MADD: Multi-Agent Drug Discovery Orchestra

Hit identification is a central challenge in early drug discovery, traditionally requiring substantial experimental resources. Recent advances in artificial intelligence, particularly large language models (LLMs), have enabled virtual screening methods that reduce costs and improve efficiency. However, the growing complexity of these tools has limited their accessibility to wet-lab researchers. Multi-agent systems offer a promising solution by combining the interpretability of LLMs with the precision of specialized models and tools. In this work, we present MADD, a multi-agent system that builds and executes customized hit identification pipelines from natural language queries. MADD employs four coordinated agents to handle key subtasks in de novo compound generation and screening. We evaluate MADD across seven drug discovery cases and demonstrate its superior performance compared to existing LLM-based solutions. Using MADD, we pioneer the application of AI-first drug design to five biological targets and release the identified hit molecules. Finally, we introduce a new benchmark of query-molecule pairs and docking scores for over three million compounds to contribute to the agentic future of drug design.

Hybrid Generative AI for De Novo Design of Co-Crystals with Enhanced Tabletability

Co-crystallization is an accessible way to control physicochemical characteristics of organic crystals, which finds many biomedical applications. In this work, we present Generative Method for Co-crystal Design (GEMCODE), a novel pipeline for automated co-crystal screening based on the hybridization of deep generative models and evolutionary optimization for broader exploration of the target chemical space. GEMCODE enables fast de novo co-crystal design with target tabletability profiles, which is crucial for the development of pharmaceuticals. With a series of experimental studies highlighting validation and discovery cases, we show that GEMCODE is effective even under realistic computational constraints. Furthermore, we explore the potential of language models in generating co-crystals. Finally, we present numerous previously unknown co-crystals predicted by GEMCODE and discuss its potential in accelerating drug development.

Oil reservoir recovery factor assessment using Bayesian networks based on advanced approaches to analogues clustering

The work focuses on the modelling and imputation of oil and gas reservoirs parameters, specifically, the problem of predicting the oil recovery factor (RF) using Bayesian networks (BNs). Recovery forecasting is critical for the oil and gas industry as it directly affects a company's profit. However, current approaches to forecasting the RF are complex and computationally expensive. In addition, they require vast amount of data and are difficult to constrain in the early stages of reservoir development. To address this problem, we propose a BN approach and describe ways to improve parameter predictions' accuracy. Various training hyperparameters for BNs were considered, and the best ones were used. The approaches of structure and parameter learning, data discretization and normalization, subsampling on analogues of the target reservoir, clustering of networks and data filtering were considered. Finally, a physical model of a synthetic oil reservoir was used to validate BNs' predictions of the RF. All approaches to modelling based on BNs provide full coverage of the confidence interval for the RF predicted by the physical model, but at the same time require less time and data for modelling, which demonstrates the possibility of using in the early stages of reservoirs development. The main result of the work can be considered the development of a methodology for studying the parameters of reservoirs based on Bayesian networks built on small amounts of data and with minimal involvement of expert knowledge. The methodology was tested on the example of the problem of the recovery factor imputation.