Pretraining Graph Transformers with Atom-in-a-Molecule Quantum Properties for Improved ADMET Modeling

We evaluate the impact of pretraining Graph Transformer architectures on atom-level quantum-mechanical features for the modeling of absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties of drug-like compounds. We compare this pretraining strategy with two others: one based on molecular quantum properties (specifically the HOMO-LUMO gap) and one using a self-supervised atom masking technique. After fine-tuning on Therapeutic Data Commons ADMET datasets, we evaluate the performance improvement in the different models observing that models pretrained with atomic quantum mechanical properties produce in general better results. We then analyse the latent representations and observe that the supervised strategies preserve the pretraining information after finetuning and that different pretrainings produce different trends in latent expressivity across layers. Furthermore, we find that models pretrained on atomic quantum mechanical properties capture more low-frequency laplacian eigenmodes of the input graph via the attention weights and produce better representations of atomic environments within the molecule. Application of the analysis to a much larger non-public dataset for microsomal clearance illustrates generalizability of the studied indicators. In this case the performances of the models are in accordance with the representation analysis and highlight, especially for the case of masking pretraining and atom-level quantum property pretraining, how model types with similar performance on public benchmarks can have different performances on large scale pharmaceutical data.

Analysis of Atom-level pretraining with QM data for Graph Neural Networks Molecular property models

Despite the rapid and significant advancements in deep learning for Quantitative Structure-Activity Relationship (QSAR) models, the challenge of learning robust molecular representations that effectively generalize in real-world scenarios to novel compounds remains an elusive and unresolved task. This study examines how atom-level pretraining with quantum mechanics (QM) data can mitigate violations of assumptions regarding the distributional similarity between training and test data and therefore improve performance and generalization in downstream tasks. In the public dataset Therapeutics Data Commons (TDC), we show how pretraining on atom-level QM improves performance overall and makes the activation of the features distributes more Gaussian-like which results in a representation that is more robust to distribution shifts. To the best of our knowledge, this is the first time that hidden state molecular representations are analyzed to compare the effects of molecule-level and atom-level pretraining on QM data.

MEET: A Monte Carlo Exploration-Exploitation Trade-off for Buffer Sampling

Data selection is essential for any data-based optimization technique, such as Reinforcement Learning. State-of-the-art sampling strategies for the experience replay buffer improve the performance of the Reinforcement Learning agent. However, they do not incorporate uncertainty in the Q-Value estimation. Consequently, they cannot adapt the sampling strategies, including exploration and exploitation of transitions, to the complexity of the task. To address this, this paper proposes a new sampling strategy that leverages the exploration-exploitation trade-off. This is enabled by the uncertainty estimation of the Q-Value function, which guides the sampling to explore more significant transitions and, thus, learn a more efficient policy. Experiments on classical control environments demonstrate stable results across various environments. They show that the proposed method outperforms state-of-the-art sampling strategies for dense rewards w.r.t. convergence and peak performance by 26% on average.