Visualization tools can help synthetic biologists and molecular programmers understand the complex reactive pathways of nucleic acid reactions, which can be designed for many potential applications and can be modelled using a continuous-time Markov chain (CTMC). Here we present ViDa, a new visualization approach for DNA reaction trajectories that uses a 2D embedding of the secondary structure state space underlying the CTMC model. To this end, we integrate a scattering transform of the secondary structure adjacency, a variational autoencoder, and a nonlinear dimensionality reduction method. We augment the training loss with domain-specific supervised terms that capture both thermodynamic and kinetic features. We assess ViDa on two well-studied DNA hybridization reactions. Our results demonstrate that the domain-specific features lead to significant quality improvements over the state-of-the-art in DNA state space visualization, successfully separating different folding pathways and thus providing useful insights into dominant reaction mechanisms.

翻译：可视化工具可帮助合成生物学家与分子程序员理解核酸反应的复杂反应路径，这类反应可被设计用于多种潜在应用，并可通过连续时间马尔可夫链（CTMC）进行建模。本文提出ViDa——一种针对DNA反应轨迹的新型可视化方法，该方法采用CTMC模型所依赖的二级结构状态空间的二维嵌入技术。为此，我们融合了二级结构邻接矩阵的散射变换、变分自编码器以及非线性降维方法。我们利用同时捕捉热力学与动力学特征的领域特异性监督项对训练损失进行增强。在两个广泛研究的DNA杂交反应上评估ViDa，结果表明：相较于DNA状态空间可视化的当前最优方法，领域特异性特征带来了显著的质量提升，成功分离了不同折叠路径，从而为揭示主导反应机制提供了有价值的信息。