# Graph Multi-Similarity Learning for Molecular Property Prediction

arXiv: https://arxiv.org/abs/2401.17615 · HTML: https://mlsanity.com/paper/2401.17615/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 32 of its 64 references that are in the map.
- First posted on arXiv 31 Jan 2024.

## Builds on (most cited first, 30 of 32)

- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [FaceNet: A Unified Embedding for Face Recognition and Clustering](https://mlsanity.com/paper/1503.03832/) (2015)
- [Unsupervised Feature Learning via Non-Parametric Instance-level Discrimination](https://mlsanity.com/paper/1805.01978/) (2018)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [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)
- [Self-supervised Learning: Generative or Contrastive](https://mlsanity.com/paper/2006.08218/) (2020)
- [A Survey on Contrastive Self-supervised Learning](https://mlsanity.com/paper/2011.00362/) (2020)
- [Deep Metric Learning via Lifted Structured Feature Embedding](https://mlsanity.com/paper/1511.06452/) (2015)
- [Deep metric learning using Triplet network](https://mlsanity.com/paper/1412.6622/) (2014)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)
- [Multi-Similarity Loss with General Pair Weighting for Deep Metric Learning](https://mlsanity.com/paper/1904.06627/) (2019)
- [GPT-GNN: Generative Pre-Training of Graph Neural Networks](https://mlsanity.com/paper/2006.15437/) (2020)
- [Graph Self-Supervised Learning: A Survey](https://mlsanity.com/paper/2103.00111/) (2021)
- [Pre-training Molecular Graph Representation with 3D Geometry](https://mlsanity.com/paper/2110.07728/) (2021)
- [ChemRL-GEM: Geometry Enhanced Molecular Representation Learning for Property Prediction](https://mlsanity.com/paper/2106.06130/) (2021)
- [3D Infomax improves GNNs for Molecular Property Prediction](https://mlsanity.com/paper/2110.04126/) (2021)
- [When Does Self-Supervision Help Graph Convolutional Networks?](https://mlsanity.com/paper/2006.09136/) (2020)
- [Deep Metric Learning with Angular Loss](https://mlsanity.com/paper/1708.01682/) (2017)
- [N-Gram Graph: Simple Unsupervised Representation for Graphs, with Applications to Molecules](https://mlsanity.com/paper/1806.09206/) (2018)
- [MoCL: Data-driven Molecular Fingerprint via Knowledge-aware Contrastive Learning from Molecular Graph](https://mlsanity.com/paper/2106.04509/) (2021)
- [GeomGCL: Geometric Graph Contrastive Learning for Molecular Property Prediction](https://mlsanity.com/paper/2109.11730/) (2021)
- [Self-Supervised Graph Representation Learning via Global Context Prediction](https://mlsanity.com/paper/2003.01604/) (2020)
- [Chemical-Reaction-Aware Molecule Representation Learning](https://mlsanity.com/paper/2109.09888/) (2021)
- [Attention-wise masked graph contrastive learning for predicting molecular property](https://mlsanity.com/paper/2206.08262/) (2022)
- [Motif-based Graph Representation Learning with Application to Chemical Molecules](https://mlsanity.com/paper/2208.04529/) (2022)
- [3D Graph Contrastive Learning for Molecular Property Prediction](https://mlsanity.com/paper/2208.06360/) (2022)
- [Advancing Drug Discovery with Enhanced Chemical Understanding via Asymmetric Contrastive Multimodal Learning](https://mlsanity.com/paper/2311.06456/) (2023)
- [Pairwise Similarity Learning is SimPLE](https://mlsanity.com/paper/2310.09449/) (2023)
- [Denoising Multi-Similarity Formulation: A Self-paced Curriculum-Driven Approach for Robust Metric Learning](https://mlsanity.com/paper/2211.11751/) (2022)

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

- [TransPeakNet: Solvent-Aware 2D NMR Prediction via Multi-Task Pre-Training and Unsupervised Learning](https://mlsanity.com/paper/2403.11353/) (2024)

## Abstract (arXiv)

Enhancing accurate molecular property prediction relies on effective and proficient representation learning. It is crucial to incorporate diverse molecular relationships characterized by multi-similarity (self-similarity and relative similarities) between molecules. However, current molecular representation learning methods fall short in exploring multi-similarity and often underestimate the complexity of relationships between molecules. Additionally, previous multi-similarity approaches require the specification of positive and negative pairs to attribute distinct predefined weights to different relative similarities, which can introduce potential bias. In this work, we introduce Graph Multi-Similarity Learning for Molecular Property Prediction (GraphMSL) framework, along with a novel approach to formulate a generalized multi-similarity metric without the need to define positive and negative pairs. In each of the chemical modality spaces (e.g.,molecular depiction image, fingerprint, NMR, and SMILES) under consideration, we first define a self-similarity metric (i.e., similarity between an anchor molecule and another molecule), and then transform it into a generalized multi-similarity metric for the anchor through a pair weighting function. GraphMSL validates the efficacy of the multi-similarity metric across MoleculeNet datasets. Furthermore, these metrics of all modalities are integrated into a multimodal multi-similarity metric, which showcases the potential to improve the performance. Moreover, the focus of the model can be redirected or customized by altering the fusion function. Last but not least, GraphMSL proves effective in drug discovery evaluations through post-hoc analyses of the learnt representations.