arXiv:2607.13984stat.MLcs.LG2026-07

用神经网络建模肿瘤生长与脱落时间,融合基因数据提升预测精度。

Multimodal Empirical Bayes Variational Autoencoders for Joint Longitudinal and Time-to-Event Modeling

论文配图:Multimodal Empirical Bayes Variational Autoencoders for Joint Longitudinal and Time-to-Event Modeling
图 1 · 摘自论文原文
  • 用贝叶斯先验正则化个体潜变量,结合神经解码器模拟肿瘤体积变化。
  • 联合模型准确复现肿瘤分布和脱落模式,基因条件先验提升个体预测性能。
  • 适合药理学建模、精准医疗中的多源数据整合,尤其关注基因与治疗响应关系。

纵向肿瘤测量、脱落信息与遗传协变量为治疗反应提供了互补信息,但如何在统一群体建模框架中整合这些数据仍具挑战。本文将经验贝叶斯变分自编码器(EB-VAE)扩展至纵向与生存事件联合建模,并在肿瘤生长数据上评估其性能。该框架通过协变量条件化的经验贝叶斯先验对个体间差异进行建模,解码器将潜变量映射为肿瘤体积轨迹;为处理信息性脱落,解码器引入危险率模型,实现肿瘤生长与脱落时间的联合预测。比较了全神经与半机制混合解码器,结果表明混合解码器在保持与神经解码器相当先验预测性能的同时,恢复的治疗效应参数与已有非线性混合效应模型估计结果一致。联合模型在保留个体数据中准确重现肿瘤体积分布与脱落模式,基因条件先验在黑色素瘤与乳腺癌实验中均提升了个体水平先验预测。稳定性选择识别出多个生物学合理的遗传标志物,包括BRAF、NRAS、NF1和MDM2的改变。结果表明,EB-VAE为药理学应用中融合神经动态、机制结构、生存分析与高维协变量提供了一个灵活的概率框架。

原文摘要 · Abstract (English)

Longitudinal tumor measurements, dropout information, and genetic covariates provide complementary information about treatment response, but integrating these data sources within a single population modeling framework remains challenging. We extend the empirical Bayes variational autoencoder (EB-VAE) framework to joint longitudinal and time-to-event modeling and evaluate it on tumor growth data. The framework represents inter-individual variability using latent individual effects regularized by a covariate-conditioned empirical Bayes prior, while a decoder maps these latent effects to tumor-volume trajectories. To account for informative dropout, the decoder was augmented with a hazard model, yielding joint predictions of tumor growth and time to dropout. We further compared fully neural and hybrid semi-mechanistic decoder formulations and incorporated genomic covariates through a genetics-conditioned prior adaptation. The hybrid decoder recovered treatment-effect parameters broadly consistent with previously reported nonlinear mixed-effects estimates, while achieving prior predictive performance comparable to the neural decoder. The joint model reproduced both tumor-volume distributions and dropout patterns in held-out individuals, and genetic conditioning improved individual-level prior predictions in both cutaneous melanoma and breast cancer experiments. Stability selection identified several biologically plausible genetic indicators, including alterations in BRAF, NRAS, NF1, and MDM2. These results demonstrate that EB-VAE provides a flexible probabilistic framework for combining neural dynamics, mechanistic structure, time-to-event modeling, and high-dimensional covariates in pharmacometric applications.

药理建模联合建模贝叶斯肿瘤生长

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