# Improving Molecular Properties Prediction Through Latent Space Fusion

arXiv: https://arxiv.org/abs/2310.13802 · HTML: https://mlsanity.com/paper/2310.13802/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 18 of its 29 references that are in the map.
- First posted on arXiv 20 Oct 2023.

## Builds on (most cited first, 18 of 18)

- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Optuna: A Next-generation Hyperparameter Optimization Framework](https://mlsanity.com/paper/1907.10902/) (2019)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Textbooks Are All You Need](https://mlsanity.com/paper/2306.11644/) (2023)
- [Directional Message Passing for Molecular Graphs](https://mlsanity.com/paper/2003.03123/) (2020)
- [TinyStories: How Small Can Language Models Be and Still Speak Coherent English?](https://mlsanity.com/paper/2305.07759/) (2023)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)
- [ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction](https://mlsanity.com/paper/2010.09885/) (2020)
- [Pre-training Molecular Graph Representation with 3D Geometry](https://mlsanity.com/paper/2110.07728/) (2021)
- [Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction](https://mlsanity.com/paper/1811.02633/) (2018)
- [Large-Scale Chemical Language Representations Capture Molecular Structure and Properties](https://mlsanity.com/paper/2106.09553/) (2021)
- [ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction](https://mlsanity.com/paper/2106.06130/) (2021)
- [N-Gram Graph: Simple Unsupervised Representation for Graphs, with Applications to Molecules](https://mlsanity.com/paper/1806.09206/) (2018)
- [Molecular Property Prediction: A Multilevel Quantum Interactions Modeling Perspective](https://mlsanity.com/paper/1906.11081/) (2019)
- [Molecular Hypergraph Grammar with its Application to Molecular Optimization](https://mlsanity.com/paper/1809.02745/) (2018)
- [MHG-GNN: Combination of Molecular Hypergraph Grammar with Graph Neural Network](https://mlsanity.com/paper/2309.16374/) (2023)
- [Beyond Chemical Language: A Multimodal Approach to Enhance Molecular Property Prediction](https://mlsanity.com/paper/2306.14919/) (2023)

## Built on by (most cited first, 1 of 1)

- [LLM-Fusion: A Novel Multimodal Fusion Model for Accelerated Material Discovery](https://mlsanity.com/paper/2503.01022/) (2025)

## Abstract (arXiv)

Pre-trained Language Models have emerged as promising tools for predicting molecular properties, yet their development is in its early stages, necessitating further research to enhance their efficacy and address challenges such as generalization and sample efficiency. In this paper, we present a multi-view approach that combines latent spaces derived from state-of-the-art chemical models. Our approach relies on two pivotal elements: the embeddings derived from MHG-GNN, which represent molecular structures as graphs, and MoLFormer embeddings rooted in chemical language. The attention mechanism of MoLFormer is able to identify relations between two atoms even when their distance is far apart, while the GNN of MHG-GNN can more precisely capture relations among multiple atoms closely located. In this work, we demonstrate the superior performance of our proposed multi-view approach compared to existing state-of-the-art methods, including MoLFormer-XL, which was trained on 1.1 billion molecules, particularly in intricate tasks such as predicting clinical trial drug toxicity and inhibiting HIV replication. We assessed our approach using six benchmark datasets from MoleculeNet, where it outperformed competitors in five of them. Our study highlights the potential of latent space fusion and feature integration for advancing molecular property prediction. In this work, we use small versions of MHG-GNN and MoLFormer, which opens up an opportunity for further improvement when our approach uses a larger-scale dataset.