# Multi-View Molecular Representation Learning with Hierarchical Graphs and Contextualized Fingerprints

arXiv: https://arxiv.org/abs/2609.15611 · HTML: https://mlsanity.com/paper/2609.15611/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 16 of its 42 references that are in the map.
- First posted on arXiv 14 Sep 2026.

## Builds on (most cited first, 16 of 16)

- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [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)
- [Multi-Task Learning Using Uncertainty to Weigh Losses for Scene Geometry and Semantics](https://mlsanity.com/paper/1705.07115/) (2017)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [Smarter, Better, Faster, Longer: A Modern Bidirectional Encoder for Fast, Memory Efficient, and Long Context Finetuning and Inference](https://mlsanity.com/paper/2412.13663/) (2024)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)
- [OGB-LSC: A Large-Scale Challenge for Machine Learning on Graphs](https://mlsanity.com/paper/2103.09430/) (2021)
- [GPT-GNN: Generative Pre-Training of Graph Neural Networks](https://mlsanity.com/paper/2006.15437/) (2020)
- [Graph Contrastive Learning Automated](https://mlsanity.com/paper/2106.07594/) (2021)
- [Pre-training Molecular Graph Representation with 3D Geometry](https://mlsanity.com/paper/2110.07728/) (2021)
- [Geometric Deep Learning on Molecular Representations](https://mlsanity.com/paper/2107.12375/) (2021)
- [Fragment-based Pretraining and Finetuning on Molecular Graphs](https://mlsanity.com/paper/2310.03274/) (2023)
- [Subgraph Aggregation for Out-of-Distribution Generalization on Graphs](https://mlsanity.com/paper/2410.22228/) (2024)

## Abstract (arXiv)

Molecular property prediction requires representations that generalize from limited labeled data to structurally novel compounds. Existing molecular pretraining methods often rely on a single view: graph-based approaches model atom-bond topology but provide limited fragment-level supervision, whereas fingerprint descriptors encode chemical patterns but are typically used as fixed auxiliary features. We propose HiFi-Mol, a multi-view framework that separately pretrains a hierarchical graph encoder and a contextualized fingerprint encoder before downstream integration. The graph branch uses fragment-aware masking with multi-resolution supervision to capture substructure-aware representations, while the fingerprint branch tokenizes active entries from seven fingerprint families and applies masked language modeling to learn contextualized embeddings. During fine-tuning, HiFi-Mol combines projected multi-resolution graph features with fingerprint embeddings for downstream prediction. Evaluated on MoleculeNet benchmarks under the scaffold split, HiFi-Mol achieves a 2.77% improvement in average ROC-AUC over the best baseline across eight classification tasks while maintaining competitive performance on three regression tasks. Further analyses reveal that fragment-aware masking improves graph representation quality, and classification results demonstrate dataset-dependent strengths of the individual graph and fingerprint variants, confirming that the two views provide complementary predictive signals.