# Topology-Driven Generative Completion of Lacunae in Molecular Data

arXiv: https://arxiv.org/abs/2208.00063 · HTML: https://mlsanity.com/paper/2208.00063/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 11 of its 37 references that are in the map.
- First posted on arXiv 29 Jul 2022.

## Builds on (most cited first, 11 of 11)

- [Generative Adversarial Networks](https://mlsanity.com/paper/2203.00667/) (2022)
- [Auto-Encoding Variational Bayes](https://mlsanity.com/paper/1312.6114/) (2013)
- [Molecular De Novo Design through Deep Reinforcement Learning](https://mlsanity.com/paper/1704.07555/) (2017)
- [A roadmap for the computation of persistent homology](https://mlsanity.com/paper/1506.08903/) (2015)
- [Multi-Objective De Novo Drug Design with Conditional Graph Generative Model](https://mlsanity.com/paper/1801.07299/) (2018)
- [giotto-tda: A Topological Data Analysis Toolkit for Machine Learning and Data Exploration](https://mlsanity.com/paper/2004.02551/) (2020)
- [Deep learning for molecular design - a review of the state of the art](https://mlsanity.com/paper/1903.04388/) (2019)
- [Generative Models for Automatic Chemical Design](https://mlsanity.com/paper/1907.01632/) (2019)
- [Scaffold-constrained molecular generation](https://mlsanity.com/paper/2009.07778/) (2020)
- [Topological Descriptors Help Predict Guest Adsorption in Nanoporous Materials](https://mlsanity.com/paper/2001.05972/) (2020)
- [Fibres of Failure: Classifying errors in predictive processes](https://mlsanity.com/paper/1803.00384/) (2018)

## Abstract (arXiv)

We introduce an approach to the targeted completion of lacunae in molecular data sets which is driven by topological data analysis, such as Mapper algorithm. Lacunae are filled in using scaffold-constrained generative models trained with different scoring functions. The approach enables addition of links and vertices to the skeletonized representations of the data, such as Mapper graph, and falls in the broad category of network completion methods. We illustrate application of the topology-driven data completion strategy by creating a lacuna in the data set of onium cations extracted from USPTO patents, and repairing it.