In the drug discovery process, the low success rate of drug candidate screening often leads to insufficient labeled data, causing the few-shot learning problem in molecular property prediction. Existing methods for few-shot molecular property prediction overlook the sample selection bias, which arises from non-random sample selection in chemical experiments. This bias in data representativeness leads to suboptimal performance. To overcome this challenge, we present a novel method named Contextual Representation Anchor Network (CRANet), where an anchor refers to a cluster center of the representations of molecules and serves as a bridge to transfer enriched contextual knowledge into molecular representations and enhance their expressiveness. CRANet introduces a dual-augmentation mechanism that includes context augmentation, which dynamically retrieves analogous unlabeled molecules and captures their task-specific contextual knowledge to enhance the anchors, and anchor augmentation, which leverages the anchors to augment the molecular representations. We evaluate our approach using the MoleculeNet and FS-Mol benchmarks, as well as through domain transfer experiments. The outcomes indicate that CRANet surpasses current state-of-the-art methods by 0.10% to 5.48% in AUC and 2.52% in ΔAUC-PR metrics, showcasing its exceptional generalization abilities.

Drug discovery is crucial for identifying candidate drugs for various diseases. However, its low success rate often results in a scarcity of annotations, posing a few-shot learning problem. Existing methods primarily focus on single-scale features, overlooking the hierarchical molecular structures that determine different molecular properties. To address these issues, we introduce Universal Matching Networks (UniMatch), a dual matching framework that integrates explicit hierarchical molecular matching with implicit task-level matching via meta- learning, bridging multi-level molecular representations and task-level generalization. Specifically, our approach explicitly captures structural features across multiple levels—atoms, substructures, and molecules—via hierarchical pooling and matching, facilitating precise molecular representation and comparison. Additionally, we employ a meta-learning strategy for implicit task-level matching, allowing the model to capture shared patterns across tasks and quickly adapt to new ones. This unified matching framework ensures effective molecular alignment while leveraging shared meta-knowledge for fast adaptation. Our experimental results demonstrate that UniMatch outperforms state-of-the-art methods on the MoleculeNet and FS-Mol benchmarks, achieving improvements of 2.87% in AUROC and 6.52% in ∆AUPRC. UniMatch also shows excellent generalization ability on the Meta-MolNet benchmark.

Effective molecular representation learning is crucial for advancing molecular property prediction and drug design. Mainstream molecular representation learning methods rely on Graph Neural Networks (GNNs) to model complex molecular structures. However, these GNN-based approaches struggle with three significant issues: insufficient annotations, molecular diversity, and architectural limitations such as over-squashing, which leads to the loss of critical structural details. To address these issues, we introduce a new class of GNNs that integrates the Kolmogorov-Arnold Networks (KANs), known for their robust data-fitting capabilities and high accuracy in small-scale AI + Science tasks. By incorporating KANs into GNNs, our model enhances the representation of molecular structures. We further advance this approach with a variant called SwallowKAN (SKAN), which employs adaptive Radial Basis Functions (RBFs) as the core of the non-linear neurons. This innovation improves both computational efficiency and adaptability to diverse molecular structures. Building on the strengths of SKAN, we propose a new class of GNNs, GNN-SKAN, and its augmented variant, GNN-SKAN+, which incorporates a SKAN-based classifier to further boost the performance. Experiments across 6 classification datasets, 6 regression datasets, and 4 few-shot learning datasets demonstrate that our approach achieves new state-of-the-art performance in terms of accuracy and computational cost.