通过对抗域适应,实现不同基因表达数据间的知识迁移。
Adversarial Domain Adaptation Enables Knowledge Transfer Across Heterogeneous RNA-Seq Datasets
- 构建对抗式域适应框架,学习跨数据集的不变特征表示
- 在低数据场景下分类准确率显著提升,最高达18.7%改善
- 适用于小样本癌症分类,尤其适合数据稀缺的研究场景
从RNA测序(RNA-seq)数据中准确预测表型对诊断、生物标志物发现和个性化医疗至关重要。深度学习模型虽表现出优于传统机器学习的潜力,但其性能依赖于大规模标注数据集。在转录组学中,此类数据常受限,导致过拟合与泛化能力差。通过将知识从大而通用的数据集迁移至小数据集可缓解此问题。然而,由于预处理流程异质性及目标表型差异,跨数据集的知识迁移仍具挑战。本研究提出一种基于深度学习的域适应框架,实现从大型通用数据集向小型数据集在癌症类型分类中的有效知识迁移。该方法通过联合优化分类与域对齐目标,学习域不变的潜在空间。为确保训练稳定性和数据稀缺下的鲁棒性,采用带有适当正则化的对抗训练。探索了利用有标签或无标签目标样本的监督与非监督变体。在TCGA、ARCHS4和GTEx三个大规模转录组数据集上评估了跨队列知识迁移能力。实验结果表明,相较于非自适应基线,分类准确率持续提升,尤其在低数据条件下表现显著。总体而言,本工作凸显域适应在转录组学中高效知识迁移的重要作用,支持在数据受限条件下实现稳健的表型预测。
原文摘要 · Abstract (English)
Accurate phenotype prediction from RNA sequencing (RNA-seq) data is essential for diagnosis, biomarker discovery, and personalized medicine. Deep learning models have demonstrated strong potential to outperform classical machine learning approaches, but their performance relies on large, well-annotated datasets. In transcriptomics, such datasets are frequently limited, leading to over-fitting and poor generalization. Knowledge transfer from larger, more general datasets can alleviate this issue. However, transferring information across RNA-seq datasets remains challenging due to heterogeneous preprocessing pipelines and differences in target phenotypes. In this study, we propose a deep learning-based domain adaptation framework that enables effective knowledge transfer from a large general dataset to a smaller one for cancer type classification. The method learns a domain-invariant latent space by jointly optimizing classification and domain alignment objectives. To ensure stable training and robustness in data-scarce scenarios, the framework is trained with an adversarial approach with appropriate regularization. Both supervised and unsupervised approach variants are explored, leveraging labeled or unlabeled target samples. The framework is evaluated on three large-scale transcriptomic datasets (TCGA, ARCHS4, GTEx) to assess its ability to transfer knowledge across cohorts. Experimental results demonstrate consistent improvements in cancer and tissue type classification accuracy compared to non-adaptive baselines, particularly in low-data scenarios. Overall, this work highlights domain adaptation as a powerful strategy for data-efficient knowledge transfer in transcriptomics, enabling robust phenotype prediction under constrained data conditions.
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