MVKTrans: Multi-View Knowledge Transfer for Robust Multiomics Classification

The distinct characteristics of multiomics data, including complex interactions within and across biological layers and disease heterogeneity (e.g., heterogeneity in etiology and clinical symptoms), drive us to develop novel designs to address unique challenges in multiomics prediction. In this paper, we propose the multi-view knowledge transfer learning (MVKTrans) framework, which transfers intra- and inter-omics knowledge in an adaptive manner by reviewing data heterogeneity and suppressing bias transfer, thereby enhancing classification performance. Specifically, we design a graph contrastive module that is trained on unlabeled data to effectively learn and transfer the underlying intra-omics patterns to the supervised task. This unsupervised pretraining promotes learning general and unbiased representations for each modality, regardless of the downstream tasks. In light of the varying discriminative capacities of modalities across different diseases and/or samples, we introduce an adaptive and bi-directional cross-omics distillation module. This module automatically identifies richer modalities and facilitates dynamic knowledge transfer from more informative to less informative omics, thereby enabling a more robust and generalized integration. Extensive experiments on four real biomedical datasets demonstrate the superior performance and robustness of MVKTrans compared to the state-of-the-art. Code and data are available at https://github.com/Yaolab-fantastic/MVKTrans.

Can Large Language Models Empower Molecular Property Prediction?

Molecular property prediction has gained significant attention due to its transformative potential in multiple scientific disciplines. Conventionally, a molecule graph can be represented either as a graph-structured data or a SMILES text. Recently, the rapid development of Large Language Models (LLMs) has revolutionized the field of NLP. Although it is natural to utilize LLMs to assist in understanding molecules represented by SMILES, the exploration of how LLMs will impact molecular property prediction is still in its early stage. In this work, we advance towards this objective through two perspectives: zero/few-shot molecular classification, and using the new explanations generated by LLMs as representations of molecules. To be specific, we first prompt LLMs to do in-context molecular classification and evaluate their performance. After that, we employ LLMs to generate semantically enriched explanations for the original SMILES and then leverage that to fine-tune a small-scale LM model for multiple downstream tasks. The experimental results highlight the superiority of text explanations as molecular representations across multiple benchmark datasets, and confirm the immense potential of LLMs in molecular property prediction tasks. Codes are available at \url{https://github.com/ChnQ/LLM4Mol}.