Synthetic biologists and molecular programmers design novel nucleic acid reactions, with many potential applications. Good visualization tools are needed to help domain experts make sense of the complex outputs of folding pathway simulations of such reactions. Here we present ViDa, a new approach for visualizing DNA reaction folding trajectories over the energy landscape of secondary structures. We integrate a deep graph embedding model with common dimensionality reduction approaches, to map high-dimensional data onto 2D Euclidean space. We assess ViDa on two well-studied and contrasting DNA hybridization reactions. Our preliminary results suggest that ViDa's visualization successfully separates trajectories with different folding mechanisms, thereby providing useful insight to users, and is a big improvement over the current state-of-the-art in DNA kinetics visualization.

翻译：合成生物学家和分子程序设计师致力于设计新型核酸反应，这些反应具有诸多潜在应用潜力。为帮助领域专家理解此类反应折叠路径模拟的复杂输出，亟需优质的视觉化工具。本文提出ViDa——一种基于二级结构能量景观对DNA反应折叠轨迹进行可视化的新方法。我们融合深度图嵌入模型与常见降维技术，将高维数据映射至二维欧氏空间。通过两个经充分研究的对比性DNA杂交反应对ViDa进行评估，初步结果表明，ViDa的可视化能够成功区分不同折叠机制的轨迹，从而为用户提供有价值的洞见，且相较当前最先进的DNA动力学可视化方法实现了重大改进。