MolGraph-xLSTM: A graph-based dual-level xLSTM framework with multi-head mixture-of-experts for enhanced molecular representation and interpretability

Abstract

Predicting molecular properties is essential for drug discovery, and computational methods can greatly enhance this process. Molecular graphs have become a focus for representation learning, with Graph Neural Networks (GNNs) widely used. However, GNNs often struggle with capturing long-range dependencies. To address this, we propose MolGraph-xLSTM, a novel graph-based xLSTM model that enhances feature extraction and effectively models molecule long-range interactions. Our approach processes molecular graphs at two scales: atom-level and motif-level. For atom-level graphs, a GNN-based xLSTM framework with jumping knowledge extracts local features and aggregates multilayer information to capture both local and global patterns effectively. Motif-level graphs provide complementary structural information for a broader molecular view. Embeddings from both scales are refined via a multi-head mixture of experts (MHMoE), further enhancing expressiveness and performance. We validate MolGraph-xLSTM on 10 molecular property prediction datasets, covering both classification and regression tasks. Our model demonstrates consistent performance across all datasets, with improvements of up to 7.03% on the BBBP dataset for classification and 7.54% on the ESOL dataset for regression compared to baselines. On average, MolGraph-xLSTM achieves an AUROC improvement of 3.18\% for classification tasks and an RMSE reduction of 3.83\% across regression datasets compared to the baseline methods. These results confirm the effectiveness of our model, offering a promising solution for molecular representation learning for drug discovery.