# Visualizing DNA reaction trajectories with deep graph embedding approaches

Source: [Visualizing DNA reaction trajectories with deep graph embedding approaches](<https://www.sota2.com/research/paper/68fa5f4b1e209131ce9e8c6e>)

Collection index: [llms.txt](<https://www.sota2.com/research/llms.txt>)

Data updated: 2025-10-25T19:12:53.591Z

Authors: Chenwei Zhang, Khanh Dao Duc, Anne Condon

Published: 2023-11-06T05:06:35.000Z

## Abstract

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.

## Recorded benchmark results

A research result applies to its stated dataset, split, metric and evaluation configuration. Compare like-for-like settings, preserve the metric's unit and direction, and distinguish paper-reported results from independent reproduction. The best result recorded here is not a claim of exhaustive, current global coverage.

## Original sources and implementation

[Original paper](<https://arxiv.org/abs/2311.03409>)

[PDF](<https://arxiv.org/pdf/2311.03409.pdf>)