# TrustMol: Trustworthy Inverse Molecular Design via Alignment with Molecular Dynamics

arXiv: https://arxiv.org/abs/2402.16930 · HTML: https://mlsanity.com/paper/2402.16930/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 17 of its 41 references that are in the map.
- First posted on arXiv 26 Feb 2024.

## Builds on (most cited first, 17 of 17)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [SGDR: Stochastic Gradient Descent with Warm Restarts](https://mlsanity.com/paper/1608.03983/) (2016)
- [Auto-Encoding Variational Bayes](https://mlsanity.com/paper/1312.6114/) (2013)
- [Simple and Scalable Predictive Uncertainty Estimation using Deep Ensembles](https://mlsanity.com/paper/1612.01474/) (2016)
- [On the Spectral Bias of Neural Networks](https://mlsanity.com/paper/1806.08734/) (2018)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Equivariant Diffusion for Molecule Generation in 3D](https://mlsanity.com/paper/2203.17003/) (2022)
- [Frequency Principle: Fourier Analysis Sheds Light on Deep Neural Networks](https://mlsanity.com/paper/1901.06523/) (2019)
- [pymoo: Multi-objective Optimization in Python](https://mlsanity.com/paper/2002.04504/) (2020)
- [Geometric Latent Diffusion Models for 3D Molecule Generation](https://mlsanity.com/paper/2305.01140/) (2023)
- [Symmetry-adapted generation of 3d point sets for the targeted discovery of molecules](https://mlsanity.com/paper/1906.00957/) (2019)
- [E(n) Equivariant Normalizing Flows](https://mlsanity.com/paper/2105.09016/) (2021)
- [A 3D Generative Model for Structure-Based Drug Design](https://mlsanity.com/paper/2203.10446/) (2022)
- [Inverse design of 3d molecular structures with conditional generative neural networks](https://mlsanity.com/paper/2109.04824/) (2021)
- [LIMO: Latent Inceptionism for Targeted Molecule Generation](https://mlsanity.com/paper/2206.09010/) (2022)
- [Autoinverse: Uncertainty Aware Inversion of Neural Networks](https://mlsanity.com/paper/2208.13780/) (2022)

## Abstract (arXiv)

Data-driven generation of molecules with desired properties, also known as inverse molecular design (IMD), has attracted significant attention in recent years. Despite the significant progress in the accuracy and diversity of solutions, existing IMD methods lag behind in terms of trustworthiness. The root issue is that the design process of these methods is increasingly more implicit and indirect, and this process is also isolated from the native forward process (NFP), the ground-truth function that models the molecular dynamics. Following this insight, we propose TrustMol, an IMD method built to be trustworthy. For this purpose, TrustMol relies on a set of technical novelties including a new variational autoencoder network. Moreover, we propose a latent-property pairs acquisition method to effectively navigate the complexities of molecular latent optimization, a process that seems intuitive yet challenging due to the high-frequency and discontinuous nature of molecule space. TrustMol also integrates uncertainty-awareness into molecular latent optimization. These lead to improvements in both explainability and reliability of the IMD process. We validate the trustworthiness of TrustMol through a wide range of experiments.