jirí Sedlár; Tomás Pluskal; Jirí Damborský; Stanislav Mazurenko; Josef Sivic (ICLR, 2024)

MassSpecGym: A benchmark for the discovery and identification of molecules. - Roman Bushuiev; Anton Bushuiev; Niek F. de Jonge; Adamo Young; Fleming Kretschmer; Raman Samusevich; Janne Heirman; Fei Wang 062; Luke Zhang; Kai Dührkop; Marcus Ludwig; Nils A. Haupt; et al. (NeurIPS, 2024)

Revealing data leakage in protein interaction benchmarks. - Anton Bushuiev; Roman Bushuiev; Jirí Sedlár; Tomás Pluskal; Jirí Damborský; Stanislav Mazurenko; Josef Sivic (CoRR, 2024)

Training on test proteins improves fitness, structure, and function prediction. - Anton Bushuiev; Roman Bushuiev; Nikola Zadorozhny; Raman Samusevich; Hannes Stärk; Jirí Sedlár; Tomás Pluskal; Josef Sivic (CoRR, 2024)

Machine Learning for Protein-Protein and Protein-Ligand Interactions (Dagstuhl Seminar 24451). - Anne-Florence Bitbol; Jennifer Listgarten; Tomás Pluskal; Anton Bushuiev; Roman Bushuiev (Dagstuhl Reports, 2024)

An evaluation methodology for machine learning-based tandem mass spectra similarity prediction. - Michael Strobel 002; Alberto Gil-de-la-Fuente; Mohammad Reza Shahneh; Yasin El Abiead; Roman Bushuiev; Anton Bushuiev; Tomás Pluskal; Mingxun Wang 001 (BMC Bioinform., 2025)