Predicting Nanorobot Shapes via Generative Models

TL;DR

This paper introduces a method to predict nanorobot shapes by combining low- and high-fidelity data using a generative model, aiming to improve assembly yield in DNA nanotechnology.

Contribution

It develops a two-step generative modeling approach that leverages low- and high-fidelity data to predict nanorobot structures, using MolGAN and QM9 datasets for demonstration.

Findings

Successfully biased the generative model towards desired node degrees

Demonstrated approach using MolGAN and QM9 datasets

Paves the way for better nanorobot shape prediction

Abstract

The field of DNA nanotechnology has made it possible to assemble, with high yields, different structures that have actionable properties. For example, researchers have created components that can be actuated. An exciting next step is to combine these components into multifunctional nanorobots that could, potentially, perform complex tasks like swimming to a target location in the human body, detect an adverse reaction and then release a drug load to stop it. However, as we start to assemble more complex nanorobots, the yield of the desired nanorobot begins to decrease as the number of possible component combinations increases. Therefore, the ultimate goal of this work is to develop a predictive model to maximize yield. However, training predictive models typically requires a large dataset. For the nanorobots we are interested in assembling, this will be difficult to collect. This is because high-fidelity data, which allows us to characterize the shape and size of individual structures, is very time-consuming to collect, whereas low-fidelity data is readily available but only captures bulk statistics for different processes. Therefore, this work combines low- and high-fidelity data to train a generative model using a two-step process. We first use a relatively small, high-fidelity dataset to train a generative model. At run time, the model takes low-fidelity data and uses it to approximate the high-fidelity content. We do this by biasing the model towards samples with specific properties as measured by low-fidelity data. In this work we bias our distribution towards a desired node degree of a graphical model that we take as a surrogate representation of the nanorobots that this work will ultimately focus on. We have not yet accumulated a high-fidelity dataset of nanorobots, so we leverage the MolGAN architecture [1] and the QM9 small molecule dataset [2-3] to demonstrate our approach.