# InversionGNN: A Dual Path Network for Multi-Property Molecular Optimization

arXiv: https://arxiv.org/abs/2503.01488 · HTML: https://mlsanity.com/paper/2503.01488/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 47 of its 68 references that are in the map.
- First posted on arXiv 3 Mar 2025.

## Builds on (most cited first, 30 of 47)

- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Convex optimization](https://mlsanity.com/paper/2106.01946/) (2021)
- [Multi-Task Learning as Multi-Objective Optimization](https://mlsanity.com/paper/1810.04650/) (2018)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Junction Tree Variational Autoencoder for Molecular Graph Generation](https://mlsanity.com/paper/1802.04364/) (2018)
- [MolGAN: An implicit generative model for small molecular graphs](https://mlsanity.com/paper/1805.11973/) (2018)
- [Flow Network based Generative Models for Non-Iterative Diverse Candidate Generation](https://mlsanity.com/paper/2106.04399/) (2021)
- [Graph Convolutional Policy Network for Goal-Directed Molecular Graph Generation](https://mlsanity.com/paper/1806.02473/) (2018)
- [GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation](https://mlsanity.com/paper/2001.09382/) (2020)
- [GuacaMol: Benchmarking Models for De Novo Molecular Design](https://mlsanity.com/paper/1811.09621/) (2018)
- [Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development](https://mlsanity.com/paper/2102.09548/) (2021)
- [Pareto Multi-Task Learning](https://mlsanity.com/paper/1912.12854/) (2019)
- [Hierarchical Generation of Molecular Graphs using Structural Motifs](https://mlsanity.com/paper/2002.03230/) (2020)
- [Optimization of Molecules via Deep Reinforcement Learning](https://mlsanity.com/paper/1810.08678/) (2018)
- [Constrained Graph Variational Autoencoders for Molecule Design](https://mlsanity.com/paper/1805.09076/) (2018)
- [Deep Reinforcement Learning for De-Novo Drug Design](https://mlsanity.com/paper/1711.10907/) (2017)
- [MARS: Markov Molecular Sampling for Multi-objective Drug Discovery](https://mlsanity.com/paper/2103.10432/) (2021)
- [Objective-Reinforced Generative Adversarial Networks (ORGAN) for Sequence Generation Models](https://mlsanity.com/paper/1705.10843/) (2017)
- [Multi-Objective De Novo Drug Design with Conditional Graph Generative Model](https://mlsanity.com/paper/1801.07299/) (2018)
- [Multi-Objective GFlowNets](https://mlsanity.com/paper/2210.12765/) (2022)
- [Exploring Chemical Space with Score-based Out-of-distribution Generation](https://mlsanity.com/paper/2206.07632/) (2022)
- [Learning Multimodal Graph-to-Graph Translation for Molecular Optimization](https://mlsanity.com/paper/1812.01070/) (2018)
- [GraphEBM: Molecular Graph Generation with Energy-Based Models](https://mlsanity.com/paper/2102.00546/) (2021)
- [ZeroG: Investigating Cross-dataset Zero-shot Transferability in Graphs](https://mlsanity.com/paper/2402.11235/) (2024)
- [ChemBO: Bayesian Optimization of Small Organic Molecules with Synthesizable Recommendations](https://mlsanity.com/paper/1908.01425/) (2019)
- [The Synthesizability of Molecules Proposed by Generative Models](https://mlsanity.com/paper/2002.07007/) (2020)

## Built on by (most cited first, 2 of 2)

- [Learning the Interaction Prior for Protein-Protein Interaction Prediction: A Model-Agnostic Approach](https://mlsanity.com/paper/2605.09964/) (2026)
- [PharmAgent: Constraint-Aware Search with Frozen Language Models for Molecular Optimization](https://mlsanity.com/paper/2610.05431/) (2026)

## Abstract (arXiv)

Exploring chemical space to find novel molecules that simultaneously satisfy multiple properties is crucial in drug discovery. However, existing methods often struggle with trading off multiple properties due to the conflicting or correlated nature of chemical properties. To tackle this issue, we introduce InversionGNN framework, an effective yet sample-efficient dual-path graph neural network (GNN) for multi-objective drug discovery. In the direct prediction path of InversionGNN, we train the model for multi-property prediction to acquire knowledge of the optimal combination of functional groups. Then the learned chemical knowledge helps the inversion generation path to generate molecules with required properties. In order to decode the complex knowledge of multiple properties in the inversion path, we propose a gradient-based Pareto search method to balance conflicting properties and generate Pareto optimal molecules. Additionally, InversionGNN is able to search the full Pareto front approximately in discrete chemical space. Comprehensive experimental evaluations show that InversionGNN is both effective and sample-efficient in various discrete multi-objective settings including drug discovery.