# Cross-Modal Learning for Chemistry Property Prediction: Large Language Models Meet Graph Machine Learning

arXiv: https://arxiv.org/abs/2408.14964 · HTML: https://mlsanity.com/paper/2408.14964/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 46 of its 69 references that are in the map.
- First posted on arXiv 27 Aug 2024.

## Builds on (most cited first, 30 of 46)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Semi-Supervised Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1609.02907/) (2016)
- [Graph Attention Networks](https://mlsanity.com/paper/1710.10903/) (2017)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [PaLM: Scaling Language Modeling with Pathways](https://mlsanity.com/paper/2204.02311/) (2022)
- [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)
- [Tree of Thoughts: Deliberate Problem Solving with Large Language Models](https://mlsanity.com/paper/2305.10601/) (2023)
- [Pre-train, Prompt, and Predict: A Systematic Survey of Prompting Methods in Natural Language Processing](https://mlsanity.com/paper/2107.13586/) (2021)
- [DeBERTa: Decoding-enhanced BERT with Disentangled Attention](https://mlsanity.com/paper/2006.03654/) (2020)
- [Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering](https://mlsanity.com/paper/1606.09375/) (2016)
- [Multitask Prompted Training Enables Zero-Shot Task Generalization](https://mlsanity.com/paper/2110.08207/) (2021)
- [PaLM 2 Technical Report](https://mlsanity.com/paper/2305.10403/) (2023)
- [Spectral Networks and Locally Connected Networks on Graphs](https://mlsanity.com/paper/1312.6203/) (2013)
- [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)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Gated Graph Sequence Neural Networks](https://mlsanity.com/paper/1511.05493/) (2015)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [SchNet: A continuous-filter convolutional neural network for modeling quantum interactions](https://mlsanity.com/paper/1706.08566/) (2017)
- [Directional Message Passing for Molecular Graphs](https://mlsanity.com/paper/2003.03123/) (2020)
- [Provably Powerful Graph Networks](https://mlsanity.com/paper/1905.11136/) (2019)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)
- [Diffusion-Convolutional Neural Networks](https://mlsanity.com/paper/1511.02136/) (2015)
- [Cormorant: Covariant Molecular Neural Networks](https://mlsanity.com/paper/1906.04015/) (2019)

## Built on by (most cited first, 4 of 4)

- [Large Language Models Meet Text-Attributed Graphs: A Survey of Integration Frameworks and Applications](https://mlsanity.com/paper/2510.21131/) (2025)
- [MolMix: A Simple Yet Effective Baseline for Multimodal Molecular Representation Learning](https://mlsanity.com/paper/2410.07981/) (2024)
- [Towards Agentic Intelligence for Materials Science](https://mlsanity.com/paper/2602.00169/) (2026)
- [ChemAmp: Amplified Chemistry Tools via Composable Agents](https://mlsanity.com/paper/2505.21569/) (2025)

## Abstract (arXiv)

In the field of chemistry, the objective is to create novel molecules with desired properties, facilitating accurate property predictions for applications such as material design and drug screening. However, existing graph deep learning methods face limitations that curb their expressive power. To address this, we explore the integration of vast molecular domain knowledge from Large Language Models (LLMs) with the complementary strengths of Graph Neural Networks (GNNs) to enhance performance in property prediction tasks. We introduce a Multi-Modal Fusion (MMF) framework that synergistically harnesses the analytical prowess of GNNs and the linguistic generative and predictive abilities of LLMs, thereby improving accuracy and robustness in predicting molecular properties. Our framework combines the effectiveness of GNNs in modeling graph-structured data with the zero-shot and few-shot learning capabilities of LLMs, enabling improved predictions while reducing the risk of overfitting. Furthermore, our approach effectively addresses distributional shifts, a common challenge in real-world applications, and showcases the efficacy of learning cross-modal representations, surpassing state-of-the-art baselines on benchmark datasets for property prediction tasks.