Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models. - Daniil Polykovskiy; Alexander Zhebrak; Benjamín Sánchez-Lengeling; Sergey Golovanov; Oktai Tatanov; Stanislav Belyaev; Rauf Kurbanov; Aleksey Artamonov; Vladimir Aladinskiy; Mark Veselov; Artur Kadurin; Sergey I. Nikolenko; et al. (CoRR, 2018)

Fair Evaluation in Concept Normalization: a Large-scale Comparative Analysis for BERT-based Models. - Elena Tutubalina; Artur Kadurin; Zulfat Miftahutdinov (COLING, 2020)

Drug and Disease Interpretation Learning with Biomedical Entity Representation Transformer. - Zulfat Miftahutdinov; Artur Kadurin; Roman Kudrin; Elena Tutubalina (ECIR (1), 2021)

Medical concept normalization in clinical trials with drug and disease representation learning. - Zulfat Miftahutdinov; Artur Kadurin; Roman Kudrin; Elena Tutubalina (Bioinform., 2021)

Graph-Enriched Biomedical Entity Representation Transformer. - Andrey Sakhovskiy; Natalia Semenova; Artur Kadurin; Elena Tutubalina (CLEF, 2023)

Gradual Optimization Learning for Conformational Energy Minimization. - Artem Tsypin; Leonid Ugadiarov; Kuzma Khrabrov; Manvel Avetisian; Alexander Telepov; Egor Rumiantsev; Alexey Skrynnik; Aleksandr I. Panov; Dmitry P. Vetrov; Elena Tutubalina; Artur Kadurin (CoRR, 2023)

FREED++: Improving RL Agents for Fragment-Based Molecule Generation by Thorough Reproduction. - Alexander Telepov; Artem Tsypin; Kuzma Khrabrov; Sergey Yakukhnov; Pavel Strashnov; Petr Zhilyaev; Egor Rumiantsev; Daniel Ezhov; Manvel Avetisian; Olga Popova; Artur Kadurin (Trans. Mach. Learn. Res., 2023)

MineralImage5k: A benchmark for zero-shot raw mineral visual recognition and description. - Sergey Nesteruk; Julia Agafonova; Igor Pavlov; Maxim Gerasimov; Nikolay Latyshev; Denis Dimitrov; Andrey Kuznetsov; Artur Kadurin; Pavel Plechov (Comput. Geosci., 2023)

Lost in Translation: Chemical Language Models and the Misunderstanding of Molecule Structures. - Veronika Ganeeva; Andrey Sakhovskiy; Kuzma Khrabrov; Andrey V. Savchenko; Artur Kadurin; Elena Tutubalina (EMNLP (Findings), 2024)

Chemical Language Models Have Problems with Chemistry: A Case Study on Molecule Captioning Task. - Veronika Ganeeva; Kuzma Khrabrov; Artur Kadurin; Andrey V. Savchenko; Elena Tutubalina (Tiny Papers @ ICLR, 2024)

Gradual Optimization Learning for Conformational Energy Minimization. - Artem Tsypin; Leonid Ugadiarov; Kuzma Khrabrov; Alexander Telepov; Egor Rumiantsev; Alexey Skrynnik; Aleksandr Panov; Dmitry P. Vetrov; Elena Tutubalina; Artur Kadurin (ICLR, 2024)

Biomedical Entity Representation with Graph-Augmented Multi-Objective Transformer. - Andrey Sakhovskiy; Natalia Semenova; Artur Kadurin; Elena Tutubalina (NAACL-HLT (Findings), 2024)

$ nabla^2$DFT: A Universal Quantum Chemistry Dataset of Drug-Like Molecules and a Benchmark for Neural Network Potentials. - Kuzma Khrabrov; Anton Ber; Artem Tsypin; Konstantin Ushenin; Egor Rumiantsev; Alexander Telepov; Dmitry Protasov; Ilya Shenbin; Anton Alekseev 001; Mikhail Shirokikh; Sergey I. Nikolenko; Elena Tutubalina; et al. (NeurIPS, 2024)

∇2DFT: A Universal Quantum Chemistry Dataset of Drug-Like Molecules and a Benchmark for Neural Network Potentials. - Kuzma Khrabrov; Anton Ber; Artem Tsypin; Konstantin Ushenin; Egor Rumiantsev; Alexander Telepov; Dmitry Protasov; Ilya Shenbin; Anton Alekseev 001; Mikhail Shirokikh; Sergey I. Nikolenko; Elena Tutubalina; et al. (CoRR, 2024)

AFToolkit: a framework for molecular modeling of proteins with AlphaFold-derived representations. - Maria Sindeeva; Alexander Telepov; Nikita Ivanisenko; Tatiana I Shashkova; Kuzma Khrabrov; Artem Tsypin; Artur Kadurin; Olga L. Kardymon (Briefings Bioinform., 2025)

LAGNet: better electron density prediction for LCAO-based data and drug-like substances. - Konstantin Ushenin; Kuzma Khrabrov; Artem Tsypin; Anton Ber; Egor Rumiantsev; Artur Kadurin (J. Cheminformatics, 2025)