# Analyzing Learned Molecular Representations for Property Prediction

arXiv: https://arxiv.org/abs/1904.01561 · HTML: https://mlsanity.com/paper/1904.01561/

## Key facts

- Cited by 375 papers in the map (data through 14 Oct 2026).
- First posted on arXiv 2 Apr 2019.

## Built on by (most cited first, 30 of 375)

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- [Motif-based Graph Self-Supervised Learning for Molecular Property Prediction](https://mlsanity.com/paper/2110.00987/) (2021)
- [3D Infomax improves GNNs for Molecular Property Prediction](https://mlsanity.com/paper/2110.04126/) (2021)
- [LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset](https://mlsanity.com/paper/2402.09391/) (2024)
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- [One Transformer Can Understand Both 2D & 3D Molecular Data](https://mlsanity.com/paper/2210.01765/) (2022)
- [A Comprehensive Survey on Deep Graph Representation Learning](https://mlsanity.com/paper/2304.05055/) (2023)
- [ComENet: Towards Complete and Efficient Message Passing for 3D Molecular Graphs](https://mlsanity.com/paper/2206.08515/) (2022)
- [Permutation invariant graph-to-sequence model for template-free retrosynthesis and reaction prediction](https://mlsanity.com/paper/2110.09681/) (2021)
- [Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching](https://mlsanity.com/paper/2206.13602/) (2022)
- [MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design](https://mlsanity.com/paper/2203.14500/) (2022)
- [GeomGCL: Geometric Graph Contrastive Learning for Molecular Property Prediction](https://mlsanity.com/paper/2109.11730/) (2021)
- [Structure-aware Interactive Graph Neural Networks for the Prediction of Protein-Ligand Binding Affinity](https://mlsanity.com/paper/2107.10670/) (2021)
- [SafeDrug: Dual Molecular Graph Encoders for Recommending Effective and Safe Drug Combinations](https://mlsanity.com/paper/2105.02711/) (2021)
- [DrugOOD: Out-of-Distribution (OOD) Dataset Curator and Benchmark for AI-aided Drug Discovery -- A Focus on Affinity Prediction Problems with Noise Annotations](https://mlsanity.com/paper/2201.09637/) (2022)
- [Few-shot Conformal Prediction with Auxiliary Tasks](https://mlsanity.com/paper/2102.08898/) (2021)
- [Molecular Contrastive Learning with Chemical Element Knowledge Graph](https://mlsanity.com/paper/2112.00544/) (2021)
- [A new perspective on building efficient and expressive 3D equivariant graph neural networks](https://mlsanity.com/paper/2304.04757/) (2023)
- [Molformer: Motif-based Transformer on 3D Heterogeneous Molecular Graphs](https://mlsanity.com/paper/2110.01191/) (2021)
- [Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language](https://mlsanity.com/paper/2303.03363/) (2023)
- [Can Large Language Models Empower Molecular Property Prediction?](https://mlsanity.com/paper/2307.07443/) (2023)

## Abstract (arXiv)

Advancements in neural machinery have led to a wide range of algorithmic solutions for molecular property prediction. Two classes of models in particular have yielded promising results: neural networks applied to computed molecular fingerprints or expert-crafted descriptors, and graph convolutional neural networks that construct a learned molecular representation by operating on the graph structure of the molecule. However, recent literature has yet to clearly determine which of these two methods is superior when generalizing to new chemical space. Furthermore, prior research has rarely examined these new models in industry research settings in comparison to existing employed models. In this paper, we benchmark models extensively on 19 public and 16 proprietary industrial datasets spanning a wide variety of chemical endpoints. In addition, we introduce a graph convolutional model that consistently matches or outperforms models using fixed molecular descriptors as well as previous graph neural architectures on both public and proprietary datasets. Our empirical findings indicate that while approaches based on these representations have yet to reach the level of experimental reproducibility, our proposed model nevertheless offers significant improvements over models currently used in industrial workflows.