# Clustering Molecular Energy Landscapes by Adaptive Network Embedding

arXiv: https://arxiv.org/abs/2401.10972 · HTML: https://mlsanity.com/paper/2401.10972/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 5 of its 24 references that are in the map.
- First posted on arXiv 19 Jan 2024.

## Builds on (most cited first, 5 of 5)

- [Distributed Representations of Words and Phrases and their Compositionality](https://mlsanity.com/paper/1310.4546/) (2013)
- [node2vec: Scalable Feature Learning for Networks](https://mlsanity.com/paper/1607.00653/) (2016)
- [DeepWalk: Online Learning of Social Representations](https://mlsanity.com/paper/1403.6652/) (2014)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Identifying Transition States of Chemical Kinetic Systems using Network Embedding Techniques](https://mlsanity.com/paper/2010.15760/) (2020)

## Abstract (arXiv)

In order to efficiently explore the chemical space of all possible small molecules, a common approach is to compress the dimension of the system to facilitate downstream machine learning tasks. Towards this end, we present a data driven approach for clustering potential energy landscapes of molecular structures by applying recently developed Network Embedding techniques, to obtain latent variables defined through the embedding function. To scale up the method, we also incorporate an entropy sensitive adaptive scheme for hierarchical sampling of the energy landscape, based on Metadynamics and Transition Path Theory. By taking into account the kinetic information implied by a system's energy landscape, we are able to interpret dynamical node-node relationships in reduced dimensions. We demonstrate the framework through Lennard-Jones (LJ) clusters and a human DNA sequence.