Author name cluster

Daniil Polykovskiy

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4 papers

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AAAI Conference 2025 Conference Paper

BindGPT: A Scalable Framework for 3D Molecular Design via Language Modeling and Reinforcement Learning

Artem Zholus
Maksim Kuznetsov
Roman Schutski
Rim Shayakhmetov
Daniil Polykovskiy
Sarath Chandar
Alex Zhavoronkov

Generating novel active molecules for a given protein is an extremely challenging task for generative models that requires an understanding of the complex physical interactions between the molecule and its environment. This paper presents a novel generative model, BindGPT, which uses a conceptually simple but powerful approach to create 3D molecules within the protein's binding site. Our model produces molecular graphs and conformations jointly, eliminating the need for an extra graph reconstruction step. We pre-train BindGPT on a large-scale dataset and fine-tune it with reinforcement learning using scores from external simulation software. We demonstrate how a single pre-trained language model can serve at the same time as a 3D molecular generative model, a conformer generator conditioned on the molecular graph, and a pocket-conditioned 3D molecule generator. Notably, the model does not make any representational equivariance assumptions about the domain of generation. We show how such a simple conceptual approach combined with pre-training and scaling can perform on par or better than the current best-specialized diffusion models, language models, and graph neural networks while being two orders of magnitude cheaper to sample.

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AAAI Conference 2025 Conference Paper

nach0-pc: Multi-task Language Model with Molecular Point Cloud Encoder

Maksim Kuznetsov
Airat Valiev
Alex Aliper
Daniil Polykovskiy
Elena Tutubalina
Rim Shayakhmetov
Zulfat Miftahutdinov

Recent advancements have integrated Language Models (LMs) into a drug discovery pipeline. However, existing models mostly work with SMILES and SELFIES chemical string representations, which lack spatial features vital for drug discovery. Additionally, attempts to translate chemical 3D structures into text format encounter issues such as excessive length and insufficient atom connectivity information. To address these issues, we introduce nach0-pc, a model combining domain-specific encoder and textual representation to handle spatial arrangement of atoms effectively. Our approach utilizes a molecular point cloud encoder for concise and order-invariant structure representation. We introduce a novel pre-training scheme for molecular point clouds to distillate the knowledge from spatial molecular structures datasets. After fine-tuning within both single-task and multi-task frameworks, nach0-pc demonstrates performance comparable with other diffusion models in terms of generated samples quality across several established spatial molecular generation tasks. Notably, our model is a multi-task approach, in contrast to diffusion models being limited to single tasks. Additionally, it is capable of processing point cloud-related data, which language models are not capable of handling due to memory limitations. These lead to our model having reduced training and inference time while maintaining on par performance.

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AAAI Conference 2021 Conference Paper

MolGrow: A Graph Normalizing Flow for Hierarchical Molecular Generation

Maksim Kuznetsov
Daniil Polykovskiy

We propose a hierarchical normalizing flow model for generating molecular graphs. The model produces new molecular structures from a single-node graph by recursively splitting every node into two. All operations are invertible and can be used as plug-and-play modules. The hierarchical nature of the latent codes allows for precise changes in the resulting graph: perturbations in the top layer cause global structural changes, while perturbations in the consequent layers change the resulting molecule marginally. The proposed model outperforms existing generative graph models on the distribution learning task. We also show successful experiments on global and constrained optimization of chemical properties using latent codes of the model.

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NeurIPS Conference 2019 Conference Paper

A Prior of a Googol Gaussians: a Tensor Ring Induced Prior for Generative Models

Maxim Kuznetsov
Daniil Polykovskiy
Dmitry Vetrov
Alex Zhebrak

Generative models produce realistic objects in many domains, including text, image, video, and audio synthesis. Most popular models—Generative Adversarial Networks (GANs) and Variational Autoencoders (VAEs)—usually employ a standard Gaussian distribution as a prior. Previous works show that the richer family of prior distributions may help to avoid the mode collapse problem in GANs and to improve the evidence lower bound in VAEs. We propose a new family of prior distributions—Tensor Ring Induced Prior (TRIP)—that packs an exponential number of Gaussians into a high-dimensional lattice with a relatively small number of parameters. We show that these priors improve Fréchet Inception Distance for GANs and Evidence Lower Bound for VAEs. We also study generative models with TRIP in the conditional generation setup with missing conditions. Altogether, we propose a novel plug-and-play framework for generative models that can be utilized in any GAN and VAE-like architectures.

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