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, such as 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 delta AUPRC. UniMatch also shows excellent generalization ability on the Meta-MolNet benchmark.

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 (CRA), 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. CRA 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 on the MoleculeNet and FS-Mol benchmarks, as well as in domain transfer experiments. The results demonstrate that CRA outperforms the state-of-the-art by 2.60% and 3.28% in AUC and $\Delta$AUC-PR metrics, respectively, and exhibits superior generalization capabilities.

In multi-task learning, we often encounter the case when the presence of labels across samples exhibits irregular patterns: samples can be fully labeled, partially labeled or unlabeled. Taking drug analysis as an example, multiple toxicity properties of a drug molecule may not be concurrently available due to experimental limitations. It triggers a demand for a new training and inference mechanism that could accommodate irregularly present labels and maximize the utility of any available label information. In this work, we focus on the two-label learning task, and propose a novel training and inference framework, Dual-Label Learning (DLL). The DLL framework formulates the problem into a dual-function system, in which the two functions should simultaneously satisfy standard supervision, structural duality and probabilistic duality. DLL features a dual-tower model architecture that explicitly captures the information exchange between labels, aimed at maximizing the utility of partially available labels in understanding label correlation. During training, label imputation for missing labels is conducted as part of the forward propagation process, while during inference, labels are regarded as unknowns of a bivariate system of equations and are solved jointly. Theoretical analysis guarantees the feasibility of DLL, and extensive experiments are conducted to verify that by explicitly modeling label correlation and maximizing the utility of available labels, our method makes consistently better predictions than baseline approaches by up to a 10% gain in F1-score or MAPE. Remarkably, our method provided with data at a label missing rate as high as 60% can achieve similar or even better results than baseline approaches at a label missing rate of only 10%.

Block-wise missing data poses significant challenges in real-world data imputation tasks. Compared to scattered missing data, block-wise gaps exacerbate adverse effects on subsequent analytic and machine learning tasks, as the lack of local neighboring elements significantly reduces the interpolation capability and predictive power. However, this issue has not received adequate attention. Most SOTA matrix completion methods appeared less effective, primarily due to overreliance on neighboring elements for predictions. We systematically analyze the issue and propose a novel matrix completion method ``BlockEcho" for a more comprehensive solution. This method creatively integrates Matrix Factorization (MF) within Generative Adversarial Networks (GAN) to explicitly retain long-distance inter-element relationships in the original matrix. Besides, we incorporate an additional discriminator for GAN, comparing the generator's intermediate progress with pre-trained MF results to constrain high-order feature distributions. Subsequently, we evaluate BlockEcho on public datasets across three domains. Results demonstrate superior performance over both traditional and SOTA methods when imputing block-wise missing data, especially at higher missing rates. The advantage also holds for scattered missing data at high missing rates. We also contribute on the analyses in providing theoretical justification on the optimality and convergence of fusing MF and GAN for missing block data.