Albert Bou

Albert Bou, Matteo Bettini, Sebastian Dittert et al.

PyTorch has ascended as a premier machine learning framework, yet it lacks a native and comprehensive library for decision and control tasks suitable for large development teams dealing with complex real-world data and environments. To address this issue, we propose TorchRL, a generalistic control library for PyTorch that provides well-integrated, yet standalone components. We introduce a new and flexible PyTorch primitive, the TensorDict, which facilitates streamlined algorithm development across the many branches of Reinforcement Learning (RL) and control. We provide a detailed description of the building blocks and an extensive overview of the library across domains and tasks. Finally, we experimentally demonstrate its reliability and flexibility and show comparative benchmarks to demonstrate its computational efficiency. TorchRL fosters long-term support and is publicly available on GitHub for greater reproducibility and collaboration within the research community. The code is open-sourced on GitHub.

Nikolai Schapin, Carles Navarro, Albert Bou et al.

Binding affinity optimization is crucial in early-stage drug discovery. While numerous machine learning methods exist for predicting ligand potency, their comparative efficacy remains unclear. This study evaluates the performance of classical tree-based models and advanced neural networks in protein-ligand binding affinity prediction. Our comprehensive benchmarking encompasses 2D models utilizing ligand-only RDKit embeddings and Large Language Model (LLM) ligand representations, as well as 3D neural networks incorporating bound protein-ligand conformations. We assess these models across multiple standard datasets, examining various predictive scenarios including classification, ranking, regression, and active learning. Results indicate that simpler models can surpass more complex ones in specific tasks, while 3D models leveraging structural information become increasingly competitive with larger training datasets containing compounds with labelled affinity data against multiple targets. Pre-trained 3D models, by incorporating protein pocket environments, demonstrate significant advantages in data-scarce scenarios for specific binding pockets. Additionally, LLM pretraining on 2D ligand data enhances complex model performance, providing versatile embeddings that outperform traditional RDKit features in computational efficiency. Finally, we show that combining 2D and 3D model strengths improves active learning outcomes beyond current state-of-the-art approaches. These findings offer valuable insights for optimizing machine learning strategies in drug discovery pipelines.

Albert Bou, Morgan Thomas, Sebastian Dittert et al.

In recent years, reinforcement learning (RL) has emerged as a valuable tool in drug design, offering the potential to propose and optimize molecules with desired properties. However, striking a balance between capabilities, flexibility, reliability, and efficiency remains challenging due to the complexity of advanced RL algorithms and the significant reliance on specialized code. In this work, we introduce ACEGEN, a comprehensive and streamlined toolkit tailored for generative drug design, built using TorchRL, a modern RL library that offers thoroughly tested reusable components. We validate ACEGEN by benchmarking against other published generative modeling algorithms and show comparable or improved performance. We also show examples of ACEGEN applied in multiple drug discovery case studies. ACEGEN is accessible at \url{https://github.com/acellera/acegen-open} and available for use under the MIT license.

Morgan Thomas, Albert Bou, Jose Carlos Gómez-Tamayo et al.

Chemical language models, combined with reinforcement learning (RL), have shown significant promise to efficiently traverse large chemical spaces for drug discovery. However, the performance of various RL algorithms and their best practices for practical drug discovery are still unclear. Here, starting from the principles of the REINFORCE algorithm, we investigate the effect of different components from RL theory including experience replay, hill-climbing, baselines to reduce variance, and alternative reward shaping. We propose a new regularization method more aligned to REINFORCE than current standard practices, and demonstrate how RL hyperparameters can be fine-tuned for effectiveness and efficiency. Lastly, we apply our learnings to practical drug discovery by demonstrating enhanced learning efficiency on frontier binding affinity models by using Boltz2 as a reward model. We share our RL models used in the ACEGEN repository, and hope the experiments here act as a guide to researchers applying RL to chemical language models for drug discovery.

Morgan Thomas, Albert Bou, Gianni De Fabritiis

Chemical Language Models (CLMs) leveraging reinforcement learning (RL) have shown promise in de novo molecular design, yet often suffer from mode collapse, limiting their exploration capabilities. Inspired by Test-Time Training (TTT) in large language models, we propose scaling TTT for CLMs to enhance chemical space exploration. We introduce MolExp, a novel benchmark emphasizing the discovery of structurally diverse molecules with similar bioactivity, simulating real-world drug design challenges. Our results demonstrate that scaling TTT by increasing the number of independent RL agents follows a log-linear scaling law, significantly improving exploration efficiency as measured by MolExp. In contrast, increasing TTT training time yields diminishing returns, even with exploration bonuses. We further evaluate cooperative RL strategies to enhance exploration efficiency. These findings provide a scalable framework for generative molecular design, offering insights into optimizing AI-driven drug discovery.

Albert Bou, Sebastian Dittert, Gianni De Fabritiis

Advancing reinforcement learning (RL) requires tools that are flexible enough to easily prototype new methods while avoiding impractically slow experimental turnaround times. To match the first requirement, the most popular RL libraries advocate for highly modular agent composability, which facilitates experimentation and development. To solve challenging environments within reasonable time frames, scaling RL to large sampling and computing resources has proved a successful strategy. However, this capability has been so far difficult to combine with modularity. In this work, we explore design choices to allow agent composability both at a local and distributed level of execution. We propose a versatile approach that allows the definition of RL agents at different scales through independent reusable components. We demonstrate experimentally that our design choices allow us to reproduce classical benchmarks, explore multiple distributed architectures, and solve novel and complex environments while giving full control to the user in the agent definition and training scheme definition. We believe this work can provide useful insights to the next generation of RL libraries.