通过自适应跨组学知识迁移,提升多组学分类的准确性和鲁棒性。
MVKTrans: Multi-View Knowledge Transfer for Robust Multiomics Classification
- 基于图对比学习在无标签数据上预训练,提取各组学通用特征。
- 在四个真实生物数据集上表现优于现有方法,提升分类性能。
- 适合研究疾病异质性、需融合多组学数据的生物医学工作者。
多组学数据具有层内与层间复杂交互关系及疾病异质性(如病因和临床症状差异),带来独特挑战。本文提出多视图知识迁移框架MVKTrans,通过自适应地转移组内与组间知识,缓解数据异质性并抑制偏差传播,从而提升分类性能。具体地,设计一个在无标签数据上训练的图对比模块,有效学习并传递底层组内模式至有监督任务,促进各模态生成通用且无偏表示。针对不同疾病/样本中各模态判别能力不一的问题,引入自适应双向跨组学蒸馏模块,自动识别信息量更丰富的模态,并动态实现从高信息模态向低信息模态的知识传递,增强整合的鲁棒性与泛化性。在四个真实生物医学数据集上的大量实验表明,MVKTrans显著优于当前最优方法。代码与数据见https://github.com/Yaolab-fantastic/MVKTrans。
原文摘要 · Abstract (English)
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.
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